PaperBLAST
PaperBLAST Hits for metacyc::SGL_RS08600-MONOMER glycerate dehydrogenase (EC 1.1.1.29) (Synechocystis sp. (strain PCC 6803 / Kazusa)) (554 a.a., MNLAWLQGLS...)
Show query sequence
>metacyc::SGL_RS08600-MONOMER glycerate dehydrogenase (EC 1.1.1.29) (Synechocystis sp. (strain PCC 6803 / Kazusa))
MNLAWLQGLSLGLLSPPAPALLIFRSFTMAKVLVSDSIDQVGIDILKQVAQVDVKTGLSE
AEIIDIVPEYDAIMLRSATKVTEKIIQAGSQLKIIGRAGVGVDNIDVPAATRQGIVVVNS
PEGNTIAAAEHALAMMMALARHIPDANKSVKESKWERKQFIGTEVYKKTLGVVGLGKIGS
HVAGVAKAMGMKLLAYDPFISQERADQIGCTLVDLDLLFSEADFITLHIPKTPETANLIN
AETLAKMKPTARIINCSRGGIIDEEALVTAIETAQIGGAALDVFAQEPLGESRLREFSNV
ILTPHLGASTEEAQVNVAVDVAEQIRDVLLGLPARSAVNIPGLTPDVMEKLRPYLKLAET
LGTLVGQLAGGRIDRLTVCLQGDLAEYTNSQPLVVAAIKGLLSQALRERVNYVNAAIEAK
ERGIRVIETKDASVRDYSGSLHLKATGTMGEHSATGALLSNGEIRITDVDEFPINVPPNN
YMLFTLHRDMPGIIGKIGSLLGSFNVNIASMQVGRKIVRGDAIMALSLDDPLPDGLLSEI
TKVAGIRDAYTVKL
Running BLASTp...
Found 252 similar proteins in the literature:
hprA / P73821 glycerate dehydrogenase (EC 1.1.1.29) from Synechocystis sp. (strain PCC 6803 / Kazusa) (see paper)
sll1908 phosphoglycerate dehydrogenase from Synechocystis sp. PCC 6803
100% identity, 100% coverage
- Regulatory Diversity and Functional Analysis of Two-Component Systems in Cyanobacterium Synechocystis sp. PCC 6803 by GC-MS Based Metabolomics
Shi, Frontiers in microbiology 2020 - “...acid 10.15 slr1124 gpmB , phosphoserine phosphatase, involved in glycine, serine and threonine metabolism 1.96 sll1908 serA , D-3-phosphoglycerate dehydrogenase / 2-oxoglutarate reductase 1.73 Pyruvic acid 3.76 slr0721 me , encoding a malic enzyme, involved in pyruvate metabolism 1.70 sll1721 pdhB , pyruvate dehydrogenase E1 component...”
- First proteomic study of S-glutathionylation in cyanobacteria
Chardonnet, Journal of proteome research 2015 (PubMed)- “...in oxidative stress tolerance and 3-phosphoglycerate dehydrogenase (Sll1908) acting on amino acids metabolism, was confirmed by biochemical studies on the...”
- “...(PrxII, Sll1621) and 3-phosphoglycerate dehydrogenase (PGDH, Sll1908), has been validated in vitro using recombinant proteins. Article EXPERIMENTAL SECTION...”
- Redox regulation by reversible protein S-thiolation in bacteria
Loi, Frontiers in microbiology 2015 - “...mapped by mass spectrometry. In addition, the peroxiredoxin PrxII (Sll1621) and the 3-phosphoglycerate dehydrogenase PGDH (Sll1908) could be S -glutathionylated by BioGSSG in vitro (Chardonnet et al., 2015 ). Figure 5 Redox proteomics methods to study protein S -glutathionylation at a global scale . Mass spectrometry-based...”
- The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008 - “...g18360 slr0293 sll0171 slr0879 slr1096 sll1931 slr0006 sll1908 all4607 all4609 all4608 alr4745 alr4806 alr2765 alr1890 At4g33010 At1g11860 At2g35370 At3g17240...”
SYNPCC7002_A1246 D-3-phosphoglycerate dehydrogenase from Synechococcus sp. PCC 7002
78% identity, 95% coverage
alr1890 phosphoglycerate dehydrogenase from Nostoc sp. PCC 7120
79% identity, 95% coverage
- Proteomic De-Regulation in Cyanobacteria in Response to Abiotic Stresses
Babele, Frontiers in microbiology 2019 - “...of abiotic stresses. It was reported that the enzymes cysteine synthase (all2521) and D-3-phosphoglycerate dehydrogenase (alr1890) are drastically down-regulated under UV-B stress, which may negatively influence the amino acid biosynthesis pathway. In our study, we found down-regulation of D-3-phosphoglycerate dehydrogenase in Anabaena L31 under UV-B stress...”
- Induction and differential expression of certain novel proteins in Anabaena L31 under UV-B radiation stress
Babele, Frontiers in microbiology 2015 - “...7.6 110 IPR001926 Cysteine synthase/cystathionine beta-synthase P -phosphate-binding site 4.2.99.8 Down 12 D -3-phosphoglycerate dehydrogenase alr1890 17229382 526 55841.6 5.7 106 IPR006236 D -3-Phosphoglycerate_DH 1.1.1.95 Down Unknown proteins 11 Hypothetical protein all4050 all4050 17231542 324 37259.4 5 104 IPR007903 PRC_barrel Up 4 Hypothetical protein all3797 all3797...”
- “...of all living organisms. In this context, our data show that D -3-phosphoglycerate dehydrogenase ( alr1890) and cysteine synthase (all2521) are down regulated under UV-B stress and thus may adversely affect the amino acid biosynthesis pathway. Down regulation of D -3-phosphoglycerate dehydrogenase which catalyzes the formation...”
- The photorespiratory glycolate metabolism is essential for cyanobacteria and might have been conveyed endosymbiontically to plants
Eisenhut, Proceedings of the National Academy of Sciences of the United States of America 2008 - “...all4607 all4609 all4608 alr4745 alr4806 alr2765 alr1890 At4g33010 At1g11860 At2g35370 At3g17240 At4g37930 At1g23310 At1g68010 At4g33010 (At3g16950*) slr1840...”
GKIL_0932 phosphoglycerate dehydrogenase from Gloeobacter kilaueensis JS1
69% identity, 95% coverage
- Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i
Saw, PloS one 2013 - “...resistance pathway, revealed by the presence of vanB (GKIL_3597), vanX (GKIL_1509 and GKIL_1879), and serA (GKIL_0932). GVIO, however, only has a copy of vanX (gll1805) and serA (gvip294), and is missing vanB . Five essential gene products are in fact required for high-level vancomycin resistance, specifically...”
gvip294 D-3-phosphoglycerate dehydrogenase from Gloeobacter violaceus PCC 7421
68% identity, 95% coverage
- Cultivation and complete genome sequencing of Gloeobacter kilaueensis sp. nov., from a lava cave in Kīlauea Caldera, Hawai'i
Saw, PloS one 2013 - “...GKIL_1879), and serA (GKIL_0932). GVIO, however, only has a copy of vanX (gll1805) and serA (gvip294), and is missing vanB . Five essential gene products are in fact required for high-level vancomycin resistance, specifically VanR, VanS, VanH, VanX, and either VanA, VanB or VanD [28] [30]...”
MA0592 phosphoglycerate dehydrogenase from Methanosarcina acetivorans C2A
47% identity, 95% coverage
DET0599 D-3-phosphoglycerate dehydrogenase from Dehalococcoides ethenogenes 195
47% identity, 95% coverage
ZMO1685 D-3-phosphoglycerate dehydrogenase from Zymomonas mobilis subsp. mobilis ZM4
44% identity, 95% coverage
- Comprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering
Asefi, Microbial cell factories 2024 - “...(AhpC). It was discovered that ZMNPs hydrolysate tolerance was influenced by increased cysteine production (including ZMO1685 (serA1), ZMO1684 (serC), and ZMO0748 (cysK)) and the activation of stress response genes [ 118 ]. In silico genome-scale metabolic modeling and mathematical modeling are two of the most potent...”
- Molecular mechanism of enhanced ethanol tolerance associated with hfq overexpression in Zymomonas mobilis
Tang, Frontiers in bioengineering and biotechnology 2022 - “...alpha chain 1.89 ZMO1000 metE 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase 2.12 2.56 ZMO1684 serC Phosphoserine aminotransferase 1.09 1.28 ZMO1685 serA1 D-3-phosphoglycerate dehydrogenase 1.55 1.83 Heat shock response ZMO0016 grpE GrpE protein 1.10 1.06 ZMO0246 hslV ATP-dependent protease subunit HslV 2.06 2.21 ZMO0247 hslU Heat shock protein atpase subunit HslU...”
- “...in ZM4- hfq was observed in other genes involved in cysteine biosynthesis, including serA1 ( ZMO1685 ) and serC ( ZMO1684 ) ( Table 1 ; Figure 2 , Supplementary Table S4 ). However, such upregulated gene cluster was not induced under the condition without ethanol...”
- A plasmid-free Zymomonas mobilis mutant strain reducing reactive oxygen species for efficient bioethanol production using industrial effluent of xylose mother liquor
Geng, Frontiers in bioengineering and biotechnology 2022 - “...expression results showed that three genes associated with cysteine synthesis were upregulated in ZMNP, including ZMO1685 ( serA1 ) and ZMO1684 ( serC ) for L-serine synthesis, and ZMO0748 ( cysK ) that could catalyze O-acety-L-serine and the sulfur assimilation product H 2 S to synthesize...”
- Model-driven analysis of mutant fitness experiments improves genome-scale metabolic models of Zymomonas mobilis ZM4
Ong, PLoS computational biology 2020 - “...ZMO1128, ZMO1182, ZMO1851 Isoprenoid Precursor biosynthesis M56 0.293 3 PGCD_f, PSERT_f, PSP_L_f 3 ZMO1137, ZMO1684, ZMO1685 Serine biosynthesis M57 0.247 6 ADEt2rpp_r, ADEtex_r , HPN1_f, HPN2_f, HPN3_f , EX_ade_e_f 3 ZMO0873, ZMO0874, ZMO0969 Hopanoid biosynthesis M60 0.119 11 ADCL_f, ADCS_f, AKP1_f, DHFS_f, DHNPA2r_f , DHPS2_f, EX_gcald_e_f...”
- Proteomic and metabolomic analysis of the cellular biomarkers related to inhibitors tolerance in Zymomonas mobilis ZM4
Chang, Biotechnology for biofuels 2018 - “...Of the 31 DEPs, 15 DEPs (ZMO1485, ZZM4_0141, ZMO0495, ZMO0472, Pgi, ZMO0070, ZMO0758, ZMO0487, Mfd, ZMO1685, CysH, ZMO0075, ZMO0474, LeuC, and ZMO1124) were simultaneously up-regulated; wherein, ZMO1485 showed the highest fold change with an average value of 11.95, followed by ZMO0472 with average 10.25-fold change and...”
- “...and LeuC have the maximal interaction numbers with other DEPs, followed by GabD, CysH, and ZMO1685. Here, proteinprotein interactions are determined if the two proteins have been documented to be neighborhood proteins, fusion proteins, co-expression proteins, etc. with a confidence score more than 0.40. Fig.4 Heat...”
- Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Yang, Biotechnology for biofuels 2018 - “...ZMO1657 G to A (K176K) 17150281715028 ZMO1659 ( ftsH ) G to A (V68I) 17392261739226 ZMO1685 ( serA ) A to G (T93A) 18900211890021 ZMO1842 ( nosX ) C to T (G277D) 18946041894604 ZMO1848 C to T (K347K) 19173601917360 ZMO1862 C to T (A33T) 19453901945390 ZMO1886...”
Athe_2125 phosphoglycerate dehydrogenase from Caldicellulosiruptor bescii DSM 6725
43% identity, 95% coverage
A7Z657 D-3-phosphoglycerate dehydrogenase from Bacillus velezensis (strain DSM 23117 / BGSC 10A6 / LMG 26770 / FZB42)
43% identity, 95% coverage
BSU23070 D-3-phosphoglycerate dehydrogenase from Bacillus subtilis subsp. subtilis str. 168
P35136 D-3-phosphoglycerate dehydrogenase from Bacillus subtilis (strain 168)
43% identity, 95% coverage
RLV_6165 phosphoglycerate dehydrogenase from Rhizobium leguminosarum bv. viciae
43% identity, 94% coverage
serA / GB|AAC83943.1 phosphoglycerate dehydrogenase; EC 1.1.1.95 from Bacillus subtilis (see paper)
serA / AAC83943.1 phosphoglycerate dehydrogenase from Bacillus subtilis (see 3 papers)
43% identity, 95% coverage
MMP1588 D-3-phosphoglycerate dehydrogenase from Methanococcus maripaludis S2
43% identity, 95% coverage
RSP_1352 D-3-phosphoglycerate dehydrogenase from Rhodobacter sphaeroides 2.4.1
44% identity, 90% coverage
SMc00641 PUTATIVE D-3-PHOSPHOGLYCERATE DEHYDROGENASE PROTEIN from Sinorhizobium meliloti 1021
Q92MA3 D-3-phosphoglycerate dehydrogenase from Rhizobium meliloti (strain 1021)
42% identity, 94% coverage
BAB1_1697 ATP/GTP-binding site motif A (P-loop):Amino acid-binding ACT:D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain:... from Brucella melitensis biovar Abortus 2308
43% identity, 93% coverage
- Brucella abortus Depends on l-Serine Biosynthesis for Intracellular Proliferation
Révora, Infection and immunity 2020 (secret) - Evaluation of the effects of erythritol on gene expression in Brucella abortus
Rodríguez, PloS one 2012 - “...COG0683E BAB1_1794 0.56 0.38 Leu/Ile/Val-binding family protein COG0683E BAB2_0282 0.55 0.33 Leu/Ile/Val-binding family protein COG0683E BAB1_1697 2.67 7.98 D-3-phosphoglycerate dehydrogenase COG0111EH BAB1_1699 - 5.80 Phosphoserine aminotransferase COG1932EH BAB1_1502 2.15 2.57 Carbamoyl phosphate synthase small subunit COG0505EF BAB1_1508 2.11 2.54 Carbamoyl phosphate synthase large subunit COG0458EF BAB2_0640...”
- “...7.95 BAB1_1502 Carbamoyl phosphate synthase small subunit 3.65 BAB1_1508 Carbamoyl phosphate synthase large subunit 2.20 BAB1_1697 D-3-phosphoglycerate dehydrogenase 3.30 BAB1_1699 Phosphoserin aminotransferase 4.65 BAB1_1813 Putative transaldolase 4.40 BAB2_0364 Fructose-1,6-bisphosphatase 4.15 BAB2_0367 Triosephosphate isomerase 2 (TIM 2) 8.05 BAB2_0371 Erythritol-4-phosphate-dehydrogenase 9.25 BAB2_0375 Phosphoribulokinase ABC transporter ATPase 3.60...”
- Intracellular adaptation of Brucella abortus
Lamontagne, Journal of proteome research 2009 - “...synthesis SSU S17 34 BAB1_1699 AA synthesis SerC 35 BAB1_1236 Protein synthesis LSU L15p 35 BAB1_1697 AA synthesis SerA-1 36 BAB1_1259 Protein synthesis SSU S7 36 BAB1_1845 Stress response CtpA 37 BAB1_0811 Protein synthesis LSU L13 37 BAB1_2130 Stress response DnaJ 38 BAB1_1254 Protein synthesis LSU...”
A4XJ21 D-3-phosphoglycerate dehydrogenase from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
42% identity, 93% coverage
ATU_RS17200 phosphoglycerate dehydrogenase from Agrobacterium fabrum str. C58
42% identity, 93% coverage
Dshi_3318 D-3-phosphoglycerate dehydrogenase from Dinoroseobacter shibae DFL 12
44% identity, 91% coverage
SH1200 D-3-phosphoglycerate dehydrogenase from Staphylococcus haemolyticus JCSC1435
42% identity, 95% coverage
- First Case of Staphylococci Carrying Linezolid Resistance Genes from Laryngological Infections in Poland
Michalik, Pathogens (Basel, Switzerland) 2021 - “...arcC allel 1; cfxE allel 1; hemH allel 1; leuB allel 1; RiboseABC allel 4; SH1200 allel 1; SH1431 allel 5) not applicable mecA only III fib, hla, hlb pathogens-10-00335-t002_Table 2 Table 2 Antimicrobial susceptibility profiles and antibiotic resistance genes of S. aureus and S. haemolyticus...”
- Incorporating Statistical Test and Machine Intelligence Into Strain Typing of Staphylococcus haemolyticus Based on Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry
Chung, Frontiers in microbiology 2019 - “...We defined the strain typing of S. haemolyticus by sequencing seven housekeeping genes, namely arc, SH1200, hemH, leuB, SH1431, cfxE , and RiboseABC (Panda et al., 2016 ). The sequencing results of these genes were used to assign the sequence types of S. haemolyticus throughout the...”
- Identification of Novel Sequence Types among Staphylococcus haemolyticus Isolated from Variety of Infections in India
Panda, PloS one 2016 - “...to NCBI GenBank under accession numbers KM985504KM985522 and KX073468KX073483 for arc, KM985523KM985541 and KX073484KX073499 for SH1200, KM985542KM985560 and KX073500KX073515 for hemH, KM985561KM985579 and KX073516KX073531 for leuB, KM985580 -KM985598 and KX073532KX073547 for SH1431, KM985599KM985617 and KX073548KX073563 for cfxE, KP019681KP019699 and KX073564KX073579 for Ribose ABC, respectively. Data Availability...”
- “...to NCBI GenBank under accession numbers KM985504KM985522 and KX073468KX073483 for arc, KM985523KM985541 and KX073484KX073499 for SH1200, KM985542KM985560 and KX073500KX073515 for hemH, KM985561KM985579 and KX073516KX073531 for leuB, KM985580 -KM985598 and KX073532KX073547 for SH1431, KM985599KM985617 and KX073548KX073563 for cfxE, KP019681KP019699 and KX073564KX073579 for Ribose ABC, respectively. Introduction Staphylococcus...”
- Analysis of nosocomial Staphylococcus haemolyticus by MLST and MALDI-TOF mass spectrometry
Kornienko, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases 2016 (PubMed)- “...novel variant of MLST scheme including the tpiA, pta, sh1200, rphE, tphK, mvaK1, and arc loki was tested. The discriminatory power was estimated by the...”
- “.... haemo lyticus clinical isolates in accordance ( tpiA pta sh1200 rphE tphK mvaK1 arcC ) MLST scheme: (a) clonal grouping of S . haemolyticus isolates based on...”
DA471_RS00355 phosphoglycerate dehydrogenase from Staphylococcus aureus
SAR1801 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
41% identity, 95% coverage
SA1545 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus N315
41% identity, 95% coverage
- Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
Scherr, Infection and immunity 2013 - “...SA1818 SA0155 SA2475 SA0712 SA0687 SA2278 SA1235 SA0024 SA1545 SA1553 SA0616 SA0024 SA2342 SA0409 SA0251 SA1825 SA0200 SA1401 SA1820 SA1596 SA1182 SA1435 SA1364...”
- Staphylococcal IgM enzyme-linked immunosorbent assay for diagnosis of periprosthetic joint infections
Artini, Journal of clinical microbiology 2011 - “...revised in 1983). SSPA from Staphylococcus strain SA1545 (a slime-producing clinical isolate) was prepared as previously reported, with important modifications...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...diester phosphodiesterase sa_c2220s1920_a_at * 5.5 2.5 2.5 SA1514 glycerol-3-phosphate dehydrogenase, NAD-dependent sa_c2448s2032_a_at 2.5 2.5 2.5 SA1545 short chain dehydrogenase/reductase family oxidoreductase sa_c2493s2074_a_at 6.6 5 5 SA1560 2-oxoisovalerate dehydrogenase sa_c2497s2076_a_at 8.5 5 2.5 SA1561 2-oxoisovalerate dehydrogenase sa_c2501s2080_a_at 3.9 2.5 5 SA1562 2-oxoisovalerate dehydrogenase sa_c3114s2669_a_at 4.5 2.5 2.5...”
- Transcriptional signature following inhibition of early-stage cell wall biosynthesis in Staphylococcus aureus
O'Neill, Antimicrobial agents and chemotherapy 2009 - “...SA1235 SA1236 SA1238 SA1254 SA1255 SA1256 SA1257 SA1532 SA1545 SA1546 SA1691 SA1858 SA1859 SA1860 SA1861 SA1862 SA1863 SA1864 SA1865 SA1866 SA2112 SA2221 SA2235...”
- Transcriptome analysis of the responses of Staphylococcus aureus to antimicrobial peptides and characterization of the roles of vraDE and vraSR in antimicrobial resistance
Pietiäinen, BMC genomics 2009 - “...4.2 5.3 3.3 VraSR, VCM Hypothetical protein SA1517 citC 4.9 5.8 3.1 VCM Isocitrate dehydrogenase SA1545 serA 4.6 2.5 VCM Similar to soluble hydrogenase 42 kD subunit SA1549 htrA 2.9 3.0 2.0 VraSR, VCM Similar to serine proteinase Do, heat-shock protein HtrA SA1599 3.2 2.4 Similar...”
SACOL1773 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus COL
NWMN_1617 D-3-phosphoglycerate dehydrogenase from Staphylococcus aureus subsp. aureus str. Newman
41% identity, 95% coverage
CCNA_03322 D-3-phosphoglycerate dehydrogenase from Caulobacter crescentus NA1000
CC3215 D-3-phosphoglycerate dehydrogenase from Caulobacter crescentus CB15
42% identity, 94% coverage
- The complex logic of stringent response regulation in Caulobacter crescentus: starvation signalling in an oligotrophic environment
Boutte, Molecular microbiology 2011 - “...l ysA mar414 CCNA_02296 ( Huitema et al , 2006 ) 1166 NA1000 serA mar414 CCNA_03322 ( Huitema et al , 2006 ) 1164 NA1000 CCNA1419 mar414 CCNA_01419 ( Huitema et al , 2006 ) 1250 NA1000 gltB CCNA_03722 This work 1183 NA1000 cysE hMu CCNA_02734...”
- Whole-genome transcriptional analysis of heavy metal stresses in Caulobacter crescentus
Hu, Journal of bacteriology 2005 - “...degradation CC0957 CC0958 CC0959 CC0960 Serine biosynthesis CC3215 CC3216 LPSa synthesis CC0118 CC1985 Annotation Chromate 8448 HU ET AL. ACKNOWLEDGMENTS This...”
- Transcriptional profiling of Caulobacter crescentus during growth on complex and minimal media
Hottes, Journal of bacteriology 2004 - “...dehydrogenase, putA 3.74 3.78 Serine synthesis CC3215, D-3-phosphoglycerate dehydrogenase, serA CC3216, phosphoserine aminotransferase, serC 0.23 0.27 0.22 0.24...”
MPNT_20138 phosphoglycerate dehydrogenase from Candidatus Methylacidithermus pantelleriae
41% identity, 95% coverage
NJ7G_0555 phosphoglycerate dehydrogenase from Natrinema sp. J7-2
41% identity, 94% coverage
Q9Z564 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Streptomyces coelicolor (see paper)
SCO5515 probable D-3-phosphoglycerate dehydrogenase from Streptomyces coelicolor A3(2)
40% identity, 94% coverage
mru_0678 phosphoglycerate dehydrogenase SerA from Methanobrevibacter ruminantium M1
39% identity, 95% coverage
ARB_07891 uncharacterized protein from Trichophyton benhamiae CBS 112371
41% identity, 91% coverage
HVO_2968 D-3-phosphoglycerate dehydrogenase from Haloferax volcanii DS2
39% identity, 95% coverage
A9PEK1 D-3-phosphoglycerate dehydrogenase from Populus trichocarpa
40% identity, 88% coverage
SERA2_ARATH / O04130 D-3-phosphoglycerate dehydrogenase 2, chloroplastic; PGDH; EC 1.1.1.95 from Arabidopsis thaliana (Mouse-ear cress) (see 3 papers)
O04130 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Arabidopsis thaliana (see 3 papers)
NP_564034 D-3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
AT1G17745 PGDH (3-PHOSPHOGLYCERATE DEHYDROGENASE); phosphoglycerate dehydrogenase from Arabidopsis thaliana
39% identity, 84% coverage
- function: Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
disruption phenotype: No visible phenotype. - The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense
Bulgakov, Scientific reports 2018 - “...Required to activate the iron superoxide dismutases (FeSOD) 20.6 Chaperone Functions along with Cpn60 19 O04130 (SERA2_ARATH) D-3-phosphoglycerate dehydrogenase 2, chloroplastic Amino-acid biosynthesis 2.51 Primary metabolism 20 Q9M9K1 (PMG2_ARATH) 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 2 Glycolysis 2.10.5 Primary metabolism 21 Q42592 (APXS_ARATH) L-ascorbate peroxidase S, chloroplastic/mitochondrial Plays a...”
- Iron-dependent modifications of the flower transcriptome, proteome, metabolome, and hormonal content in an Arabidopsis ferritin mutant
Sudre, Journal of experimental botany 2013 - “...metabolism 1 O80988 At2g26080 3.4 6.3 3.1 Glycine dehydrogenase 1 454/9/9 11 114.7/6.2 111.4/6.2 2 O04130 At1g17745 3.0 d -3-Phosphoglycerate-DH 625/12/8 17 66.8/5.8 71.3/5.7 3 Q9ZPF5 At4g08870 3.3 3.6 Putative arginase 834/36/18 48 38.1/5.9 35.4/6.2 Mn 4 F4I7I0 At1g17290 2.4 Alanine aminotransferase 723/15/13 28 60.4/5.9 56.5/5.6...”
- Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana.
Yoshida, The Journal of biological chemistry 2020 - GeneRIF: Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana.
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - GeneRIF: In the present study, two Arabidopsis PGDH isoforms were inhibited by L-serine but were activated by L-amino acids such as L-homocysteine in vitro.
- “.... Accession numbers for each amino acid sequence are as follows: AtPGDH1, NP_195146 (EMBL/GenBank/DDBJ); AtPGDH2, NP_564034 (EMBL/GenBank/DDBJ); AtPGDH3, NP_566637 (EMBL/GenBank/DDBJ); AhPGDH, BAF91727.1 (EMBL/GenBank/DDBJ); MtPGDH, 1YGY chain A (PDB); RnPGDH, CAA66374.1 (EMBL/GenBank/DDBJ); HsPGDH, NP_006614.2 (EMBL/GenBank/DDBJ) and EcPGDH 1YBA chain A (PDB). Reagents Nicotine amide adenine dinucleotide (NAD)...”
- Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.
Toujani, Plant physiology 2013 - GeneRIF: Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots.
- Transcriptomic and Metabolomic Analysis of a Pseudomonas-Resistant versus a Susceptible Arabidopsis Accession
Orf, International journal of molecular sciences 2022 - “...( Supplementary Table S1 ). Increased expression of a G3P-consuming G3P dehydrogenase 2 ( PGDH2, AT1G17745 ; Supplementary Table S1 ) in Col-0 in only was observed. 3. Discussion Here, we report on the dynamic response of the metabolome and transcriptome of resistant (C24) and susceptible...”
- Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance
Höhner, Plant physiology 2021 - “...respective metabolite or enzyme in WT and pgdh3 mutant plants. Accession numbers PGDH1 (At4g34200), PGDH2 (At1g17745), PGDH3 (At3g19480), pgdh3-1 mutant (SM_3_37584; Toujani etal., 2013 ), pgdh3-2 (GK-877F12; Toujani etal., 2013 ), npq4-1 (Li et al., 2000), npq2-1 aka aba1-6 CS3772 ( Niyogi etal., 1998 ). Supplemental...”
- Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
Yoshida, The Journal of biological chemistry 2020 (secret) - Target of Rapamycin Regulates Genome Methylation Reprogramming to Control Plant Growth in Arabidopsis
Zhu, Frontiers in genetics 2020 - “...ribosome in RAP vs. DMSO group. Gene id Methylation ratio Status Regions Annotation Carbon metabolism AT1G17745 0.0065 Hypo Promoter PGDH2| Allosteric substrate binding domain AT3G52200 0.3913 Hypo Exon/intron LTA3| 2-oxoacid dehydrogenase acyltransferase AT5G08300 0.5078 Hypo Promoter ATP-citrate lyase/succinyl-CoA ligase AT1G04410 0.5323 Hypo Promoter MDH1| Lactate dehydrogenase/glycoside...”
- Phosphoserine Aminotransferase1 Is Part of the Phosphorylated Pathways for Serine Biosynthesis and Essential for Light and Sugar-Dependent Growth Promotion
Wulfert, Frontiers in plant science 2018 - “...families. The Arabidopsis genome contains three genes for the PGDH ( At4g34200 , PGDH1 ; At1g17745 , PGDH2 ; At3g19480 , PGDH3 ), two genes for the PSAT ( At4g35630 , PSAT1 , and At2g17630 , PSAT2 ) and one gene for the PSP ( At1g18640...”
- Identification and Biochemical Characterization of the Serine Biosynthetic Enzyme 3-Phosphoglycerate Dehydrogenase in Marchantia polymorpha
Akashi, Frontiers in plant science 2018 - “...identity with MtPGDH. AtPGDH1 (At4g34200) and AtPGDH3 (At3g19480) are inhibited by L -serine, while AtPGDH2 (At1g17745) is not ( Benstein et al., 2013 ; Okamura and Hirai, 2017 ). The expression of genes encoding the three AtPGDH isozymes shows different organ specificity. AtPDGH1 is expressed in...”
- A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses
Alqurashi, Proteomes 2017 - “...patterns between the two treatments. Three proteins, ubiquinol-cytochrome C reductase hinge (UQCRH, AT1G15120), D-3-phosphoglycerate dehydrogenase (AT1G17745) and NADH:cytochrome B5 reductase 1 (Cyt b 5R, AT5G17770), belonging to the molecular function category oxidoreductase activity ( Table S2 ), showed differential accumulation in response to either ABA or...”
- “...Number Protein Name ANOVA ( p -Value) FC 5 min FC 20 min 1. Metabolism AT1G17745 D-3-phosphoglycerate dehydrogenase 2 0.0089 0.1 0.1 AT5G26780 Serine hydroxymethyltransferase 2 0.036 2.1 13 AT3G61440 Cysteine synthase C1 0.00074 ns 5 AT4G14880 O-acetylserine (thiol) lyase isoform A1 0.015 0.1 7.9 AT5G23300...”
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - “...domain. Arabidopsis thaliana expresses three PGDH isoforms and these are encoded by PGDH1 (At4g34200), PGDH2 (At1g17745), and PGDH3 (At3g19480) 1 (henceforth designated AtPGDH1 , AtPGDH2 , and AtPGDH3 , respectively). Although AtPGDH1 and AtPGDH3, but not AtPGDH2, are inhibited by l -serine 1 , the related...”
- “...dark) at 22C. Preparation of recombinant enzymes Full-length cDNA clones of AtPGDH1 (At4g34200) and AtPGDH2 (At1g17745) were obtained from RIKEN Bio Resource Center (accession code pda02295 and pda04481, respectively) 44 , 45 . Full-length cDNA of AtPGDH3 (At3g19480) was synthesized using a PrimeScript II High Fidelity...”
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F6I5Y5 D-3-phosphoglycerate dehydrogenase from Vitis vinifera
41% identity, 80% coverage
XP_002283022 D-3-phosphoglycerate dehydrogenase 3, chloroplastic from Vitis vinifera
40% identity, 86% coverage
A0A2R6X868 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Marchantia polymorpha (see paper)
40% identity, 83% coverage
XP_002518687 D-3-phosphoglycerate dehydrogenase 1, chloroplastic from Ricinus communis
B9RYA3 D-3-phosphoglycerate dehydrogenase from Ricinus communis
40% identity, 88% coverage
- Domestication Syndrome Is Investigated by Proteomic Analysis between Cultivated Cassava (Manihot esculenta Crantz) and Its Wild Relatives
An, PloS one 2016 - “...beta, mitochondrial-like Brachypodium distachyon XP_003567942 59.12/6.00 1.100.08(-) 1.080.09(-) 215 d-3-phosphoglycerate dehydrogenase, putative R . communis XP_002518687 7.65/63.10 1.230.15(+) 1.160.10(+) 216 d-3-phosphoglycerate dehydrogenase, putative R . communis XP_002518687 7.65/63.10 1.100.09(+) 1.020.07(+) 217 * ATP synthase subunit beta, mitochondrial; P17614 5.95/59.86 1.550.16(+) 1.340.16(-) 218 ATP synthase subunit beta...”
- “...precursor, putative- R . communis XP_002526228 4.89/31.87 66/1 376 d-3-phosphoglycerate dehydrogenase, putative R . communis XP_002518687 7.65/63.10 421/4 385 ATP synthase subunit beta, mitochondrial P17614 5.95/59.86 342/2 386 Enolase 2 Q9LEI9 5.92/47.91 75/1 389 sinapyl alcohol dehydrogenase Populus tremuloides AAK58693 6.23/38.99 67/1 394 ADPglucose pyrophosphorylase Oryza...”
- Proteomic and biochemical analyses of the cotyledon and root of flooding-stressed soybean plants
Komatsu, PloS one 2013 - “...unguiculata] Glyma16g27210.1 ABB89042 54243 5.63 1795 168 35 880 55 d-3-phosphoglycerate dehydrogenase [Ricinus communis] Glyma10g40750.1 XP_002518687 62859 6.32 41 2 14 878 56 (No significant hits to report) 57 argininosuccinate synthase,putative [Ricinus communis] Glyma05g03190.1 XP_002521168 52641 6.55 16 2 13 774 58 pyruvate decarboxylase 1 [Lotus...”
- Proteomic Analysis of Embryo Isolated From Mature Jatropha curcas L. Seeds
Ramzan, Frontiers in plant science 2022 - “...AT2G33040.1 Jcr4S01672.20 Ferredoxin B9SCU0 AT2G27510.1 Jcr4S01794.30 Chlorophyll a-b binding protein B9SID9 AT5G54270.1 Jcr4S01456.10 Phosphoglycerate dehydrogenase B9RYA3 AT4G34200.1 We identified four cytosolic isoforms of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) (Jcr4S07385.10, Jcr4S00953.40, Jcr4S00273.150, and Jcr4S00205.140) that catalyze the formation of 1,3-bisphosphoglycerate (BPGA) from Gly-3-P. In rapeseeds, the specific expression of...”
A2YVQ8 D-3-phosphoglycerate dehydrogenase from Oryza sativa subsp. indica
39% identity, 84% coverage
- TMT-based quantitative proteomics analysis of defense responses induced by the Bph3 gene following brown planthopper infection in rice
Qing, BMC plant biology 2024 - “...encoding up-regulated proteins (A2XFY5, B8B674, B8B186, A2WX74, A2WU38, B8BDJ3, A2YXK8, A28P7, B8AK41, B8ABR1, A2WP38, and A2YVQ8) were up-regulated, and 2 out of 3 genes encoding down-regulated proteins (A2XK95, A2WRZ6, and B8AQ36) were down-regulated at the mRNA level (Fig. 7 b). Following BPH infection of R582 for...”
LOC101246616 D-3-phosphoglycerate dehydrogenase 3, chloroplastic-like from Solanum lycopersicum
40% identity, 88% coverage
- Comparative Analyses of Tomato yellow leaf curl virus C4 Protein-Interacting Host Proteins in Healthy and Infected Tomato Tissues
Kim, The plant pathology journal 2016 - “...PREDICTED: Solanum lycopersicum asparagine--tRNA ligase, chloroplastic/mitochondrial-like (LOC101254276), mRNA XM_004236228.1 PREDICTED: Solanum lycopersicum d-3-phosphoglycerate dehydrogenase, chloroplastic-like (LOC101246616), mRNA NM_001246911.1 Solanum lycopersicum flavonoid biosynthesis oxidoreductase protein (LOC100736526), mRNA NM_001246909.1 Solanum lycopersicum carotenoid cleavage dioxygenase 1-2 (CCD1-2), mRNA KC184125.1 PREDICTED: Solanum lycopersicum 3-dehydroquinate synthase-like (LOC101252666), mRNA XM_004241576.1 PREDICTED: Solanum...”
Q6ZAA5 D-3-phosphoglycerate dehydrogenase from Oryza sativa subsp. japonica
38% identity, 84% coverage
A0A1Z4EAX3 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Beta vulgaris (see paper)
38% identity, 84% coverage
Q8TYK0 D-3-phosphoglycerate dehydrogenase from Methanopyrus kandleri (strain AV19 / DSM 6324 / JCM 9639 / NBRC 100938)
40% identity, 95% coverage
GRMZM2G009323 D-3-phosphoglycerate dehydrogenase from Zea mays
39% identity, 85% coverage
LOC100280688 uncharacterized protein LOC100280688 from Zea mays
38% identity, 84% coverage
LOC107808555 D-3-phosphoglycerate dehydrogenase 2, chloroplastic from Nicotiana tabacum
38% identity, 82% coverage
VDAG_01596 D-3-phosphoglycerate dehydrogenase from Verticillium dahliae VdLs.17
39% identity, 79% coverage
A0A1Z4EAX4 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Beta vulgaris (see paper)
39% identity, 84% coverage
A3BE72 D-3-phosphoglycerate dehydrogenase from Oryza sativa subsp. japonica
40% identity, 85% coverage
SERA1_ARATH / O49485 D-3-phosphoglycerate dehydrogenase 1, chloroplastic; Protein EMBRYO SAC DEVELOPMENT ARREST 9; EC 1.1.1.95 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
O49485 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Arabidopsis thaliana (see 4 papers)
NP_195146 D-3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
AT4G34200 EDA9 (embryo sac development arrest 9); ATP binding from Arabidopsis thaliana
38% identity, 87% coverage
- function: Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB). Required for mature pollen development.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
disruption phenotype: Embryo lethal when homozygous. - The Shared Proteome of the Apomictic Fern Dryopteris affinis ssp. affinis and Its Sexual Relative Dryopteris oreades
Ojosnegros, International journal of molecular sciences 2022 - “...195-2609_5_ORF2 Q41932 PSBQ2 Oxygen-evolving enhancer protein 3-2, chloroplastic 24 230 3.05 10 77 Reproduction 229414-114_3_ORF1 O49485 EDA9 D-3-phosphoglycerate dehydrogenase 1, chloroplastic 68 918 0 Reproduction 155382-187_1_ORF2 F4I6W4 PGM2 Phosphoglucomutase (alpha-D-glucose-1,6-bisphosphate-dependent) 68 915 0 Reproduction 40155-402_5_ORF3 Q38905 PRF5 Profilin-5 14 62 8.5 10 59 Reproduction 65126-313_6_ORF2 O81644...”
- Sexual and Apogamous Species of Woodferns Show Different Protein and Phytohormone Profiles
Fernández, Frontiers in plant science 2021 - “...At1g63130 1,010 62277-321_4_ORF2 90 Q9CAN0 3.09193E-32 2.00 5.1 7 D-3-phosphoglycerate dehydrogenase 1 918 229414-114_3_ORF1 68 O49485 0 1.00 23 14 DC1 domain-containing protein 919 167954-169_4_ORF1 68 O80763 8.1609E-154 1.58 5.4 3 Dihydrolipoyl dehydrogenase 1 867 143453-204_6_ORF2 [2] 63 A8MS68 0 1.58 13 9 Membrane-associated progesterone binding...”
- Disclosing proteins in the leaves of cork oak plants associated with the immune response to Phytophthora cinnamomi inoculation in the roots: A long-term proteomics approach
Coelho, PloS one 2021 - “...beta chain protein 2 ACLB2 O04499 0.098 0.195 0.009 0.9 2,3-bisphosphoglycerate-independent phosphoglycerate mutase 1 PMG1/iPGAM O49485 0.575 1.064 0.041 0.9 D-3-phosphoglycerate dehydrogenase 1, chloroplastic SERA1 Q9LF37 0.038 0.074 0.041 0.9 Chaperone protein ClpB3, chloroplastic CLPB3 Q9STX5 0.175 0.389 0.041 0.9 Endoplasmin homolog ENPL Q9M040 0.171 0.336...”
- Proteome Changes Reveal the Protective Roles of Exogenous Citric Acid in Alleviating Cu Toxicity in Brassica napus L.
Ju, International journal of molecular sciences 2021 - “...increased abundance, while NADP-dependent glyceraldehyde-3-phosphate dehydrogenase (P93338), two fructose-bisphosphate aldolases (P16096, O65581), D-3-phosphoglycerate dehydrogenase 1 (O49485), and glyceraldehyde-3-phosphate dehydrogenase A (P12858) were decreased ( Table 1 ). Under heavy metal stress, plants have developed complex and intricate regulatory network mechanisms to positively modulate the metabolic pathways...”
- “...ligase [ADP-forming] subunit beta (O82662), exhibited increased abundance under Cu stress, whereas D-3-phosphoglycerate dehydrogenase 1 (O49485) exhibited decreased abundance under a low concentration of Cu. Interestingly, however, exogenous CA treatment promoted the alleviation of Cu stress symptoms. A previous proteomic study in O. glazioviana subjected to...”
- Gel-based proteomic map of Arabidopsis thaliana root plastids and mitochondria
Grabsztunowicz, BMC plant biology 2020 - “...synthase 82, 83, 102 P47999, At2g43750 D-3-phosphoglycerate dehydrogenase 1 18, 2224, 30, 4547, 54, 55 O49485, At4g34200 Diaminopimelate decarboxylase 2 56 Q94A94, At5g11880 Diaminopimelate epimerase 86 Q9LFG2, At3g53580 Dihydroxy-acid dehydratase 30, 43, 45 Q9LIR4, At3g23940 Glutamine synthetase 55 Q43127, At5g35630 Homoserine kinase 83, 85 Q8L7R2, At2g17265...”
- iTRAQ-based quantitative proteomic analysis reveals the lateral meristem developmental mechanism for branched spike development in tetraploid wheat (Triticum turgidum L.)
Chen, BMC genomics 2018 - “...p -value=4.15E 03 ) (Additional file 4 : Table S4). Proteins of particular interest included O49485 (W5ASV5) and P25858 (W5HB91) because these proteins are involved in metabolic pathways and post-embryonic development according to the BP analysis ( p =3.26E 02 ) (Additional file 4 : Table...”
- “...tauschii Traes_1DL_FDB539EBE W5AJW7 0.439 0.376 Q6TBX7 carotene epsilon-monooxygenase, chloroplastic Aegilops tauschii Traes_2AL_608FCBC83 W5ASV5 0.476 0.531 O49485 D-3-phosphoglycerate dehydrogenase, chloroplastic Triticum urartu TRIAE_CS42_1DS_TGACv1_080841_AA0254500 W5ALP4 0.530 0.577 O22898 long chain acyl-CoA synthetase 1 Aegilops tauschii Traes_7AL_D93FC054C W5HB91 0.551 0.319 P25858 glyceraldehyde-3-phosphate dehydrogenase 1,cytosolic Aegilops tauschii Traes_4DL_852DF544C W5EJA0 0.568...”
- Cold and Heat Stress Diversely Alter Both Cauliflower Respiration and Distinct Mitochondrial Proteins Including OXPHOS Components and Matrix Enzymes
Rurek, International journal of molecular sciences 2018 - “...3 0.18 0.01 0.40 0.09 (+2.22) 0.21 0.01 (+1.17) 3-phosphoglycerate dehydrogenase-like protein; Arabidopsis; AM NP_195146.1 O49485 At4g34200 63.6 6.16 72 5.43 7707; 1.48 31 112; 266 4 0.11 0.01 0.15 0.01 (+1.36) 0.21 0.03 (+1.91) Phosphoglycerate kinase 1; Arabidopsis; CM NP_187884.1 Q9LD57 At3g12780 50.1 5.91 43...”
- “...8 0.17 0.02 0.64 0.19 (+3.76) 0.48 0.07 (+2.82) 3-phosphoglycerate dehydrogenase-like protein; Arabidopsis; AM NP_195146.1 O49485 At4g34200 63.6 6.16 73 5.56 6778; 1.74 30 88; 237 9 0.25 0.03 0.72 0.31 (+2.88) 0.72 0.16 (+2.88) 3-phosphoglycerate dehydrogenase-like protein; Arabidopsis; AM NP_195146.1 O49485 At4g34200 63.6 6.16 74...”
- The rolB plant oncogene affects multiple signaling protein modules related to hormone signaling and plant defense
Bulgakov, Scientific reports 2018 - “...metabolism 10 Q93ZC5 (AOC4_ARATH) Allene oxide cyclase 4, chloroplastic Jasmonic acid biosynthetic process 5.40.5 11 O49485 (SERA1_ARATH) D-3-phosphoglycerate dehydrogenase 1, chloroplastic L-serine biosynthetic process Embryo development Pollen development 2.60.5 Primary metabolism 12 Q8RWV0 (TKTC1_ARATH) Transketolase-1, chloroplastic Pentose-phosphate cycle 2.80.3 Primary metabolism 13 Q9C5Y9 (Q9C5Y9_ARATH) Initiation factor...”
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- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - “...42 , 43 . Accession numbers for each amino acid sequence are as follows: AtPGDH1, NP_195146 (EMBL/GenBank/DDBJ); AtPGDH2, NP_564034 (EMBL/GenBank/DDBJ); AtPGDH3, NP_566637 (EMBL/GenBank/DDBJ); AhPGDH, BAF91727.1 (EMBL/GenBank/DDBJ); MtPGDH, 1YGY chain A (PDB); RnPGDH, CAA66374.1 (EMBL/GenBank/DDBJ); HsPGDH, NP_006614.2 (EMBL/GenBank/DDBJ) and EcPGDH 1YBA chain A (PDB). Reagents Nicotine amide...”
- Functional characterization of the plastidial 3-phosphoglycerate dehydrogenase family in Arabidopsis.
Toujani, Plant physiology 2013 - GeneRIF: Data indicate that 3-phosphoglycerate dehydrogenases PGDH (At1g17745) and EDA9 (At4g34200) were expressed preferentially in roots while 3-PGDH (At3g19480) was expressed mainly in the aerial parts and was not expressed or very poorly in roots.
- Identification of the phosphoglycerate dehydrogenase isoform EDA9 as the essential gene for embryo and male gametophyte development in Arabidopsis.
Toujani, Plant signaling & behavior 2013 - GeneRIF: Genetic and molecular evidence were provided for the essential role of EDA9 for embryo and pollen development.
- Arabidopsis phosphoglycerate dehydrogenase1 of the phosphoserine pathway is essential for development and required for ammonium assimilation and tryptophan biosynthesis.
Benstein, The Plant cell 2013 - GeneRIF: PGDH1 is essential for Arabidopsis development.
- Metabolic engineering of the serine/glycine network as a means to improve the nitrogen content of crops
Casatejada-Anchel, Plant biotechnology journal 2025 - “...To obtain the At TriOex lines overexpressing the three main PPSB genes ( AtPGDH1 , At4g34200; AtPSAT1 , At4g35630; and AtPSP1 , At1g18640), transgenic plants overexpressing the AtPGDH1 gene (Toujani etal ., 2013 ) were used as a starting material. Two constructs were obtained in order...”
- “...software. Accession numbers The Arabidopsis locus identifiers for genes used in this study are: PGDH1 (At4g34200); PSAT1 (At4g35630); PSP1 (At1g18640). Themaize locus identifiers for PGDH1 genes are: ZmPGDHX1 (Zm00001d032114); ZmPGDHX2 (Zm00001d046923); ZmPGDHX9 (Zm00001d002051) and PGDHX10 (Zm00001d026472). Author contributions RCA, ATM, ADA, NB, AAE, LPS, SRT, JK,...”
- New Insights on the Role of ß-Cyanoalanine Synthase CAS-C1 in Root Hair Elongation through Single-Cell Proteomics
Arenas-Alfonseca, Plants (Basel, Switzerland) 2023 - “...ubiquitin-activating enzyme 2 AT3G48340 CEP2 CEP2__Cysteine proteinases superfamily protein AT4G24800 ECIP1-MRF3 ECIP1 MA3 domain-containing protein AT4G34200 EDA9P-GDH1 EDA9 D-3-phosphoglycerate dehydrogenase AT1G29880 Glycyl-tRNA synthetase/glycine--tRNA ligase AT1G18500 IPMS1-MAML-4 IPMS1 methylthioalkylmalate synthase-like 4 AT1G53240 mMDH1 mMDH1 Lactate/malate dehydrogenase family protein AT3G04600 Nucleotidylyl transferase superfamily protein AT2G22780 PMDH1 PMDH1__peroxisomal NAD-malate...”
- DEFECTIVELY ORGANIZED TRIBUTARIES 5 is not required for leaf venation patterning in Arabidopsis thaliana
Vlad, The Plant journal : for cell and molecular biology 2022 - “...AT4G16230 GDSLlike lipase/acylhydrolase superfamily protein AtL er 4G62980.1 Deletion exon 4, premature stop codon Chr4 AT4g34200 PGDH1; phosphoglycerate dehydrogenase 1; EDA9 AtL er 5G70960.1 Deletion Chr5 AT5G56200 C2H2 type zinc finger transcription factor family AtL er 1G22980.1 Insertion exon 2 Chr1 Not annotated AtL er 1G47950.1...”
- Nitric oxide coordinates growth, development, and stress response via histone modification and gene expression
Ageeva-Kieferle, Plant physiology 2021 - “...hydrolase family protein, AT1G78060), auxin biosynthesis (tryptophan aminotransferase related 2, AT4G24670), serine biosynthesis (D-3-phosphoglycerate dehydrogenase, AT4G34200), and histone modification (histone-lysine N-methyltransferase SETD1B-like protein, AT5G03670; Figure 8 ; Supplemental Table S2 ). Under D conditions, only three genes are hyperacetylated and overexpressed in both mutants. One of...”
- “...related 2 TAR2 is required for reprogramming root architecture in response to low nitrogen conditions. AT4G34200 D-3-phosphoglycerate dehydrogenase AT3G50660 Cytochrome P450 superfamily protein Brassinosteroid biosynthetic pathway. AT5G03670 Histone-lysine N-methyltransferase SETD1B-like protein Histone methyltransferase that specifically methylates H3K4. ChIP-seq and RNA-seq datasets were integrated at the gene...”
- Proteins associated with the Arabidopsis thaliana plastid rhomboid-like protein RBL10
Lavell, The Plant journal : for cell and molecular biology 2021 - “...appears to influence growth and development is D-3-Phoshpoglycerate dehydrogenase 1 (PGDH1 or EDA9) encoded by At4g34200. PGDH1 catalyzes the first committed step of serine biosynthesis and out of three PGDH-encoding genes in Arabidopsis, this appears to be essential and induced under salt stress ( Rosa-Tellez et...”
- “...CPN60B, LEN1 - chaperonin 60 beta AT1G55490 64 1.906 2 11 EDA9 - D-3-phosphoglycerate dehydrogenase AT4G34200 63 1.906 2 12 SBPASE - sedoheptulose-bisphosphatase AT3G55800 42 1.906 2 13 CLPC1 - CLPC homologue 1 AT5G50920 103 1.906 2 14 ATPB - ATP synthase subunit beta ATCG00480 54...”
- Network Topological Analysis for the Identification of Novel Hubs in Plant Nutrition
Di, Frontiers in plant science 2021 - “...synthetase A0A0A0KCX8 Csa_6G077980 ARGAH1 (AT4G08900) 85% 590 34 1 0 4 Arginase A0A0A0LBW6 Csa_3G199630 EDA9 (AT4G34200) 83% 981 4 1,9E-02 33 7 D-3-phosphoglycerate dehydrogenase A0A0A0L0I0 Csa_4G285780 PA2 (AT5G06720) 53% 335 3,7 2,6E-02 33 3 1 3 Peroxidase A0A0A0KA81 Csa_6G088110 AT2G20420 88% 757 31 4 8 12...”
- High-throughput single-cell transcriptomics reveals the female germline differentiation trajectory in Arabidopsis thaliana
Hou, Communications biology 2021 - “.../ pAT4G13710: 3Venus construct, the promoter sequences of ER (AT2G26330), ERL1 (AT5G62230), ERL2 (AT5G07180) pPGDH1 (AT4G34200), and AT4G13710 were amplified, and PCR fragments were cloned into the pENTR/D-TOPO vector (Invitrogen) and the pPGDH1/AT4G13710 3Venus -N7 vectors. The pENTR clones were recombined into the destination vector pGWB604...”
- Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance
Höhner, Plant physiology 2021 - “...of the respective metabolite or enzyme in WT and pgdh3 mutant plants. Accession numbers PGDH1 (At4g34200), PGDH2 (At1g17745), PGDH3 (At3g19480), pgdh3-1 mutant (SM_3_37584; Toujani etal., 2013 ), pgdh3-2 (GK-877F12; Toujani etal., 2013 ), npq4-1 (Li et al., 2000), npq2-1 aka aba1-6 CS3772 ( Niyogi etal., 1998...”
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M1AIT2 D-3-phosphoglycerate dehydrogenase from Solanum tuberosum
38% identity, 83% coverage
- Identification of the cell wall proteins associated with the softening of Lycium barbarum L. fruit by using iTRAQ technology.
Liu, Food chemistry. Molecular sciences 2022 - “...dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial 1.2030.028 1.5640.122 0.015 1.300 K4BP29 Alpha-galactosidase 0.9190.014 0.7260.047 0.005 0.790 M1AIT2 D-3-phosphoglycerate dehydrogenase 1.0290.029 0.8010.022 0.001 0.779 M1B2K3 Phosphomannomutase 0.8690.068 1.3130.125 0.012 1.510 M1B9T8 Aspartate aminotransferase 1.0300.049 1.2370.079 0.034 1.201 M1BC44 Beta-hexosaminidase 0.8770.014 0.7240.056 0.020 0.826 M1C0V6 Fructose-bisphosphate aldolase 0.8890.034 0.7030.057...”
- “...1.349 F1DBB9 Chloroplast polyphenol oxidase 1.1690.078 0.7410.021 0.034 0.634 K7QK65 Adenosylhomocysteinase 1.0010.022 1.2560.026 0.000 1.255 M1AIT2 D-3-phosphoglycerate dehydrogenase 1.0290.029 0.8010.022 0.001 0.779 M1B9T8 Aspartate aminotransferase 1.0300.049 1.2370.079 0.034 1.201 M1C0V6 Fructose-bisphosphate aldolase 0.8890.034 0.7030.057 0.017 0.791 P50433 Serine hydroxymethyltransferase, mitochondrial 1.1070.070 0.7450.085 0.010 0.673 Fatty acid...”
- Comparative proteomics of three Chinese potato cultivars to improve understanding of potato molecular response to late blight disease
Xiao, BMC genomics 2020 - “...protein L7A-like protein 0.69 0.00 M1CGC9 3-phosphoshikimate 1-carboxyvinyltransferase 0.78 0.00 M1BTT7 Ketol-acid reductoisomerase 0.78 0.00 M1AIT2 D-3-phosphoglycerate dehydrogenase 0.79 0.00 M1CZC0 ERBB-3 BINDING PR 0.81 0.00 A0A0M4KNM3 Carotenoid 9,10(9,10)-cleavage dioxygenase 1-like protein (Fragment) 0.77 0.00 Q9ZRB6 Ci21A protein 0.38 0.00 K7VKB1 TAS14 peptide 0.42 0.00 MA...”
- “...acid biosynthesis and metabolisms such as (phosphoshikimate 1-carboxyvinyltransferase (M1CGC9), ketol-acid reductoisomerase (M1BTT7), and D-3-phosphoglycerate dehydrogenase (M1AIT2). The phosphoshikimate 1-carboxyvinyltransferase is a key enzyme of the shikimate pathway, involved in the biosynthesis of multiple aromatic compounds, including chorismite, phenylalanine, tyrosine, and tryptophan [ 37 ]. The ketol-acid...”
CHLNCDRAFT_56437 hypothetical protein from Chlorella variabilis
38% identity, 85% coverage
B6SKK1 D-3-phosphoglycerate dehydrogenase from Zea mays
38% identity, 84% coverage
MAB_3304c D-3-phosphoglycerate dehydrogenase (SerA) from Mycobacterium abscessus ATCC 19977
39% identity, 93% coverage
A0QUY2 D-3-phosphoglycerate dehydrogenase from Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155)
MSMEG_2378 D-3-phosphoglycerate dehydrogenase from Mycobacterium smegmatis str. MC2 155
MSMEG_2378, MSMEI_2318 phosphoglycerate dehydrogenase from Mycolicibacterium smegmatis MC2 155
39% identity, 94% coverage
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...ClpC1 EQ Amino acid metabolism A0QR33 hemL , MSMEG_0969, MSMEI_0943 Glutamate-1-semialdehyde 2,1-aminomutase (GSA) 0.09 0.02 A0QUY2 serA , MSMEG_2378, MSMEI_2318 d -3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) 0.48 0.64 A0R6V5 gabT , MSMEG_6685, MSMEI_6505 4-Aminobutyrate transaminase (EC 2.6.1.19) 0.09 0.1 0.23 0.23 A0QZX1 hisG , MSMEG_4180, MSMEI_4082 ATP...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...acid metabolism A0QR33 hemL , MSMEG_0969, MSMEI_0943 Glutamate-1-semialdehyde 2,1-aminomutase (GSA) 0.09 0.02 A0QUY2 serA , MSMEG_2378, MSMEI_2318 d -3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) 0.48 0.64 A0R6V5 gabT , MSMEG_6685, MSMEI_6505 4-Aminobutyrate transaminase (EC 2.6.1.19) 0.09 0.1 0.23 0.23 A0QZX1 hisG , MSMEG_4180, MSMEI_4082 ATP phosphoribosyltransferase (ATP-PRT) (ATP-PRTase)...”
- High throughput screen identifies small molecule inhibitors specific for Mycobacterium tuberculosis phosphoserine phosphatase
Arora, The Journal of biological chemistry 2014 - “...Rv2996c BCG_3017c MMAR_1715 ML1692 MUL_1952 MAF_30010 MSMEG_2378, MSMEI_2318 Rv3214 BCG_3241, BCG_3334 MMAR_1343 Rv0489 BCG_0530 MMAR_0814, MMAR_3747 ML2441c...”
- Regulation of the ald gene encoding alanine dehydrogenase by AldR in Mycobacterium smegmatis
Jeong, Journal of bacteriology 2013 - “...a molecular mass of 32 kDa and pI of 5.2, and MSMEG_2378 (SerA), with a molecular mass of 51 kDa and pI of 4.9. (B) Determination of the transcription levels of...”
- “...encoded by MSMEG_2659 (ald), MSMEG_3084 (gap), and MSMEG_2378 (serA), respectively. Since the synthesis of alanine dehydrogenase (Ald) was increased the most...”
- Mycobacterium smegmatis RoxY is a repressor of oxyS and contributes to resistance to oxidative stress and bactericidal ubiquitin-derived peptides
Daugherty, Journal of bacteriology 2011 - “...Annotationa Intermediary metabolism msmeg_2378 .........................D-3-Phosphoglycerate dehydrogenase msmeg_5121 .........................Aminotransferase,...”
- “...the wild type was reproducibly observed in the msmeg_2378 and msmeg_0642 (yliD) mutants (see Fig. S2C in the supplemental material). Since mycobacterial mutants...”
- Interactome Analysis Identifies MSMEI_3879 as a Substrate of Mycolicibacterium smegmatis ClpC1
Ogbonna, Microbiology spectrum 2023 - “...metabolism A0QR33 hemL , MSMEG_0969, MSMEI_0943 Glutamate-1-semialdehyde 2,1-aminomutase (GSA) 0.09 0.02 A0QUY2 serA , MSMEG_2378, MSMEI_2318 d -3-Phosphoglycerate dehydrogenase (EC 1.1.1.95) 0.48 0.64 A0R6V5 gabT , MSMEG_6685, MSMEI_6505 4-Aminobutyrate transaminase (EC 2.6.1.19) 0.09 0.1 0.23 0.23 A0QZX1 hisG , MSMEG_4180, MSMEI_4082 ATP phosphoribosyltransferase (ATP-PRT) (ATP-PRTase) 0.04...”
B4G011 D-3-phosphoglycerate dehydrogenase from Zea mays
40% identity, 85% coverage
- Leaf Proteomic Analysis in Seedlings of Two Maize Landraces with Different Tolerance to Boron Toxicity
Mamani-Huarcaya, Plants (Basel, Switzerland) 2023 - “...degradation A0A1D6K836 Zm00001d029848 Branched-chain amino-acid aminotransferase 2.35 0.0272 1.65 0.0241 0.70 Branched-chain amino acid biosynthesis B4G011 Zm00001d046923 d -3-phosphoglycerate dehydrogenase chloroplastic 2.31 0.0154 1.52 0.0202 0.66 Serine biosynthesis A0A1D6DW07 Zm00001d002051 d -3-phosphoglycerate dehydrogenase 1.78 0.0494 1.69 0.0175 0.95 Serine biosynthesis CARBON ASSIMILATION/CALVIN CYCLE O24574 Zm00001d004894 Ribulose...”
SERA3_ARATH / Q9LT69 D-3-phosphoglycerate dehydrogenase 3, chloroplastic; EC 1.1.1.95 from Arabidopsis thaliana (Mouse-ear cress) (see 2 papers)
Q9LT69 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Arabidopsis thaliana (see 4 papers)
AT3G19480, NP_566637 D-3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
NP_566637 D-3-phosphoglycerate dehydrogenase, putative / 3-PGDH, putative from Arabidopsis thaliana
38% identity, 89% coverage
- function: Involved in the plastidial phosphorylated pathway of serine biosynthesis (PPSB).
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
disruption phenotype: No visible phenotype. - Cyclic electron flow compensates loss of PGDH3 and concomitant stromal NADH reduction
Krämer, Scientific reports 2024 - “...|1| cutoff, respectively. The red dot represents PGDH3 transcripts. C Read coverage of the PGDH3 (AT3G19480) locus of selected bio-replicates of WT (black), pgdh3-1 (red), or pgdh3-2 (green) after read mapping. The gene structure is given under the coverage plots in blue. The dashed line indicates...”
- “...Arabidopsis thaliana ( A. thaliana ) Columbia 0 (Col-0) accession. T-DNA insertion lines pgdh3-1 (SM_3_37584; At3g19480); pgdh3-2 (GK-877F12-026469; At3g19480); pam68l-1 (SALK_143426; At5g52780) 71 and point mutation lines pgr5 hope1 (At2g05620) 26 ; pgr5 -Cas#1 (At2g05620) 27 ; npq4-1 (At1g44575) 19 used as single and after crossings...”
- Integrative transcriptomics and proteomics profiling of <i>Arabidopsis thaliana</i> elucidates novel mechanisms underlying spaceflight adaptation
Olanrewaju, Frontiers in plant science 2023 - “...1 0.27 0.033 0.35 0.01 AT3G13460 Evolutionarily conserved C-terminal region 2 0.21 0.039 0.48 0.02 AT3G19480 D-3-phosphoglycerate dehydrogenase 0.27 0.02 0.44 0.02 AT3G25920 50S large ribosomal subunit 0.34 0.011 0.82 0.01 AT3G50820 Oxygen-evolving enhancer protein 12 0.41 0.014 0.72 0.01 AT3G60770 40S ribosomal subunit 0.21 0.04...”
- The Arabidopsis T-DNA mutant SALK_008491 carries a 14-kb deletion on chromosome 3 that provides rare insights into the plant response to dynamic light stress
Lopez, Plant direct 2022 - “...membrane protein of unknown function Plasma membrane At3G19470 Fbox and associated interaction domainscontaining protein Cytosol At3G19480 PGDH3 involved in the plastid phosphorylated pathway of serine biosynthesis Plastid At3G19490 NHD1 associated as a Na + /H + antiporter that extrudes sodium in exchange for protons Plastid 2.3...”
- “...14kb deletion, we identified the plastid stromal enzyme PHOSPHOGLYCERATE DEHYDROGENASE 3 (PGDH3) encoded by locus At3g19480 . PGDH3 is one of three PGDH isoforms in Arabidopsis to function in the phosphoserine pathway (Benstein et al., 2013 ). Previous studies have shown that isoform PGDH3 is important...”
- Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance
Höhner, Plant physiology 2021 - GeneRIF: Stromal NADH supplied by PHOSPHOGLYCERATE DEHYDROGENASE3 is crucial for photosynthetic performance.
- “...homozygous genotype of previously isolated independent T-DNA insertion lines pgdh3-1 and pgdh3-2 in the PGDH3 (At3g19480) locus ( Figure2, A and B; Toujani etal., 2013 ). In the same study, no residual PGDH3 mRNA was detected in either homozygous line ( Toujani etal., 2013 ). We...”
- Biochemical insight into redox regulation of plastidial 3-phosphoglycerate dehydrogenase from Arabidopsis thaliana
Yoshida, The Journal of biological chemistry 2020 (secret) - Phosphoserine Aminotransferase1 Is Part of the Phosphorylated Pathways for Serine Biosynthesis and Essential for Light and Sugar-Dependent Growth Promotion
Wulfert, Frontiers in plant science 2018 - “...contains three genes for the PGDH ( At4g34200 , PGDH1 ; At1g17745 , PGDH2 ; At3g19480 , PGDH3 ), two genes for the PSAT ( At4g35630 , PSAT1 , and At2g17630 , PSAT2 ) and one gene for the PSP ( At1g18640 ). Deficiency in either...”
- Identification and Biochemical Characterization of the Serine Biosynthetic Enzyme 3-Phosphoglycerate Dehydrogenase in Marchantia polymorpha
Akashi, Frontiers in plant science 2018 - “...share 7581% identity with each other and 3537% identity with MtPGDH. AtPGDH1 (At4g34200) and AtPGDH3 (At3g19480) are inhibited by L -serine, while AtPGDH2 (At1g17745) is not ( Benstein et al., 2013 ; Okamura and Hirai, 2017 ). The expression of genes encoding the three AtPGDH isozymes...”
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - “...expresses three PGDH isoforms and these are encoded by PGDH1 (At4g34200), PGDH2 (At1g17745), and PGDH3 (At3g19480) 1 (henceforth designated AtPGDH1 , AtPGDH2 , and AtPGDH3 , respectively). Although AtPGDH1 and AtPGDH3, but not AtPGDH2, are inhibited by l -serine 1 , the related modes of inhibition...”
- “...were purchased from Wako Pure Chemical Industries, Ltd. (Osaka, Japan). Plant materials To clone AtPGDH3 (At3g19480) cDNA, A . thaliana accession Columbia-0 (Col-0) were grown on agar-solidified half-strength MS medium containing 0.5% sucrose, 1mM MES, and 0.1% MS vitamin solution (pH 5.8) for 3 weeks under...”
- More
- Novel regulatory mechanism of serine biosynthesis associated with 3-phosphoglycerate dehydrogenase in Arabidopsis thaliana
Okamura, Scientific reports 2017 - “...for each amino acid sequence are as follows: AtPGDH1, NP_195146 (EMBL/GenBank/DDBJ); AtPGDH2, NP_564034 (EMBL/GenBank/DDBJ); AtPGDH3, NP_566637 (EMBL/GenBank/DDBJ); AhPGDH, BAF91727.1 (EMBL/GenBank/DDBJ); MtPGDH, 1YGY chain A (PDB); RnPGDH, CAA66374.1 (EMBL/GenBank/DDBJ); HsPGDH, NP_006614.2 (EMBL/GenBank/DDBJ) and EcPGDH 1YBA chain A (PDB). Reagents Nicotine amide adenine dinucleotide (NAD) disodium salt, 3-phosphoglycerate...”
XP_042922996 uncharacterized protein from Chlamydomonas reinhardtii
38% identity, 84% coverage
MMAR_1715 D-3-phosphoglycerate dehydrogenase SerA1 from Mycobacterium marinum M
40% identity, 93% coverage
P9WNX3 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Mycobacterium tuberculosis (see 5 papers)
Rv2996c PROBABLE D-3-PHOSPHOGLYCERATE DEHYDROGENASE SERA1 (PGDH) from Mycobacterium tuberculosis H37Rv
MT3074 D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis CDC1551
BCG_3017c putative D-3-phosphoglycerate dehydrogenase serA1 from Mycobacterium bovis BCG str. Pasteur 1173P2
YP_177916 D-3-phosphoglycerate dehydrogenase from Mycobacterium tuberculosis H37Rv
40% identity, 95% coverage
- The In Vivo Transcriptomic Blueprint of Mycobacterium tuberculosis in the Lung
Coppola, Frontiers in immunology 2021 - “...in vivo expressed genes 12 (Rv3418c, Rv3023c, Rv1199c, Rv0985c, Rv3115, Rv3022c, Rv2512c, Rv0299, Rv0294, Rv3018c, Rv2996c, and Rv1908c) were not previously described as IVE-TB genes or implemented in TB vaccines or diagnostics ( Figure S1 ). Taken together, these analyses show that most potent candidate TB...”
- One-Year Old Dormant, "Non-culturable" Mycobacterium tuberculosis Preserves Significantly Diverse Protein Profile
Trutneva, Frontiers in cellular and infection microbiology 2020 - “...regulatory protein MtrA Rv1436 Probable glyceraldehyde 3-phosphate dehydrogenase Gap (GAPDH) Rv3224 Possible iron-regulated short-chain dehydrogenase/reductase Rv2996c Probable D-3-phosphoglycerate dehydrogenase SerA1 (PGDH) Rv0860 Probable fatty oxidation protein FadB Rv3841 Bacterioferritin BfrB Rv0831c Conserved protein Rv0242c Probable 3-oxoacyl-[acyl-carrier protein] reductase FabG4 Rv2971 Probable oxidoreductase Rv3280 Probable propionyl-CoA carboxylase...”
- Activity-Based Protein Profiling Reveals That Cephalosporins Selectively Active on Non-replicating Mycobacterium tuberculosis Bind Multiple Protein Families and Spare Peptidoglycan Transpeptidases
Lopez, Frontiers in microbiology 2020 - “...subunit alpha P63677 Rv1310 atpD Yes PP: ATP synthase subunit beta Intermediary metabolism enzymes P0A544 Rv2996c serA Yes PP: D-3-phosphoglycerate dehydrogenase P60176 Rv3248c sahH Yes PP: adenosylhomocysteinase; thioester hydrolase P64178 Rv1436 gap Yes PP: glyceraldehyde-3-phosphate dehydrogenase P65149 Rv3001c ilvC Yes PP: ketol-acid reductoisomerase Q10530 Rv0896 gtlA2...”
- A High Throughput Whole Blood Assay for Analysis of Multiple Antigen-Specific T Cell Responses in Human Mycobacterium tuberculosis Infection
Whatney, Journal of immunology (Baltimore, Md. : 1950) 2018 - “...Unknown Pool 41 Rv2874 DipZ 2 Membrane Pool 42 Rv2875 MPT70 1 Secreted Pool 43 Rv2996c SerA1 2 Membrane Pool 44 Rv3012c GatC 4 Membrane Pool 45 Rv3015c Rv3015c 4 Cytoplasm Pool 46 Rv3018c PPE46 PPE family Unknown Pool 47 Rv3019c EsxR (TB10.3) 1 Predicted secreted...”
- D-3-Phosphoglycerate Dehydrogenase
Grant, Frontiers in molecular biosciences 2018 - “...tuberculosis , and Homo sapiens , the gene coding for PGDH is designated as serA1, Rv2996c , and PHGDH , respectively. In this review, the designation PGDH will be used to refer to this enzyme from any species. Figure 1 The l -serine biosynthetic pathway uses...”
- Cyclipostins and Cyclophostin analogs as promising compounds in the fight against tuberculosis
Nguyen, Scientific reports 2017 - “...AmiC Rv2888c 50.9 Amidase IM/R Amidase AmiB2 Rv1263 49.1 Amidase IM/R D-3-phosphoglycerate dehydrogenase (PGDH) SerA1 Rv2996c 54.5 in vitro Methyltransferase IM/R 32 Carboxylesterase A CaeA Rv2224c 55.9 Macrophage and in vitro growth Lipase/esterase CW/CP 49 , 51 2 Penicillin-binding protein Rv1730c 55.8 -lactamase CW/CP 30 Serine...”
- “...concomitant reduction of NAD; the putative L-lactate dehydrogenase LidD2 (Rv1872c) 31 ; the methyltransferase SerA1 (Rv2996c) involved in the L-serine biosynthetic process 32 ; glyA1 (Rv1093) annotated as a serine hydroxymethyltransferase with possible role in serine to glycine conversion 33 ; and UmaA (Rv0469) a S-adenosyl-L-methionine-dependent...”
- A genome-wide structure-based survey of nucleotide binding proteins in M. tuberculosis
Bhagavat, Scientific reports 2017 - “...Rv2855 NADPH-dependent mycothiol reductase Mtr ATP Rv2858c Probable aldehyde dehydrogenase AldC AMP ADP ATP GTP Rv2996c Probable D-3-phosphoglycerate dehydrogenase SerA1 (PGDH) ADP Rv3028c Probable electron transfer flavoprotein (alpha-subunit) FixB (alpha-ETF) (electron transfer flavoprotein large subunit) (ETFLS) GTP Rv3075c Conserved protein ATP GTP Rv3273 Probable transmembrane carbonic...”
- “...described in supplementary text B. Examples of proteins Rv1017c (prsA), Rv1098c (fum), Rv3676 (crp), Rv0998, Rv2996c (serA) and Rv3710 (leuA) are discussed with two possibilities of a) identifying a new additional location on the known allosteric protein, and b) suggesting a possible new allosteric modulator for...”
- Mycobacterium tuberculosis AtsG (Rv0296c), GlmU (Rv1018c) and SahH (Rv3248c) Proteins Function as the Human IL-8-Binding Effectors and Contribute to Pathogen Entry into Human Neutrophils
Dziadek, PloS one 2016 - “...arylsulfatase), GlmU (Rv1018c; bifunctional glucosamine-1-phosphate acetyltransferase and N-acetylglucosamine-1-phosphate uridyltransferase), SahH (Rv3248c; S-adenosyl-L-homocysteine hydrolase) and SerA (Rv2996c; D-3-phosphoglycerate dehydrogenase SerA1) were selected and subjected to further analysis. Proteins and peptides identification details are provided in S1 Table in supplementary materials related to this article. Analysis of Mtb...”
- More
- Neu-Laxova syndrome is a heterogeneous metabolic disorder caused by defects in enzymes of the L-serine biosynthesis pathway
Acuna-Hidalgo, American journal of human genetics 2014 - “...(RefSeq NP_496868.1), and Mycobacterium tuberculosis (UniProt ID P9WNX3) were obtained from UniProt and Entrez. The 3D structure of wild-type human PHGDH...”
- Enhanced specialized transduction using recombineering in Mycobacterium tuberculosis
Tufariello, mBio 2014 - “...( 17 ) to result in amino acid or vitamin auxotrophy: serA1 ( Rv2996c [ MT3074 ]), metA ( Rv3341 [ MT3444 ]), panC ( Rv3602c [ MT3707 ]), leuD ( Rv2987c [ MT3065 ]), and argB ( Rv1654 [ MT1692 ]), to induce auxotrophy for...”
- High throughput screen identifies small molecule inhibitors specific for Mycobacterium tuberculosis phosphoserine phosphatase
Arora, The Journal of biological chemistry 2014 - “...ML1837 (Pseudogene) MUL_0823 MAF_07380 Rv2996c BCG_3017c MMAR_1715 ML1692 MUL_1952 MAF_30010 MSMEG_2378, MSMEI_2318 Rv3214 BCG_3241, BCG_3334 MMAR_1343...”
- Crystal structure of Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase: extreme asymmetry in a tetramer of identical subunits.
Dey, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: Mycobacterium tuberculosis D-3-phosphoglycerate dehydrogenase has extreme asymmetry in a tetramer of identical subunits
- D-3-Phosphoglycerate dehydrogenase from Mycobacterium tuberculosis is a link between the Escherichia coli and mammalian enzymes.
Dey, The Journal of biological chemistry 2005 (PubMed)- GeneRIF: analysis of D-3-Phosphoglycerate dehydrogenase from Mycobacterium tuberculosis
3dc2A / P9WNX3 Crystal structure of serine bound d-3-phosphoglycerate dehydrogenase from mycobacterium tuberculosis (see paper)
40% identity, 94% coverage
MUL_1952 D-3-phosphoglycerate dehydrogenase SerA1 from Mycobacterium ulcerans Agy99
40% identity, 93% coverage
C629_RS07285 phosphoglycerate dehydrogenase from Corynebacterium glutamicum SCgG2
cg1451 D-3-phosphoglycerate dehydrogenase from Corynebacterium glutamicum ATCC 13032
38% identity, 92% coverage
- Transcriptomic and enzymatic analysis reveals the roles of glutamate dehydrogenase in Corynebacterium glutamicum
Ge, AMB Express 2022 - “...were upregulated. In addition, the genes of serine synthesized from glyceric acid -3-P, including serA (C629_RS07285), serC (C629_RS05100), serB (C629_RS12565), and then glyA (C629_RS05820) of glycine synthesized from serine, were upregulated. Analysis of transcriptomic changes of C. glutamicum F343 elicited by gdhA gdhB double disruption When...”
- Comprehensive Analysis of C. glutamicum Anaplerotic Deletion Mutants Under Defined d-Glucose Conditions
Kappelmann, Frontiers in bioengineering and biotechnology 2020 - “...3.42e-23 CAF18800 cg0282 Conserved hypothetical protein 2.02 2.79e-08 CAF20737 cg3008 porA Porin 0.48 7.16e-06 CAF19986 cg1451 serA Phosphoglycerate dehydrogenase 0.43 5.03e-30 CAF19413 cg0812 dtsR1 Acetyl/ propionyl-CoA carboxylase beta chain 0.42 1.34e-13 All proteins with significant changes [p < 0.05, Log2(fold change) > 0.5 for upregulated proteins...”
- “...appear to accumulate intracellularly. This would also explain why the phosphoglycerate dehydrogenase encoded by serA (cg1451) was found to be significantly down-regulated in this mutant ( Table 3 ). The enzyme catalyzes the first step in the biosynthesis of l -glycine, l -serine and l -cysteine...”
- Protein S-mycothiolation functions as redox-switch and thiol protection mechanism in Corynebacterium glutamicum under hypochlorite stress
Chi, Antioxidants & redox signaling 2014 - “...Cg2862 PurLb Fructose-bisphosphate aldolase Phosphoglycerate Cg1451 SerAb dehydrogenase Cg3048 Pta Phosphate acetyltransferase Cg0147 XylB Sugar (pentulose...”
- Citrate utilization by Corynebacterium glutamicum is controlled by the CitAB two-component system through positive regulation of the citrate transport genes citH and tctCBA
Brocker, Journal of bacteriology 2009 - “...cg1581 cg1582 cg1583 cg3026 cg3027 cg3028 cg3029 cg1156 cg1451 cg0576 cg2894 cg1364 cg2157 cg1151 cg1386 cg0653 cg1147 cg1349 cg0825 cg0882 cg3420 cg2069 cg3351...”
- Functional genomics of pH homeostasis in Corynebacterium glutamicum revealed novel links between pH response, oxidative stress, iron homeostasis and methionine synthesis
Follmann, BMC genomics 2009 - “...subunit 0 -1.71 -1.11 1.1 4.2 3.4 3.3 4.9 4.7 4.0 4.0 2.5 SigH* 28 cg1451 serA Phosphoglycerate dehydrogenase 0 -0.22 -1.10 6.5 5.4 6.1 7.7 7.5 7.2 5.3 5.3 4.2 29 cg1537 ptsM PTS system mannose-specific EIIBCA component 10 -0.39 -1.06 2.6 3.5 1.8 5.9...”
- Co-ordinated regulation of gluconate catabolism and glucose uptake in Corynebacterium glutamicum by two functionally equivalent transcriptional regulators, GntR1 and GntR2
Frunzke, Molecular microbiology 2008 - “...0.99 0.90 cg1488 3-isopropylmalate dehydratase small subunit, leuD 0.10 1.23 1.09 1.27 1.15 0.98 0.98 cg1451 d -3-phosphoglycerate dehydrogenase, serA 0.12 1.10 0.86 1.00 1.09 0.67 1.14 cg2125 Uracil permease, uraA 0.14 1.11 1.22 0.86 1.10 1.03 0.98 cg0564 LSU ribosomal protein L1P 0.19 0.75 0.97...”
- Random mutagenesis in Corynebacterium glutamicum ATCC 13032 using an IS6100-based transposon vector identified the last unknown gene in the histidine biosynthesis pathway
Mormann, BMC genomics 2006 - “...proC (1) Pyrroline-5-carboxylate reductase Proline biosynthesis [98] 5 Methionine nd c nd c 13 Serine cg1451 serA (1) Phosphoglycerate dehydrogenase Serine biosynthesis [99] 17 Cysteine cg3118 cysI (2) Ferredoxin-sulfite reductase Assimilatory sulfate reduction [65] 14 Leucine cg1488 leuD (1) 3-Isopropylmalate dehydratase, small chain Leucine biosynthesis [100]...”
- Adaptation of Corynebacterium glutamicum to ammonium limitation: a global analysis using transcriptome and proteome techniques
Silberbach, Applied and environmental microbiology 2005 - “...cg0113 cg0115 cg0104 cg0104 cg0116 cg1256 cg0119 cg1437 cg0104 cg1451 cg1784 cg1783 cg1784 cg2280 cg1437 cg0303 cg1581 ureB glnA ocd ureG ureA ureC codAb codAb...”
- “...NCgl2451 NCgl1442 NCgl0625 NCgl0345 NCgl1926 NCgl0827 cg1203 cg1451 cg2361 cg0873 cg1814 cg1145 cg2453 cg3096 cg0482 cg2797 cg1693 cg0755 cg0422 cg2192 cg0984...”
AFUA_2G04490 D-3-phosphoglycerate dehydrogenase from Aspergillus fumigatus Af293
37% identity, 83% coverage
MAVA5_16825 phosphoglycerate dehydrogenase from Mycobacterium avium subsp. hominissuis A5
39% identity, 94% coverage
ML1692 D-3-phosphoglycerate dehydrogenase from Mycobacterium leprae TN
40% identity, 92% coverage
MAP3033c SerA from Mycobacterium avium subsp. paratuberculosis str. k10
39% identity, 94% coverage
ATE51_01764 phosphoglycerate dehydrogenase from Campylobacter coli
36% identity, 93% coverage
PITG_00133 phosphoserine aminotransferase, putative from Phytophthora infestans T30-4
36% identity, 15% coverage
Cj0891c D-3-phosphoglycerate dehydrogenase from Campylobacter jejuni subsp. jejuni NCTC 11168
36% identity, 93% coverage
- Cysteine Biosynthesis in Campylobacter jejuni: Substrate Specificity of CysM and the Dualism of Sulfide
Hitchcock, Biomolecules 2022 - “...Knock-out deletion mutants of cysM ( cj0912c ), cysE ( cj0763c ) and serA ( cj0891c ) were generated by replacing the majority of the open reading frame with an antibiotic resistance cassette. Mutation plasmids were generated by an isothermal assembly method, as follows. Upstream and...”
- In vivo and in silico determination of essential genes of Campylobacter jejuni
Metris, BMC genomics 2011 - “...cj0699c, cj0716, cj0764c, cj0766c, cj0767c, cj0795c, cj0798c, cj0806, cj0813, cj0821, cj0822, cj0847, cj0853c, cj0858c, cj0862c, cj0891c, cj0905c, cj0918c, cj0932c, cj0947c, cj0949c, cj0955c, cj0992c, cj0995c, cj1039, cj1044c, cj1046c, cj1048c, cj1067, cj1080c, cj1081c, cj1088c, cj1096c, cj1104, cj1114c, cj1133, cj1149c, cj1150c, cj1151c, cj1152c, cj1177c, cj1183c, cj1196c, cj1198, cj1202, cj1213c,...”
- Comparison of PCR binary typing (P-BIT), a new approach to epidemiological subtyping of Campylobacter jejuni, with serotyping, pulsed-field gel electrophoresis, and multilocus sequence typing methods
Cornelius, Applied and environmental microbiology 2010 - “...Rev: GGCTTTTCACATTCGCTTTC 404 71 serA (Cj0891c) For: GGGGTGGGCGTAGATAATGT Rev: TTTTGCAATTTCTTGCTTTCC 450 49 peb1A (Cj0921c) For: TTGATCAAGCAACAGGTGAAA...”
- Iron acquisition and regulation in Campylobacter jejuni
Palyada, Journal of bacteriology 2004 - “...ExbB2, ExbD2, TonB1, ExbB1, and ExbD1 CeuC Cft Cj0203, Cj0891c, Cj1163c, and Cj0339 Oxidative stress responses PerR KatA AhpC Tpx SodB Iron not required as...”
CJJ81176_0900 D-3-phosphoglycerate dehydrogenase from Campylobacter jejuni subsp. jejuni 81-176
36% identity, 93% coverage
DR_1291 D-3-phosphoglycerate dehydrogenase from Deinococcus radiodurans R1
36% identity, 97% coverage
SERA_MOUSE / Q61753 D-3-phosphoglycerate dehydrogenase; 3-PGDH; A10; EC 1.1.1.95 from Mus musculus (Mouse) (see paper)
Q61753 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Mus musculus (see 2 papers)
NP_058662 D-3-phosphoglycerate dehydrogenase from Mus musculus
43% identity, 74% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Does not catalyze the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
subunit: Homotetramer.
disruption phenotype: Decreased level of free serine, glycine, taurine, GABA, glutamine, and threonine in spinal cord and head. Impaired central nervous system (CNS) with shorter neural tube length and overall growth retardation. Severe atrophy at the thoracic level, particularly in the dorsal spinal cord. Poorly developed dorsal horn and adjacent mantle zone. Neurons fail to develop neurites, particularly commissural axonal fibers. - Yap/Taz activity is associated with increased expression of phosphoglycerate dehydrogenase that supports myoblast proliferation.
Meinhold, Cell and tissue research 2024 - GeneRIF: Yap/Taz activity is associated with increased expression of phosphoglycerate dehydrogenase that supports myoblast proliferation.
- Phosphoglycerate dehydrogenase activates PKM2 to phosphorylate histone H3T11 and attenuate cellular senescence.
Wu, Nature communications 2023 - GeneRIF: Phosphoglycerate dehydrogenase activates PKM2 to phosphorylate histone H3T11 and attenuate cellular senescence.
- ZEB1 Transcriptionally Activates PHGDH to Facilitate Carcinogenesis and Progression of HCC.
Wang, Cellular and molecular gastroenterology and hepatology 2023 - GeneRIF: ZEB1 Transcriptionally Activates PHGDH to Facilitate Carcinogenesis and Progression of HCC.
- Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate.
Wu, Cell research 2023 - GeneRIF: Low glucose metabolite 3-phosphoglycerate switches PHGDH from serine synthesis to p53 activation to control cell fate.
- Chemical Components of the Fruits of Morus nigra Linn.: Methyl Caffeate as a Potential Anticancer Agent by Targeting 3-Phosphoglycerate Dehydrogenase.
Wang, Journal of agricultural and food chemistry 2021 (PubMed)- GeneRIF: Chemical Components of the Fruits of Morus nigra Linn.: Methyl Caffeate as a Potential Anticancer Agent by Targeting 3-Phosphoglycerate Dehydrogenase.
- Downregulation of PHGDH expression and hepatic serine level contribute to the development of fatty liver disease.
Sim, Metabolism: clinical and experimental 2020 (PubMed)- GeneRIF: Reduced Phgdh expression and serine levels are closely associated with the development of Fatty Liver Disease.
- Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
Wilson, Cell reports 2020 - GeneRIF: Inverse Data-Driven Modeling and Multiomics Analysis Reveals Phgdh as a Metabolic Checkpoint of Macrophage Polarization and Proliferation.
- Deletion of PHGDH in adipocytes improves glucose intolerance in diet-induced obese mice.
Okabe, Biochemical and biophysical research communications 2018 (PubMed)- GeneRIF: PHGDH-mediated serine biosynthesis has important roles in adipose tissue glucose metabolism and could be a therapeutic target for diabetes in humans
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- Lectin-Based Immunophenotyping and Whole Proteomic Profiling of CT-26 Colon Carcinoma Murine Model.
Faragó, International journal of molecular sciences 2024 - “...P16110 Galectin-3 73.50 P97310 DNA replication licensing factor MCM2 81.89 Q8K009 Mitochondrial 10-formyltetrahydrofolate dehydrogenase 82.70 Q61753 D-3-phosphoglycerate dehydrogenase 100 P25206 DNA replication licensing factor MCM3 100 P52927 High mobility group protein HMGI-C 100 P14069 Protein S100-A6 100 P70202 Latexin 100 Q64437 All-trans-retinol dehydrogenase [NAD(+)] ADH7 100...”
- Sertoli cell-enriched proteins in mouse and human testicular interstitial fluid
O'Donnell, PloS one 2023 - “...Q9DCJ9 Npl N-acetylneuraminate lyase No B2RQ13 Pald1 Paladin Yes Q921X9 Pdia5 Protein disulfide-isomerase A5 Yes Q61753 Phgdh D-3-phosphoglycerate dehydrogenase Yes Q9WTX2 Prkra Interferon-inducible double-stranded RNA-dependent protein kinase activator A Yes Q4VA55 Pwwp3b PWWP domain-containing DNA repair factor 3B Yes Q3UFN2 Qpct Glutaminyl-peptide cyclotransferase Yes Q4TU85 Rhox8...”
- Identification and characterization of ARID1A-interacting proteins in renal tubular cells and their molecular regulation of angiogenesis.
Yoodee, Journal of translational medicine 2023 - “...E2R1I5 CCDC39 6.20 0.9 1/1 110.37 Cornifin-B P22528 SPRR1B 34.12 55.1 4/4 9.89 D-3-phosphoglycerate dehydrogenase Q61753 PHGDH 7.86 2.1 1/1 56.59 DCC-interacting protein 13-alpha Q8K3H0 APPL1 33.13 5.0 3/3 79.33 Desmoplakin P15924 DSP 21.59 1.0 2/2 331.77 Dolichyl-diphosphooligosaccharide protein glycosyltransferase 48kDa subunit Q29381 DDOST 28.26 2.5...”
- In-Depth Proteomic Analysis of De Novo Proteome in a Mouse Model of Alzheimer's Disease.
Wang, Journal of Alzheimer's disease : JAD 2023 - “...Actin-related protein 3B Q641P0 0.33 Brefeldin A-inhibited guanine nucleotide-exchange protein 2 A2A5R2 0.33 D-3-phosphoglycerate dehydrogenase Q61753 0.38 Heat shock 70 kDa protein 1B P17879 0.40 Xaa-Pro aminopeptidase 1 Q6P1B1 0.53 Neurofascin Q810U3 0.58 Cholesterol 24-hydroxylase Q9WVK8 0.63 Phosphatidate cytidylyltransferase 2 Q99L43 0.64 Beta-adducin Q9QYB8 0.72 Engulfment...”
- Periostin Protects Against Alcohol-related Liver Disease by Activating Autophagy by Interacting With Protein Disulfide Isomerase.
Zhang, Cellular and molecular gastroenterology and hepatology 2023 - “...beta 7 2 2 Q61696 Hspa1a Heat shock 70 kDa protein 1A 21 11 4 Q61753 Phgdh D-3-phosphoglycerate dehydrogenase 4 2 2 Q62009 Postn Periostin 43 30 30 Q62267 Sprr1b Cornifin-B 5 1 1 Q68FD5 Cltc Clathrin heavy chain 1 4 6 6 Q6PDQ2 Chd4 Chromodomain-helicase-DNA-binding...”
- Proteomic analysis reveals activation of platelet- and fibrosis-related pathways in hearts of ApoE-/- mice exposed to diesel exhaust particles.
Jung, Scientific reports 2023 - “...1.64 0.032 O88207 COL5A1 Collagen alpha-1(V) chain 1.62 0.018 Q80XB4 NRAP Nebulin-related-anchoring protein 1.62 0.044 Q61753 PHGDH D-3-phosphoglycerate dehydrogenase 1.61 0.002 P16110 LGALS3 Galectin-3 1.60 0.021 P18872 GNAO1 Guanine nucleotide-binding protein G(o) subunit alpha 1.60 0.008 Q7TQ62 PODN Podocan 1.60 0.003 P13595 NCAM1 Neural cell adhesion...”
- Intra- and Inter-individual Differences in the Human Intestinal Microbial Conversion of (-)-Epicatechin and Bioactivity of Its Major Colonic Metabolite 5-(3',4'-Dihydroxy-Phenyl)-γ-Valerolactone in Regulating Nrf2-Mediated Gene Expression.
Liu, Frontiers in nutrition 2022 - “...gamma 1, mitochondrial Idh3g 1.24 (0.265) 1.20 (0.330) P61222 ABCE1 Abce1 1.01 (0.916) 1.26 (0.074) Q61753 D-3-phosphoglycerate dehydrogenase Phgdh 1.05 (0.608) 1.20 (0.089) P39689 Cyclin-dependent kinase inhibitor 1 Cdkn1a 2.32 (0.513) 6.16 (0.093) P28033 CCAAT/enhancer-binding protein beta Cebpb 1.20 (0.427) 1.04 (0.868) O54790 Transcription factor MafG...”
- Myocardial Injury Caused by Chronic Alcohol Exposure-A Pilot Study Based on Proteomics.
Ma, Molecules (Basel, Switzerland) 2022 - “...Q3UIJ3 Uncharacterized protein Actc1 0.634 0.027 down V9GXQ2 Predicted gene 17087 Gm17087 0.710 0.027 down Q61753 D-3-phosphoglycerate dehydrogenase Phgdh 0.816 0.027 down O35604 NPC intracellular cholesterol transporter 1 Npc1 0.824 0.029 down Q8VDP3 [F-actin]-monooxygenase MICAL1 Mical1 0.832 0.032 down Q3TX70 t-SNARE coiled-coil homology domain-containing protein Stx6...”
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Phgdh / O08651 3-phosphoglycerate dehydrogenase subunit (EC 1.1.1.95) from Rattus norvegicus (see paper)
SERA_RAT / O08651 D-3-phosphoglycerate dehydrogenase; 3-PGDH; EC 1.1.1.95 from Rattus norvegicus (Rat) (see paper)
O08651 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Rattus norvegicus (see paper)
NP_113808 D-3-phosphoglycerate dehydrogenase from Rattus norvegicus
43% identity, 74% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Does not catalyze the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
subunit: Homotetramer. - Phgdh serves a protective role in Il‑1β induced chondrocyte inflammation and oxidative‑stress damage.
Huang, Molecular medicine reports 2021 - GeneRIF: Phgdh serves a protective role in Il1beta induced chondrocyte inflammation and oxidativestress damage.
- Protective effects and potential mechanisms of Pien Tze Huang on cerebral chronic ischemia and hypertensive stroke
Zhang, Chinese medicine 2010 - “...CO3 -2.80 146 Complement C3 precursor Q9JHU0 NP_075412 DPYL5 -2.93 412 Dihydropyrimidinase-related protein 5 O08651 NP_113808 SERA -2.67 67 D-3-phosphoglycerate dehydrogenase P67779 NP_114039 PHB -2.13 561 Prohibitin P10860 NP_036702 DHE3 -2.03 443 Glutamate dehydrogenase 1, mitochondrial precursor Q63270 NP_059017 ACOC +2.00 154 Cytoplasmic aconitate hydratase *...”
- Candidate proteins interacting with cytoskeleton in cells from the basal airway epithelium in vitro
Olatona, Frontiers in molecular biosciences 2024 - “...P22734 Comt Catechol O-methyltransferase 29.6 0.025 P18395 Csde1 Cold shock domain-containing protein E1 88.8 0.000 O08651 Phgdh D-3-phosphoglycerate dehydrogenase 56.5 0.351 Met-loss + Acetyl [N-Term] P55053 Fabp5 Fatty acid-binding protein 5 15.1 0.009 P05370 G6pdx Glucose-6-phosphate 1-dehydrogenase 59.3 0.526 Met-loss + Acetyl [N-Term] Q66H61 Qars1 Glutamine--tRNA...”
- Label-free proteomic analysis reveals the hepatoprotective mechanism of gypenosides in liver injury rats.
Chen, Frontiers in pharmacology 2024 - “...fibrosis ( Mackinnon et al., 2023 ). Psat1 (Uniprot ID: A0A0G2K931) and Phgdh (Uniprot ID: O08651) are critical enzymes involved in the de novo synthesis of serine, directing the glycolytic intermediate 3-phosphoglyceric acid into the pathway. Recent studies have revealed that in hepatocellular carcinoma, PHGDH has...”
- Carbonylated Proteins as Key Regulators in the Progression of Metabolic Syndrome.
Kitamura, Antioxidants (Basel, Switzerland) 2023 - “...(CAT) 16.9 7 1.46 1.39 989 Q68FS4 Cytosol aminopeptidase (LAP3) 7.9 3 2.39 2.58 999 O08651 D-3-phosphoglycerate dehydrogenase (PHGDH) 15.0 4 1.69 2.24 1598 O88989 Malate dehydrogenase (MDH1) 26.4 7 1.66 1.93 1888 Q9Z0V6 Thioredoxin-dependent peroxide reductase (PRDX3) 23.7 4 1.47 1.27 1907 P08010 Glutathione S-transferase...”
- Gephyrin Interacts with the K-Cl Cotransporter KCC2 to Regulate Its Surface Expression and Function in Cortical Neurons
Al, The Journal of neuroscience : the official journal of the Society for Neuroscience 2022 (secret) - Investigation into potential mechanisms of metabolic syndrome by integrative analysis of metabolomics and proteomics.
Chen, PloS one 2022 - “...mitochondrial Amino-acid biosynthesis. 1.475 0.0005 Pck1 P07379 Phosphoenolpyruvate carboxykinase, cytosolic [GTP] Gluconeogenesis 1.248 0.0062 Phgdh O08651 D-3-phosphoglycerate dehydrogenase Amino-acid biosynthesis 0.542 0.0037 Pycr3 Q5PQJ6 Pyrroline-5-carboxylate reductase 3 Amino-acid biosynthesis 0.77 0.0028 Retsat Q8VHE9 All-trans-retinol 13,14-reductase Retinol metabolic process 0.832 0.0024 Sdhd Q6PCT8 Succinate dehydrogenase [ubiquinone] Carbohydrate...”
- Fluoxetine Enhances Synaptic Vesicle Trafficking and Energy Metabolism in the Hippocampus of Socially Isolated Rats.
Filipović, International journal of molecular sciences 2022 - “...subunit A (PR 65), alpha isoform, isoform CRA_a Q5XI34 Ppp2r1a 1.58 10 10 D-3-phosphoglycerate dehydrogenase O08651 Phgdh 1.57 4 3 N-ethylmaleimide sensitive fusion protein, isoform CRA_b F1LQ81 Nsf 1.57 22 21 Heat shock cognate 71 kDa protein P63018 Hspa8 1.57 44 36 Heat shock 70 kDa...”
- Proteomic Analysis of the Spatio-temporal Based Molecular Kinetics of Acute Spinal Cord Injury Identifies a Time- and Segment-specific Window for Effective Tissue Repair
Devaux, Molecular & cellular proteomics : MCP 2016 - “...Q62669 Q68FY4 Q6MGC4 Q7TQ70 Cluster 5 B0BNM1 B2RYG6 O08651 Sec22b Protein name UV excision repair protein RAD23 homolog B Dihydropyrimidinase-related protein 3...”
- Influence of age on rat bone-marrow mesenchymal stem cells potential
Fafián-Labora, Scientific reports 2015 - “...and glycine-rich protein 1 7 1,0015 0,9815 1,0448 0,5131 1,2576 0,0488 0,6896 0,0389 1,2501 0,0705 O08651 D-3-phosphoglycerate dehydrogenase 3 0,8786 0,1902 0,7465 0,0308 1,1981 0,1105 1,1565 0,1448 1,0565 0,5069 Q5BJ93 Enolase 1, (Alpha) 23 1,0226 0,655 1,026 0,5722 1,054 0,2406 0,7412 0 1,2752 0,0123 Q8R4A1 ERO1-like...”
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PHGDH / O43175 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) from Homo sapiens (see 3 papers)
SERA_HUMAN / O43175 D-3-phosphoglycerate dehydrogenase; 3-PGDH; 2-oxoglutarate reductase; Malate dehydrogenase; EC 1.1.1.95; EC 1.1.1.399; EC 1.1.1.37 from Homo sapiens (Human) (see 7 papers)
O43175 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Homo sapiens (see 8 papers)
44% identity, 72% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate and the reversible oxidation of (S)-malate to oxaloacetate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
catalytic activity: (R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH + H(+) (RHEA:49612)
catalytic activity: (S)-malate + NAD(+) = oxaloacetate + NADH + H(+) (RHEA:21432)
subunit: Homotetramer. - Comparative Analysis of Acquired Resistance to Bortezomib in Prostate Cancer Cells Using Proteomic and Bioinformatic Tools.
Seker, Journal of cellular and molecular medicine 2025 - “...ribosomal protein L21 4 2.877 0.694 18621.909 P49006 MARCKSL1 MARCKSrelated protein 5 2.872 0.931 19585.837 O43175 PHGDH D3phosphoglycerate dehydrogenase 20 2.867 0.708 57391.960 P60891 PRPS1 Ribosephosphate pyrophosphokinase 1 5 2.820 0.679 35347.547 P49756 RBM25 RNAbinding protein 25 5 2.723 0.781 100527.802 P17174 GOT1 Aspartate aminotransferase_ cytoplasmic...”
- A Proteomic Approach Identified TFEB as a Key Player in the Protective Action of Novel CB2R Bitopic Ligand FD22a against the Deleterious Effects Induced by β-Amyloid in Glial Cells.
Polini, Cells 2024 - “...1.20 1641 P68371 TUBB4B Tubulin beta-4B chain 142 31 13 4.79 50,255 0.0043 0.51 1725 O43175 PHGDH D-3-phosphoglycerate dehydrogenase 56 12 6 6.29 57,356 0.0005 1.81 1726 P28329 CHAT Choline O-acetyltransferase 73 9 8 8.9 83,852 0.0282 0.74 1730 P78371 CCT2 T-complex protein 1 subunit beta...”
- Single-Cell Patch-Clamp/Proteomics of Human Alzheimer's Disease iPSC-Derived Excitatory Neurons Versus Isogenic Wild-Type Controls Suggests Novel Causation and Therapeutic Targets.
Ghatak, Advanced science (Weinheim, Baden-Wurttemberg, Germany) 2024 - “...in the TCA cycle not previously proposed, as discussed further below. Another upregulated protein, SERA (O43175, or D3phosphoglycerate dehydrogenase or PDGDH), catalyzes reversible oxidation of 3phosphoDglycerate to 3phosphonooxypyruvate, the first step of the phosphorylated l serine biosynthesis pathway, 2hydroxyglutarate to 2oxoglutarate, or (S)malate to oxaloacetate in...”
- Downregulation of AHNAK2 inhibits cell cycle of lung adenocarcinoma cells by interacting with RUVBL1
Li, Thoracic cancer 2023 - “...smooth muscle (ACTA2) 228 0.25 10 P49411 Elongation factor Tu, mitochondrial (TUFM) 483 0.29 11 O43175 D3phosphoglycerate dehydrogenase (PHGDH) 429 0.18 12 P17844 Probable ATPdependent RNA helicase DDX5 (DDX5) 428 0.26 13.1 Q06830 Peroxiredoxin1 (PRDX1) 361 0.75 13.2 P32119 Peroxiredoxin2 (PRDX2) 214 0.33 14 O14980 Exportin1...”
- The mitotic surveillance pathway requires PLK1-dependent 53BP1 displacement from kinetochores
Burigotto, 2023 - Towards unravelling biological mechanisms behind radiation-induced oral mucositis via mass spectrometry-based proteomics.
Subedi, Frontiers in oncology 2023 - “...synthase 2 1,51 5,54E-03 9,16 4,75E-16 Q15646 OASL 2-5-oligoadenylate synthase-like protein 100 2,30E-16 4,26 9,31E-13 O43175 PHGDH D-3-phosphoglycerate dehydrogenase 0,418 3,77E-12 0,452 3,14E-05 P00749 PLAU Urokinase-type plasminogen activator 1,50 1,86E-02 1,89 3,89E-03 P06702 S100A9 Protein S100-A9 1,57 3,05E-03 1,55 3,91E-02 Q5K651 SAMD9 Sterile alpha motif domain-containing...”
- Effects of Natural Products on Enzymes Involved in Ferroptosis: Regulation and Implications.
Zuo, Molecules (Basel, Switzerland) 2023 - “...3 [ 31 ] CS O75390 Citrate synthase [ 32 ] Glucose metabolism Inhibit PHGDH O43175 D-3-phosphoglycerate dehydrogenase [ 33 ] G6PD P11413 Glucose-6-phosphate 1-dehydrogenase [ 34 ] Promote PHKG2 P15735 Phosphorylase kinase subunit gamma-2 [ 35 ] Mevalonate pathway Promote SQLE Q14534 Squalene monooxygenase [...”
- Analysis of local extracellular matrix identifies different aetiologies behind bicuspid and tricuspid aortic valve degeneration and suggests therapies.
Beusch, Cellular and molecular life sciences : CMLS 2023 - “...Signal transducer and activator of transcription 1-alpha/beta 8.5510 7 0.69 Q8TAD2 IL17D Interleukin-17D 0.0046 0.66 O43175 PHGDH D-3-phosphoglycerate dehydrogenase 0.0052 0.66 P78527 PRKDC DNA-dependent protein kinase catalytic subunit 8.7410 4 0.65 P31150 GDI1 Rab GDP dissociation inhibitor alpha 5.2410 4 0.65 O60504 SORBS3 Vinexin 0.0035 0.64...”
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XP_849835 D-3-phosphoglycerate dehydrogenase isoform X6 from Canis lupus familiaris
43% identity, 74% coverage
- Proteomics-based analysis of invasion-related proteins in malignant gliomas
Maruo, Neuropathology : official journal of the Japanese Society of Neuropathology 2013 - “...protein 3 XP_544332 94582/7.08 24 275.93 Metabolic enzyme (Energy pathway, hydrolase activity) 16 D-3-phosphoglycerate dehydrogenase-like XP_849835 56545.8/6.19 17 141.56 Metabolic enzyme (Energy pathway, catalytic activity) 17 Aldehyde dehydrogenase, mitochondrial isoform 2 (ALDH2) XP_853628 56763.1/6.63 25 176.99 Metabolic enzyme (Energy pathway, catalytic activity) 18 Heterogeneous nuclear ribonucleoprotein...”
A5GFY8 D-3-phosphoglycerate dehydrogenase from Sus scrofa
42% identity, 74% coverage
Q5EAD2 D-3-phosphoglycerate dehydrogenase from Bos taurus
43% identity, 73% coverage
B7P3M8 D-3-phosphoglycerate dehydrogenase (Fragment) from Ixodes scapularis
38% identity, 81% coverage
HP0397 phosphoglycerate dehydrogenase (serA) from Helicobacter pylori 26695
O25158 D-3-phosphoglycerate dehydrogenase from Helicobacter pylori (strain ATCC 700392 / 26695)
35% identity, 88% coverage
B3KSC3 D-3-phosphoglycerate dehydrogenase from Homo sapiens
44% identity, 66% coverage
LOC105252893 D-3-phosphoglycerate dehydrogenase from Camponotus floridanus
40% identity, 73% coverage
XP_017888762 D-3-phosphoglycerate dehydrogenase isoform X2 from Ceratina calcarata
39% identity, 79% coverage
- The effect of maternal care on gene expression and DNA methylation in a subsocial bee
Arsenault, Nature communications 2018 - “...to genes encoding a STE20-like serine/threonine-protein kinase (SLK; Ccalc.v2_009097, XP_017892454), a D-3-phosphoglycerate dehydrogenase (PHGDH; Ccalc.v2_011692, XP_017888762), and a 6-phosphofructo-2-kinase (PFKFB1; Ccalc.v2_011841, XP_017879076). Each of these represents a candidate for localized involvement of DNA methylation in gene regulation associated with maternal care in C. calcarata . Discussion...”
7dkmA / O43175 Phgdh covalently linked to oridonin (see paper)
47% identity, 55% coverage
- Ligands: (1beta,6beta,7beta,8alpha,9beta,10alpha,13alpha,14r,16beta)-1,6,7,14-tetrahydroxy-7,20-epoxykauran-15-one; nicotinamide-adenine-dinucleotide (7dkmA)
PF1394 phosphoglycerate dehydrogenase from Pyrococcus furiosus DSM 3638
47% identity, 54% coverage
TK1966 D-3-phosphoglycerate dehydrogenase from Thermococcus kodakaraensis KOD1
47% identity, 54% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...into account, we then searched for putative 2-hydroxyacid dehydrogenases. Three candidate genes (TK0551, TK0683, and TK1966), all encoding proteins of the d -lactate dehydrogenase (LDH) family, were found on the T. kodakarensis genome. TK0551 and TK0683 displayed 42% identity, TK0683 and TK1966 displayed 45% identity, and...”
- “...( 30 ), respectively. In addition, the T. kodakarensis genome harbors homologs of 3-phosphoglycerate dehydrogenase (TK1966), phosphoserine aminotransferase, and phosphoserine phosphatase. Using a TK1966 gene disruption strain, it was genetically demonstrated that 3-PGA is a precursor for serine biosynthesis ( 30 ). As T. kodakarensis harbors...”
- An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Makino, Nature communications 2016 - “...gene predicted to encode 3-phosphoglycerate dehydrogenase (SerA) is present on the genome ( Tk-serA : TK1966 (42% identical to SerA from E. coli )). We thus attempted to inactivate this pathway by disrupting the serA gene. As two other homologs with relatively high similarity, annotated as...”
- “...to glyA abolished the complementation effect by pyruvate ( Fig. 5e ), revealing that serA (TK1966) is the 3-phosphoglycerate dehydrogenase in T. kodakarensis , and that the cysteine auxotrophy observed in the serA ldhA1 ldhA2 serK -1 strain ( Fig. 2h ) was due to the...”
CG6287 uncharacterized protein from Drosophila melanogaster
46% identity, 54% coverage
- The seminal vesicle is a juvenile hormone-responsive tissue in adult male Drosophila melanogaster
Kurogi, Open biology 2024 - “...found not found Est-6 0.43701005 1.5627710 5 CG5177 not found not found Idh 0.485521317 0.002354908 CG6287 not found not found Rack1 0.502643883 0.000129842 Ogdh not found not found Obp44a not found not found Rpi not found not found Gs1 not found not found CG34107 not found...”
- Global stable-isotope tracing metabolomics reveals system-wide metabolic alternations in aging Drosophila
Wang, Nature communications 2022 - “...thereby supporting serine biosynthesis. We found that two genes involved in serine biosynthesis, CG11899 and CG6287 , were significantly increased in 30d Drosophila . Higher levels of shmt in old Drosophila heads were also observed. In addition, genes responsible for purine metabolism, including Pfas , Gart...”
- The Phosphoserine Phosphatase Alters the Free Amino Acid Compositions and Fecundity in Cyrtorhinus lividipennis Reuter
Ahmad, International journal of molecular sciences 2022 - “...(Tbp) accession: FBgn0003687, 1-pyrroline-5-carboxylate synthase (CG9018) accession: FBgn0035318, alanine-glyoxylate aminotransferase (Spat) accession: FBgn0014031, phosphoglycerate dehydrogenase (CG6287) accession: FBgn0032350, (CG11899) accession: FBgn0014427, serine racemase (CG8129) accession: FBgn0037684. Figure 5 Temporal and development variations of PSP expression in the mentioned life stages. ( A ) represents the PSP...”
- Crtc modulates fasting programs associated with 1-C metabolism and inhibition of insulin signaling
Wang, Proceedings of the National Academy of Sciences of the United States of America 2021 (secret) - Serine metabolism in the brain regulates starvation-induced sleep suppression in Drosophila melanogaster
Sonn, Proceedings of the National Academy of Sciences of the United States of America 2018 - “...( Fig. 1 E ). Heat-map analysis revealed that genes involved in serine synthesis ( CG6287 , CG11899 , and aay ) were all up-regulated after 6 and 24 h of starvation ( Fig. 1 F ). aay -Dependent Serine Synthesis Is Required for Starvation-Induced Sleep...”
- The mRNA-bound proteome of the early fly embryo
Wessels, Genome research 2016 - “...of crosslinked parental S2 cells to estimate nonspecific signal. RBP candidates Wech, GlyP, Hsc70Cb, and CG6287 could not be verified. ( C ) Enrichment of uniquely aligned CLIP sequencing reads relative to matched total RNA input for Pep and CG3800. X -axis: fraction of reads per...”
- A botanical containing freeze dried açai pulp promotes healthy aging and reduces oxidative damage in sod1 knockdown flies
Laslo, Age (Dordrecht, Netherlands) 2013 - “...Saposin related 3 -1.410.09 0.009 dsRNA transport CG6287 CG6287 3 1.780.06 0.005 Phosphoglycerate dehydrogenase CG3195 Ribosomal protein L12 3 1.930.07 0.003...”
- “...acai supplementation increased the expression of CG6287 with phosphoglycerate dehydrogenase activity, while decreasing the expression of cytochrome c...”
- Comparison of parallel high-throughput RNA sequencing between knockout of TDP-43 and its overexpression reveals primarily nonreciprocal and nonoverlapping gene expression changes in the central nervous system of Drosophila
Hazelett, G3 (Bethesda, Md.) 2012 - “...NM_001163169 No data CG4293 NM_001024984 Arginase CG4400 NM_001106731, NM_001009605 SIN3-type complex Assembly of HDAC complexes CG6287 NM_031620 Phosphoglycerate dehydrogenase Serine biosynthesis CG8223 NM_001005543 No data CG9705 NM_152790, NM_001170542 Transcription factor Unknown Clic NM_031818 Chloride intracellular channel Adult lifespan, oxidative stress dve NM_001109306 Transcription factor Copper import,...”
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TEL01S_RS09140 D-2-hydroxyacid dehydrogenase from Pseudothermotoga elfii DSM 9442 = NBRC 107921
44% identity, 54% coverage
HPR_THEMA / Q9X1C1 Hydroxypyruvate reductase; HPR; EC 1.1.1.81 from Thermotoga maritima (strain ATCC 43589 / DSM 3109 / JCM 10099 / NBRC 100826 / MSB8) (see paper)
TM1401 D-3-phosphoglycerate dehydrogenase from Thermotoga maritima MSB8
46% identity, 53% coverage
H9JRZ9 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Bombyx mori (see paper)
43% identity, 49% coverage
TRQ7_RS07315 hydroxypyruvate reductase from Thermotoga sp. RQ7
44% identity, 53% coverage
- Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation
Gautam, BMC research notes 2022 - “...FlhB d11: AAAACAGGAAGTA Frame shift, truncation 1006296 TRQ7_RS05035 Alpha-amylase i1: TTA Frame shift, run-through 1426409 TRQ7_RS07315 2-hydroxyacid dehydrogenase i1: AGAGG Frame shift, truncation SNPs 205012 TRQ7_RS01075 Methylmalonyl-CoA carboxyltransferase Transversion: GT Silent: V360 262000 TRQ7_RS01400 Hypothetical protein Transition: GA Silent: L346 323128 TRQ7_RS01715 Queuosine precursor transporter Transition:...”
1wwkA / O50095 Crystal structure of phosphoglycerate dehydrogenase from pyrococcus horikoshii ot3
44% identity, 54% coverage
- Ligand: nicotinamide-adenine-dinucleotide (1wwkA)
XP_011539528 D-3-phosphoglycerate dehydrogenase isoform X1 from Homo sapiens
42% identity, 50% coverage
- KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner.
Wang, Molecular and cellular biochemistry 2024 (PubMed)- GeneRIF: KDM4B down-regulation facilitated breast cancer cell stemness via PHGDH upregulation in H3K36me3-dependent manner.
- Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling.
Mäntyselkä, American journal of physiology. Endocrinology and metabolism 2024 (PubMed)- GeneRIF: Serine synthesis pathway enzyme PHGDH is critical for muscle cell biomass, anabolic metabolism, and mTORC1 signaling.
- PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer.
Yamamoto, Cancer research 2024 - GeneRIF: PRMT1 Sustains De Novo Fatty Acid Synthesis by Methylating PHGDH to Drive Chemoresistance in Triple-Negative Breast Cancer.
- CircPHGDH downregulation decreases papillary thyroid cancer progression through miR-122-5p/PKM2 axis.
Shen, BMC cancer 2024 - GeneRIF: CircPHGDH downregulation decreases papillary thyroid cancer progression through miR-122-5p/PKM2 axis.
- On the quaternary structure of human D-3-phosphoglycerate dehydrogenase.
Riva, Protein science : a publication of the Protein Society 2024 - GeneRIF: On the quaternary structure of human D-3-phosphoglycerate dehydrogenase.
- Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma.
Zhang, BMC medical genomics 2023 - GeneRIF: Comprehensive analysis of PHGDH for predicting prognosis and immunotherapy response in patients with endometrial carcinoma.
- PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma.
Wang, Nature communications 2023 - GeneRIF: PHGDH arginine methylation by PRMT1 promotes serine synthesis and represents a therapeutic vulnerability in hepatocellular carcinoma.
- The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer.
Gökmen-Polar, Laboratory investigation; a journal of technical methods and pathology 2023 (PubMed)- GeneRIF: The Role of ESRP1 in the Regulation of PHGDH in Estrogen Receptor-Positive Breast Cancer.
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7cvpA / O43175 The crystal structure of human phgdh from biortus.
47% identity, 40% coverage
- Ligand: nicotinamide-adenine-dinucleotide (7cvpA)
CAC0015 D-3-phosphoglycerate dehydrogenase from Clostridium acetobutylicum ATCC 824
38% identity, 54% coverage
- Metabolome remodeling during the acidogenic-solventogenic transition in Clostridium acetobutylicum
Amador-Noguez, Applied and environmental microbiology 2011 - “...cac3174, and cac3171; serine biosynthesis, cac0014, cac0015, and cac0263; asparagine synthase, cac2243; glutamine synthetase, cac2658; phenylalanine, tyrosine,...”
- Intracellular butyryl phosphate and acetyl phosphate concentrations in Clostridium acetobutylicum and their implications for solvent formation
Zhao, Applied and environmental microbiology 2005 - “...the genes encoding D-3-phosphoglycerate dehydrogenase (serA; CAC0015), alkaline phosphatase (CAC2431), pyruvate formate lyase (pflB; CAC0980), and pyruvate...”
- Transcriptional program of early sporulation and stationary-phase events in Clostridium acetobutylicum
Alsaker, Journal of bacteriology 2005 - “...LeuB (CAC3171); serine biosynthesis proteins SerA (CAC0015), SerC (CAC0014), and SerS (CAC0017); and pyridoxine biosynthesis protein PdxY (CAC0594)....”
- Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress
Alsaker, Journal of bacteriology 2004 - “...hisC (an amino acid metabolism gene), serA (CAC0015, encoding D-3-phosphoglycerate dehydrogenase, involved in amino acid metabolism), radC (CAC1241, a DNA...”
Q9UMY2 D-3-phosphoglycerate dehydrogenase (Fragment) from Homo sapiens
42% identity, 52% coverage
A5DEL5 phosphoglycerate dehydrogenase from Meyerozyma guilliermondii (strain ATCC 6260 / CBS 566 / DSM 6381 / JCM 1539 / NBRC 10279 / NRRL Y-324)
PGUG_01716 uncharacterized protein from Meyerozyma guilliermondii ATCC 6260
38% identity, 56% coverage
- In silico Prediction of Protein-Protein Interaction Network Induced by Manganese II in Meyerozyma guilliermondii
Ruas, Frontiers in microbiology 2020 - “...A5DRG2 PGUG_056863 UDP-glucose 4-epimerase 0.0 81.85 A5DQ88 PGUG_05439 Fe-S cluster assembly protein DRE2 0.0 73.44 A5DEL5 PGUG_01716 D-3-phosphoglycerate dehydrogenase 1 0.0 94.77 A5DQ39 PGUG_05390 Secreted protein 0.0 68.28 A5DQK7 PGUG_05558 Pyridoxal kinase 0.0 73.51 A5DNY7 PGUG_04988 Regulation of G-protein function 0.0 73.48 A5DBX4 PGUG_00779 Actin/actin-like protein...”
- “...manganese tolerance in differential proteomes. Pathway Accession Metabolic pathways A5DFK1 A5DDM8 A5DBX1 A5DCX8 A5DQK7 A5DQS7 A5DEL5 A5DQK9 A5DDN3 A5DQ12 A5DHQ4 A5DRG2 A5DHJ1 A5DMR7 A5DH72 A5D9X5 A5DL50 A5DQS2 A5DNZ9 Biosynthesis of secondary metabolites A5DFK1 A5DDM8 A5DQK9 A5DQS7 A5DRG2 A5DHJ1 A5DHQ4 A5DL50 A5D9X5 A5DBX1 Biosynthesis of antibiotics A5DFK1...”
- In silico Prediction of Protein-Protein Interaction Network Induced by Manganese II in Meyerozyma guilliermondii
Ruas, Frontiers in microbiology 2020 - “...PGUG_056863 UDP-glucose 4-epimerase 0.0 81.85 A5DQ88 PGUG_05439 Fe-S cluster assembly protein DRE2 0.0 73.44 A5DEL5 PGUG_01716 D-3-phosphoglycerate dehydrogenase 1 0.0 94.77 A5DQ39 PGUG_05390 Secreted protein 0.0 68.28 A5DQK7 PGUG_05558 Pyridoxal kinase 0.0 73.51 A5DNY7 PGUG_04988 Regulation of G-protein function 0.0 73.48 A5DBX4 PGUG_00779 Actin/actin-like protein 0.0...”
BMF77_03393 hydroxyacid dehydrogenase from Dolichospermum sp. UHCC 0315A
40% identity, 54% coverage
NCU01439 D-3-phosphoglycerate dehydrogenase 1 from Neurospora crassa OR74A
38% identity, 57% coverage
- The nutrient-sensing GCN2 signaling pathway is essential for circadian clock function by regulating histone acetylation under amino acid starvation
Liu, eLife 2023 - “...). For example, amino acid synthesis genes his-3 (NCU03139), arg-1 (NCU02639), trp-3 (NCU08409), and ser-2 (NCU01439) were upregulated in the WT strain, but unchanged in the cpc-1 KO strain under amino acid starvation ( Figure 7A, C ). Figure 7. Circadian clock control of CPC-1-activated metabolic...”
- “...to Input DNA. ( D ) RT-qPCR analysis showing that amino acid synthetic gene ser-2 (NCU01439) was activated by CPC-1 and was rhythmic expressed with 3 mM 3-AT treatment ( n = 3; WT: p = 2.25E05, cpc-1 KO : p > 0.05). ( E )...”
- Effect of itaconic acid production on Neurospora crassa in consolidated bioprocessing of cellulose
Zhao, Microbial cell factories 2023 - “...and metabolism were upregulated, mainly aliphatic, acidic and basic amino acid, such as NCU01429 and NCU01439 in glycine, serine, and threonine metabolism; NCU02727 and NCU06558 in glycine degradation; NCU04118 and NCU08162 in aspartic acid metabolism; NCU04754 in valine metabolism; NCU02954 and NCU03118 in lysine synthesis; NCU01195...”
8wprA / Q7WRR2 Anabaena mcyi r166a with prebound NAD and malate
40% identity, 54% coverage
- Ligand: nicotinamide-adenine-dinucleotide (8wprA)
Q8U3Y2 glyoxylate reductase (NADP+) (EC 1.1.1.79); hydroxypyruvate reductase (EC 1.1.1.81) from Pyrococcus furiosus (see paper)
PF0319 putative phosphoglycerate dehydrogenase from Pyrococcus furiosus DSM 3638
36% identity, 53% coverage
5aovA / Q8U3Y2 Ternary crystal structure of pyrococcus furiosus glyoxylate hydroxypyruvate reductase in presence of glyoxylate (see paper)
36% identity, 53% coverage
- Ligands: nadp nicotinamide-adenine-dinucleotide phosphate; glyoxylic acid (5aovA)
YP_009328950 D-3-phosphoglycerate dehydrogenase, type2 from Cedratvirus A11
38% identity, 56% coverage
- The Viral Fraction Metatranscriptomes of Lake Baikal
Potapov, Microorganisms 2022 - “...Ran-like GTP-binding protein YP_009001029 7.6 10 12 Cedratvirus A11 Protein Accession e-value D-3-phosphoglycerate dehydrogenase, type2 YP_009328950 1.7 10 99 DNA-directed RNA polymerase subunit RPB2 YP_009329295 2.4 10 14 Adenylosuccinate synthetase YP_009329210 7.8 10 14 dTDPD-glucose 4,6-dehydratase YP_009329097 4.2 10 11 ABC2 type transporter superfamily protein YP_009329403...”
SPCC364.07 D-3 phosphoglycerate dehydrogenase (predicted) from Schizosaccharomyces pombe
P87228 Putative D-3-phosphoglycerate dehydrogenase from Schizosaccharomyces pombe (strain 972 / ATCC 24843)
35% identity, 59% coverage
- Receptor for activated C-kinase (RACK1) homolog Cpc2 facilitates the general amino acid control response through Gcn2 kinase in fission yeast
Tarumoto, The Journal of biological chemistry 2013 - “...Gene Forward primer Reverse primer his4 SPAC56E4.03 SPCC364.07 SPAC10F6.13c arg3 dld1 lys3 leu3 SPBC19F5.04 cdk9 18 S rRNA cpc2 snoU24b TAGATCAGGTGCCGACAAAG...”
- “...genes as the GAAC genes (his4, SPAC56E4.03, SPCC364.07, SPAC10F6.13c, arg3, dld1, lys3, leu3, SPBC19F5.04) and checked their expression levels by quantitative...”
- Mfc1 is a novel forespore membrane copper transporter in meiotic and sporulating cells
Beaudoin, The Journal of biological chemistry 2011 - “...SPAC139.05 SPAC27D7.10c SPBC1198.01 SPBC1711.08 SPCC364.07 SPAC750.01 SPAC589.02c SPBC119.03 SPAC1B3.03c SPBC428.11 SPBC660.16 SPBC1289.14 SPBC1198.14c...”
- Response of Schizosaccharomyces pombe to zinc deficiency
Dainty, Eukaryotic cell 2008 - “...(SPBC359.03c, SPBC359.01) and biosynthesis (apt1, eca39, SPCC364.07, SPBC428.11, SPBPB2B2.05, SPAP8A3.07c). Furthermore, the mRNA levels of several genes whose...”
- “...pan6 SPAC11D3.02c SPBC21C3.08c SPBPB10D8.01 aes1 SPCC364.07 SPBP8B7.05c apt1 SPAC23C4.06c SPBC8E4.01c SPAC11D3.13 rpl3002 rpl31 SPBC359.01 SPCC330.06c eca39...”
- Proteasome regulation of petite-negativity in fission yeast.
Amberg, bioRxiv : the preprint server for biology 2024 - “...SPCC1827.06c 0.26 0.029 aspartate semialdehyde dehydrogenase Hom2 O60155 prs1 0.24 0.036 cytoplasmic proline-tRNA ligase Prs1 P87228 SPCC364.07 0.24 0.030 D-3 phosphoglycerate dehydrogenase Ser3 Q10284 sks2 0.24 0.039 heat shock protein, Hsp70 family, ribosome associated Sks2 O94514 nop56 0.24 0.029 U3 snoRNP-associated protein Nop56 P32747 ura3 0.23...”
CDIF630erm_01131 D-2-hydroxyacid dehydrogenase from Clostridioides difficile
CD0995 putative D-3-phosphoglycerate dehydrogenase from Clostridium difficile 630
37% identity, 55% coverage
- Metabolic Reprogramming of Clostridioides difficile During the Stationary Phase With the Induction of Toxin Production
Hofmann, Frontiers in microbiology 2018 - “...were also present at high levels over the whole cultivation time in the proteomic approach. CDIF630erm_01131 is annotated to encode a hydroxypyruvate reductase (Hpr), an enzyme which catalyzes the reversible reaction from D -glycerate to hydroxypyruvate with NADP + as cofactor in the serine metabolism (...”
- “...the reaction from 3-phosphoglycerate to L -serine: in the first step, the protein encoded by CDIF630erm_01131 acts as 3-phosphoglycerate dehydrogenase and catalyzes the reaction from 3-phosphoglycerate to 3-phosphohydroxypyruvate. In the second step, a phosphoserine transaminase encoded by CDIF630erm_01130 catalyzes the further reaction to 3-phosphoserine with the...”
- Global transcriptional control by glucose and carbon regulator CcpA in Clostridium difficile
Antunes, Nucleic acids research 2012 - “...decarboxylase; thrC (CD2118), threonine synthase, thrB (CD2119), homoserine kinase; tdcB (CD2514), threonine dehydratase II; serA (CD0995), putative D-3-phosphoglycerate dehydrogenase; sdaB (CD3222), L-serine dehydratase; cysE (CD1595), serine acetyltransferase; cysK (CD1594), O -acetylserine sulphydrylase; iscS2 (CD1279), cysteine desulphurase; oppBCADF (CD0853CD0857), oligopeptide ABC transporter; CD2177CD2174, cystine ABC transporter; prdF...”
A4XGF7 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding protein from Caldicellulosiruptor saccharolyticus (strain ATCC 43494 / DSM 8903 / Tp8T 6331)
37% identity, 56% coverage
SERA_YEAST / P40054 D-3-phosphoglycerate dehydrogenase 1; 3-PGDH 1; 2-oxoglutarate reductase; EC 1.1.1.95; EC 1.1.1.399 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
NP_011004 phosphoglycerate dehydrogenase SER3 from Saccharomyces cerevisiae S288C
YER081W 3-phosphoglycerate dehydrogenase, catalyzes the first step in serine and glycine biosynthesis; isozyme of Ser33p from Saccharomyces cerevisiae
36% identity, 58% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
catalytic activity: (R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH + H(+) (RHEA:49612) - A framework for application of metabolic modeling in yeast to predict the effects of nsSNV in human orthologs
Dingerdissen, Biology direct 2014 - “...Q99447 P33412 P04180 P40345 O14734 P41903 P30793 P51601 Q9Y3Q0 P47161 P14550 P14065 Q9BV23 P53750 O43175 P40054 P08243 P49090 P56937 Q12452 P22830 P16622 Q86V88 P40081 Q16769 P43599 O95336 P38858 Q8IXB1 P40564 Q15386 P53119 Q969P6 P04786 Q9Y3B8 P54964 Q9Y2H1 P53894 Q9Y2Z4 P48527 P00813 P53909 Q9UI42 P38836 Q9Y6R4 P53599...”
- Cloning, sequencing and expression of rat liver 3-phosphoglycerate dehydrogenase
Achouri, The Biochemical journal 1997 - “...accession no. L45106 ; [13]), Saccharomyces cereisiae (GenBank P40054) and Bacillus subtilis (GenBank L47648 ; [14]) are known, as is the three-dimensional...”
- “...no. L45106 ; [13]), S. cerevisiae (Scer ; GenBank P40054), B. subtilis (Bsub ; GenBank L47648 ; [14]) and rat hepatoma (the present work) are displayed in...”
- Identification of histone mutants that are defective for transcription-coupled nucleosome occupancy.
Hainer, Molecular and cellular biology 2011 - GeneRIF: Studies identified mutations altering eight histone residues (H3 residues V46, R49, V117, Q120, and K122 and H4 residues R36, I46, and S47) that strongly increase SER3 expression without reducing the transcription of the intergenic SRG1 ncDNA.
- The Paf1 complex represses SER3 transcription in Saccharomyces cerevisiae by facilitating intergenic transcription-dependent nucleosome occupancy of the SER3 promoter.
Pruneski, Eukaryotic cell 2011 - GeneRIF: Paf1 and Ctr9 repress SER3 by maintaining SRG1 transcription-dependent nucleosome occupancy.
- SCRaMbLE generates evolved yeasts with increased alkali tolerance
Ma, Microbial cell factories 2019 - “...indicating deletions of these regions in strain yML008. None amplification of PCRTags of YEL017W, YER010C, YER081W, YER118C in both synV and yML008 strains was caused by nonspecific primers. SynV strain was used as a control strain. All PCRTag primers were listed in Additional file 1 :...”
- Low toxicity of deoxynivalenol-3-glucoside in microbial cells
Suzuki, Toxins 2015 - “...expression changes revealed by DNA microarray. Systematic No. Gene Symbol Fold Change Gene Title Description YER081W SER3 0.31 3-phosphoglycerate dehydrogenase Serine and glycine biosynthesis YMR230W-A - 0.35 Putative protein of unknown function - YKL221W MCH2 0.41 Protein with similarity to mammalian monocarboxylate permeases Monocarboxylate transport YPL095C...”
- Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis
Gomes, BMC genomics 2014 - “...] have previously suggested that this activity may be present in S. cerevisiae associated to YER081W and YIL074C , which have a homologue in A. gossypii ( ACL032C ). Involved in the Ehrlich pathway of amino acids degradation, the absence of ARO9 -coded tryptophan:phenylpyruvate transaminase (2.6.1.28)...”
- Origin and consequences of the relationship between protein mean and variance
Vallania, PloS one 2014 - “...compared to YPD using genome-wide nucleosome occupancy data [33] (YAL054C, YBL015W, YBL075C, YBR139W, YBR145W, YDL097C, YER081W, YFL021W, YGL040C, YGL197W, YLR042C, YMR315W, YNL241C, YOL143C, YOR084W, YPR127W). We constructed a second set (control set) of 15 genes either stable nucleosome-bound or nucleosome-free promoters (YBR066C, YBR092C, YER056C-A, YJL200C, YKL071W,...”
- Graph ranking for exploratory gene data analysis
Gao, BMC bioinformatics 2009 - “...YJL153C YDL142C YGR256W YNR019W YLR067C YNL275W YOR349W YJR073C YJL101C YNL275W YJL088W YDR019C YOR100C YJL026W YNL036W YER081W YDR001C YDR018C YKR076W YER081W YNL071W YBR045C YJL026W YLL060C YLR237W YBR221C YJL153C YCR083W YDR001C YJL129C YLR142W Down YNL327W YNL327W YNL327W YJL178C YDR435C YFL017C YGL028C YDR044W YDL142C YER009W YNL141W YNR067C YHR128W YIL162W...”
- “...(Down) Induced (Up) Repressed (Down) YJL088W YNL327W YJL088W YCR021C YDR001C YOR095C YNL275W YGR180C YJL178C YGR036C YER081W YBR054W YMR090W YHL028W YOR298W YNR001C YOR100C YGL028C YLR343W YDR408C YLR178C YIL149C YGL156W YGL063W YJR073C YGR006W YGR180C Responses of the genes in this table are similar for genotoxic or cytotoxic stress....”
- Systems-level engineering of nonfermentative metabolism in yeast
Kennedy, Genetics 2009 - “...YPL271W YBL013W YOL017W YHR001W-A YNL055C YKL016C YJR121W YER081W YMR083W YOL067C YOR100C YNL256W YNL037C YLR071C YOR136W YKL120W YLR442C YPL075W YLR033W...”
- Preferential protection of protein interaction network hubs in yeast: evolved functionality of genetic redundancy
Kafri, Proceedings of the National Academy of Sciences of the United States of America 2008 - “...YDL160C YIL035C YOR061W YIL074C w/o serine YNL055C YER081W YIL114C YKR028W YJLO98W YDL047W YDL188C YER122C YDL226C YDL188C YDL134C slow growth B Proportion...”
- “...of double knockout of the following hubs (YER081W and YMR105C) and their respective paralogs (YIL074C and YKL127W, respectively), SSL interactions were...”
- Transcriptional reprogramming and backup between duplicate genes: is it a genomewide phenomenon?
He, Genetics 2006 - “...high numbers of protein interaction partners (94 for YER081W, 289 for YJR091C, and 128 for YMR047C) that would inappropriately influence the calculation of the...”
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CLJU_c03860 phosphoglycerate dehydrogenase from Clostridium ljungdahlii DSM 13528
40% identity, 49% coverage
ZP_02639608 D-3-phosphoglycerate dehydrogenase from Clostridium perfringens CPE str. F4969
38% identity, 54% coverage
SJAG_02313 D-3 phosphoglycerate dehydrogenase from Schizosaccharomyces japonicus yFS275
35% identity, 59% coverage
TM0327 phosphoglycerate dehydrogenase, putative from Thermotoga maritima MSB8
43% identity, 50% coverage
SER33_YEAST / P40510 D-3-phosphoglycerate dehydrogenase 2; 3-PGDH 2; 2-oxoglutarate reductase; EC 1.1.1.95; EC 1.1.1.399 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 2 papers)
YIL074C 3-phosphoglycerate dehydrogenase, catalyzes the first step in serine and glycine biosynthesis; isozyme of Ser3p from Saccharomyces cerevisiae
36% identity, 56% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
catalytic activity: (R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH + H(+) (RHEA:49612) - Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
Chen, mSystems 2021 - “...transmembrane transport CHLRE_16g682369v5 1.91 <0.001 Cu ion transmembrane transporter B21_RS14345 0.28 0.03 d -3-Phosphoglycerate dehydrogenase YIL074C 0.90 <0.001 Phosphoglycerate dehydrogenase SER33 CHLRE_16g689700v5 1.52 <0.001 Intracellular trafficking, secretion, and vesicular transport B21_RS10695 0.60 <0.001 Lactate dehydrogenase B21_RS13605 4.28 <0.001 Assimilatory sulfite reductase YJR137C 1.02 <0.001 Sulfite reductase...”
- Transcriptional profiling reveals molecular basis and novel genetic targets for improved resistance to multiple fermentation inhibitors in Saccharomyces cerevisiae
Chen, Biotechnology for biofuels 2016 - “...process (GO:0006520) YBL098W, YDL168W, YDL182W, YDR019C, YDR135C, YDR502C , YER026C, YER043C, YER091C, YGL256W , YGR209C, YIL074C, YJL101C, YJR010W, YJR137C, YJR139C, YKL001C, YKR080W, YLR058C, YLR142W , YLR180W, YLR231C, YLR303W, YMR169C , YMR189W, YMR300C, YNL135C, YNL160W, YOL058W, YOL086C, YOR184W, YOR375C YCL030C, YDR007W, YDR502C , YER091C , YGL245W, YGL256W...”
- “...YDR007W, YDR135C, YDR502C , YDR513W, YEL046C, YER043C, YER091C , YFL030W, YGL009C, YGL256W , YGR209C, YGR267C, YIL074C, YJL101C, YJR010W, YJR137C, YJR139C, YKL001C, YKR080W, YLR058C, YLR142W , YLR180W, YLR303W, YMR169C , YMR189W, YNL160W, YOL064C, YPL091W Lipid metabolic process (GO:0006629) YER026C, YER043C, YGL055W, YGR060W, YGR175C, YHR007C, YJL153C, YJL167W, YJR073C,...”
- Genome-wide metabolic re-annotation of Ashbya gossypii: new insights into its metabolism through a comparative analysis with Saccharomyces cerevisiae and Kluyveromyces lactis
Gomes, BMC genomics 2014 - “...previously suggested that this activity may be present in S. cerevisiae associated to YER081W and YIL074C , which have a homologue in A. gossypii ( ACL032C ). Involved in the Ehrlich pathway of amino acids degradation, the absence of ARO9 -coded tryptophan:phenylpyruvate transaminase (2.6.1.28) was verified...”
- Is transcription factor binding site turnover a sufficient explanation for cis-regulatory sequence divergence?
Venkataram, Genome biology and evolution 2010 - “...intergenic sequences. The tree is based on concatenation of 13 genes (YMR009W, YLR147C, YJR034W, YLR029C, YIL074C, YHR142W, YGR284C, YCL055W, YJL072C, YCR036W, YOR250C, YBR196C, YBR282W) for which homologs were identified in all species. Branch lengths show the synonymous substitution rate calculated using HYPHY and model MG94xHKY85. (...”
- Comparative transcriptomic and proteomic profiling of industrial wine yeast strains
Rossouw, Applied and environmental microbiology 2010 - “...YLR180W YDR502C YFL045C YOR184W YIL074C Coproporphyrinogen III oxidase ATP phosphoribosyltransferase Imidazoleglycerol-phosphate dehydratase Phosphoribosyl-ATP...”
- Preferential protection of protein interaction network hubs in yeast: evolved functionality of genetic redundancy
Kafri, Proceedings of the National Academy of Sciences of the United States of America 2008 - “...on galactose YKL127W YDR293C YDL160C YIL035C YOR061W YIL074C w/o serine YNL055C YER081W YIL114C YKR028W YJLO98W YDL047W YDL188C YER122C YDL226C YDL188C YDL134C...”
- “...(YER081W and YMR105C) and their respective paralogs (YIL074C and YKL127W, respectively), SSL interactions were obtained only in specific growth conditions (lack...”
- Novel cargo-binding site in the beta and delta subunits of coatomer
Michelsen, The Journal of cell biology 2007 - “...COPI subunit delta tetO7RSC6 YCR052W sec -like Chromatin remodelling; homologue of SWI/SNF subunit SWP73 ser33kanMX4 YIL074C Perinuclear accumulation serine and glycine biosynthesis snf2kanMX4 YOR290C Perinuclear accumulation SWI/SNF chromatin remodelling complex pac10kanMX4 YGR078C Perinuclear accumulation Biogenesis of microtubuli Because COPI functions as a heptameric complex, the genes...”
- Determining physical constraints in transcriptional initiation complexes using DNA sequence analysis
Shultzaberger, PloS one 2007 - “...and a predicted Met4 binding site, but their functions have not been biochemically characterized (DDR48, YIL074C, YJL060W, YHR112C). Clustering of co-regulated genes by the gene-ranking method may have identified other genes involved in sulfur utilization. 10.1371/journal.pone.0001199.g005 Figure 5 The Met4 activation model based on our analysis....”
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8q2iB / P40510 Crystal structure of ser33 in complex 2hg (2-hydroxyglutarate) and serine
36% identity, 56% coverage
- Ligands: serine; nicotinamide-adenine-dinucleotide (8q2iB)
TERTU_0393 D-3-phosphoglycerate dehydrogenase from Teredinibacter turnerae T7901
36% identity, 56% coverage
VP2593 D-3-phosphoglycerate dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
VP_RS12615 phosphoglycerate dehydrogenase from Vibrio parahaemolyticus RIMD 2210633
36% identity, 56% coverage
- Changes in global gene expression of Vibrio parahaemolyticus induced by cold- and heat-stress
Urmersbach, BMC microbiology 2015 - “...at 4 and 42C [Fig. 3 - cluster nine, 410 genes including the D-3-phosphoglycerate dehydrogenase VP2593, eam A (VP2828) a pore forming protein and glyoxalase I (VP2166)] have been found in high numbers. In addition, there are genes down-regulated across all temperatures (Fig. 3 - cluster...”
- “...amine synthesis (pyruvate family) were induced, whereas genes related to histidine (VP1137), serine (VP1324, VP1629, VP2593) and aromatic amino acid (VP2744, VP3065) families were down-regulated (Additional file 1 ). Out of 55 energy metabolism related genes only six were down-regulated in expression. Particularly, genes of electron...”
- Identification of Antibacterial Components in the Methanol-Phase Extract from Edible Herbaceous Plant Rumex madaio Makino and Their Antibacterial Action Modes
Liu, Molecules (Basel, Switzerland) 2022 - “...VP_RS07325 0.224 Acetate kinase VP_RS13930 0.206 2%2C3-bisphosphoglycerate-independent phosphoglycerate mutase VP_RS18135 0.104 Formate dehydrogenase subunit gamma VP_RS12615 0.320 Phosphate acetyltransferase VP_RS07335 0.227 Trimethylamine- N -oxide reductase TorA VP_RS15585 0.304 S-(hydroxymethyl)glutathione dehydrogenase/class III alcohol dehydrogenase VP_RS05645 0.302 Phosphoglycerate dehydrogenase VP_RS07330 0.338 Pentaheme c-type cytochrome TorC VP_RS05030 0.381 Molecular...”
GYAR_THELN / Q9C4M5 Glyoxylate reductase; EC 1.1.1.26 from Thermococcus litoralis (strain ATCC 51850 / DSM 5473 / JCM 8560 / NS-C) (see paper)
Q9C4M5 glyoxylate reductase (EC 1.1.1.26) from Thermococcus litoralis (see paper)
OCC_02245 glyoxylate reductase from Thermococcus litoralis DSM 5473
36% identity, 53% coverage
- catalytic activity: glycolate + NAD(+) = glyoxylate + NADH + H(+) (RHEA:18229)
subunit: Homodimer. - Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...TK0551 and TK0683, proteins encoded by TK0683 homologs from Thermococcales have been biochemically characterized. The OCC_02245 protein from Thermococcus litoralis and the PH0597 protein from Pyrococcus horikoshii were described as reductases preferring glyoxylate ( 31 , 32 ), while another report concluded that the proteins encoded...”
VC2481 D-3-phosphoglycerate dehydrogenase from Vibrio cholerae O1 biovar eltor str. N16961
36% identity, 56% coverage
PN96_00930 phosphoglycerate dehydrogenase from Vibrio natriegens NBRC 15636 = ATCC 14048 = DSM 759
34% identity, 56% coverage
XHV734_2726 phosphoglycerate dehydrogenase from Xanthomonas hortorum pv. vitians
36% identity, 58% coverage
ABUW_0331 phosphoglycerate dehydrogenase from Acinetobacter baumannii
35% identity, 56% coverage
VAS14_20256 phosphoglycerate dehydrogenase from Photobacterium angustum S14
35% identity, 56% coverage
APL_1452 D-3-phosphoglycerate dehydrogenase from Actinobacillus pleuropneumoniae L20
34% identity, 57% coverage
2eklA / Q972A9 Structure of st1218 protein from sulfolobus tokodaii
38% identity, 52% coverage
- Ligand: nicotinamide-adenine-dinucleotide (2eklA)
Q972A9 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Sulfurisphaera tokodaii (see paper)
ST1218 313aa long hypothetical D-3-phosphoglycerate dehydrogenase from Sulfolobus tokodaii str. 7
38% identity, 52% coverage
TK0683 glyoxylate reductase from Thermococcus kodakaraensis KOD1
35% identity, 53% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...B ) GLDH activity from glycolate to glyoxylate in cell extracts from KU216, TK0551, and TK0683 strains. Gray or white bars indicate the specific activities in extracts from cells grown under anaerobic or microaerobic conditions, respectively. ( C ) GLDH activity from glyoxylate to glycolate in...”
- “...measured toward various phosphorylated metabolites. Dehydrogenase activities of the purified TK0551 ( C ) and TK0683 ( D ) proteins were examined toward various 2-hydroxyacids. Aminotransferase activities of the purified TK0186/TK1094 proteins with various amino donor compounds in the presence of glyoxylate as the amino acceptor...”
- An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Makino, Nature communications 2016 - “...as lactate dehydrogenases (LDHs), were also present ( Tk-ldhA1 : TK0551 (29% identical), Tk-ldhA2 : TK0683 (31% identical)), we constructed a triple gene disruption strain of these genes to ensure the complete shutdown of pathway Cys2. As a result, growth without Cys was not significantly affected...”
- “...tk1449 (TK1449, metC ), Tk - serA (TK1966), Tk - ldhA1 (TK0551), Tk - ldhA2 (TK0683), Tk-cysK (TK1687), Tk-serK (TK0378), Tk-glyA (TK0528) and Tk-tdh (TK0916), their coding regions along with about 1,000bps of 5- and 3-flanking regions were amplified by PCR using T. kodakarensis KOD1 genomic...”
ETAE_2949 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein from Edwardsiella tarda EIB202
34% identity, 57% coverage
C0PKN2 phosphoglycerate dehydrogenase from Zea mays
36% identity, 61% coverage
- Quantitative iTRAQ-based proteomic analysis of phosphoproteins and ABA-regulated phosphoproteins in maize leaves under osmotic stress
Hu, Scientific reports 2015 - “...ribosome, which had the second greatest number of proteins (B8A367, C0HHU2, B6TS38, C0HIV2, B4FRM3, B4FWX5, C0PKN2, B6TPG2, B4FCE7, O04014, B4FCK4, B4FWI0), and only B4FWI0 was not regulated by ABA under osmotic stress. Moreover, the signaling pathways related to photosynthesis, such as carbon fixation in photosynthetic organisms...”
- “...C0PKH3 serine threonine-protein kinase afc3-like gGAsPPWR 0.627 1.080 Down-regulated by osmotic stress with ABA-dependent way C0PKN2 phosphoglycerate dehydrogenase gLVEPVsSTFVNLVNADYtAk 2.589 1.044 Up-regulated by osmotic stress with ABA-dependent way C4IYD7 c-type lectin receptor-like tyrosine-protein kinase at1g52310-like isoform x1 sGtsTSATsPmLPLEVRtPR 0.416 0.955 Down-regulated by osmotic stress with ABA-dependent...”
F8AEA4 glyoxylate reductase (NADP+) (EC 1.1.1.79); hydroxypyruvate reductase (EC 1.1.1.81) from Pyrococcus yayanosii (see paper)
PYCH_09300 glyoxylate reductase from Pyrococcus yayanosii CH1
36% identity, 53% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...another report concluded that the proteins encoded by PH0597, PF0319 from Pyrococcus furiosus , and PYCH_09300 from Pyrococcus yayanosii are actually HPRs ( 33 ). TK0551 homologs in Thermococcales have not yet been characterized and the physiological roles of TK0551 and TK0683 are still unclear. GLDH...”
6biiA / F8AEA4 Crystal structure of pyrococcus yayanosii glyoxylate hydroxypyruvate reductase in complex with NADP and malonate (re-refinement of 5aow) (see paper)
36% identity, 53% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (6biiA)
NE1688 D-isomer specific 2-hydroxyacid dehydrogenase from Nitrosomonas europaea ATCC 19718
37% identity, 55% coverage
A0KLT8 D-3-phosphoglycerate dehydrogenase from Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / BCRC 13018 / CCUG 14551 / JCM 1027 / KCTC 2358 / NCIMB 9240 / NCTC 8049)
36% identity, 56% coverage
- The Lysine Acetylation Modification in the Porin Aha1 of Aeromonas hydrophila Regulates the Uptake of Multidrug Antibiotics
Zhang, Molecular & cellular proteomics : MCP 2022 - “...permeability to the antibiotic. Of the 39 AMR Kac proteins, Aha1, PtsI-2, Uup, IleS, and A0KLT8 were the top five abundant Kac sites, while many proteins, such as AccC, UvrA, CheY, CueR, and GyrB, have only one altered Kac site. Most altered Kac sites were downregulated,...”
HI0465 D-3-phosphoglycerate dehydrogenase (serA) from Haemophilus influenzae Rd KW20
33% identity, 61% coverage
YPTB3189 D-3-phosphoglycerate dehydrogenase (PGDH) from Yersinia pseudotuberculosis IP 32953
YPO0914 D-3-phosphoglycerate dehydrogenase from Yersinia pestis CO92
34% identity, 60% coverage
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...YPO0906 glycine cleavage system H protein 0.377 (< 0.001) YPTB3182 (gcvT) YPO0907 aminomethyltransferase 0.526 (0.022) YPTB3189 (serA) YPO0914 D-3-phosphoglycerate dehydrogenase 1.582 (0.04) 0.517 (0.005) YPTB3214 (proC) YPO0942 putative pyrroline-5-carboxylate reductase 0.647 (0.038) YPTB3474 YPO0584 putative symporter protein 0.61 (0.007) YPTB3570 (aroQ) YPO3660 putative class II dehydroquinase...”
- New insights into how Yersinia pestis adapts to its mammalian host during bubonic plague
Pradel, PLoS pathogens 2014 - “...G3P is involved in hexose and amino-acids anabolism in Y. pestis . In particular, SerA (YPO0914, which catalyzes the first step in the biosynthesis of serine from glycerate-3P that is produced from G3P) was not necessary for plague. Whereas G3P's role in hexose and amino-acid anabolism...”
- “...to redundant genes that constitute a spare wheel system. For instance, serine biosynthesis enzyme SerA (YPO0914) was not required for virulence but its loss could be rescued by a second putative SerA (YPO1288) enzyme. Alternatively, the requirement for a limited number of genes may be because...”
- Growth of Yersinia pseudotuberculosis in human plasma: impacts on virulence and metabolic gene expression
Rosso, BMC microbiology 2008 - “...cleavage system H protein 0.377 (< 0.001) YPTB3182 (gcvT) YPO0907 aminomethyltransferase 0.526 (0.022) YPTB3189 (serA) YPO0914 D-3-phosphoglycerate dehydrogenase 1.582 (0.04) 0.517 (0.005) YPTB3214 (proC) YPO0942 putative pyrroline-5-carboxylate reductase 0.647 (0.038) YPTB3474 YPO0584 putative symporter protein 0.61 (0.007) YPTB3570 (aroQ) YPO3660 putative class II dehydroquinase 0.721 (0.036)...”
PP_5155 phosphoglycerate dehydrogenase from Pseudomonas putida KT2440
PP5155 D-3-phosphoglycerate dehydrogenase from Pseudomonas putida KT2440
35% identity, 56% coverage
- Machine learning analysis of RB-TnSeq fitness data predicts functional gene modules in Pseudomonas putida KT2440
Borchert, mSystems 2024 - “...the third step in NAD + biosynthesis from L-aspartate ( 70 ). fModule_81, contained serA (PP_5155), which plays a critical role in serine biosynthesis and NAD + /NADH recycling ( 71 ). fModule_03 contained ridA (PP_5303), a conserved deaminase that controls accumulation of reactive and toxic...”
- Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology
Puchałka, PLoS computational biology 2008 - “...putida biomass reaction should be enriched with this cofactor. The remaining false positives (PP1768, PP4909, PP5155) are involved in the serine biosynthesis pathway. We found experimentally that mutants in these genes can grow on acetate if the medium also contains l -serine. These genes can be...”
- “...on glycine, which is possible; though very slow (results not shown). One of these genes (PP5155) has also a weakly annotated isozyme (PP2335). We found out as well that several of the mutants (PP1612, PP4188-9, PP4191-4) grow in silico on glucose, which we confirmed experimentally (results...”
U3RH61 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Acanthamoeba castellanii (see paper)
33% identity, 59% coverage
lmo0078 similar to phosphoglycerate dehydrogenase from Listeria monocytogenes EGD-e
36% identity, 52% coverage
- Extreme genetic diversity in the type VII secretion system of Listeria monocytogenes suggests a role in bacterial antagonism
Bowran, Microbiology (Reading, England) 2021 - “...dehydrogenase family protein. Curiously this is the same predicted function as the gene encoded by lmo0078 in the invariant housekeeping cluster, although the two proteins have no detectable sequence identity. Two of the genes in the essC2 variable region 1 cluster encode related proteins (numbered 24...”
- Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China
Wang, BMC genomics 2019 - “...chromosomal loci adjacent to tRNA genes, including tRNA-CTT-Lys (ICDC-LM188 locus tag: A6K41_00440, the tRNA-Lys after lmo0078 ), tRNA-CGA-Ser (ICDC-LM188 locus tag: A6K41_03215, the tRNA-Ser after lmo0670 ), tRNA-CCG-Arg (ICDC-LM188 locus tag: A6K41_12845, the tRNA-Arg after lmo2466 ) and tRNA-GGT-Thr (ICDC-LM188 locus tag: A6K41_13515, the tRNA-Thr after...”
NJ56_RS09235 phosphoglycerate dehydrogenase from Yersinia ruckeri
34% identity, 60% coverage
RAYM_04224 D-2-hydroxyacid dehydrogenase from Riemerella anatipestifer RA-YM
37% identity, 53% coverage
- The Role of the Regulator Fur in Gene Regulation and Virulence of Riemerella anatipestifer Assessed Using an Unmarked Gene Deletion System
Guo, Frontiers in cellular and infection microbiology 2017 - “...fur +Fe/WT+Fe BIOSYNTHESIS OF AMINO ACIDS, COFACTORS, AND PROSTHETIC GROUPS RAYM_04219 Phosphoserine aminotransferase 1.35 1.25 RAYM_04224 D-3-phosphoglycerate dehydrogenase 1.35 1.19 RAYM_04506 Thiamine biosynthesis protein ApbE 1.84 3.37 RAYM_06215 Aminodeoxychorismate lyase 1.08 1.12 RAYM_06377 Para-aminobenzoate synthase component I 1.53 1.01 CELL ENVELOPE AND SURFACE STRUCTURES RAYM_01390 GtrA...”
- “...(Outten et al., 2004 ). Moreover, the genes Phosphoserine aminotransferase ( RAYM_04219 ), D-3-phosphoglycerate-dehydrogenase ( RAYM_04224 ) controlling the shikimate pathway were upregulated. D-3-phosphoglycerate-dehydrogenase (pabB) converts chorismate to 4-amino-4-deoxychorismate (ADC) and phosphoserine aminotransferase (pabC) converts ADC to p-aminobenzoate (PABA) and pyruvate (Green et al., 1992 )....”
YE3400 D-3-phosphoglycerate dehydrogenase from Yersinia enterocolitica subsp. enterocolitica 8081
33% identity, 60% coverage
PSPTO_5294 D-3-phosphoglycerate dehydrogenase from Pseudomonas syringae pv. tomato str. DC3000
34% identity, 56% coverage
Q6C284 phosphoglycerate dehydrogenase from Yarrowia lipolytica (strain CLIB 122 / E 150)
33% identity, 57% coverage
E4T4B2 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein from Paludibacter propionicigenes (strain DSM 17365 / JCM 13257 / WB4)
36% identity, 53% coverage
PSPPH_4885 D-3-phosphoglycerate dehydrogenase from Pseudomonas syringae pv. phaseolicola 1448A
34% identity, 56% coverage
PITG_13165 D-3-phosphoglycerate dehydrogenase, putative from Phytophthora infestans T30-4
27% identity, 86% coverage
OEOE_0025 Lactate dehydrogenase related enzyme from Oenococcus oeni PSU-1
33% identity, 56% coverage
BC3248 D-3-phosphoglycerate dehydrogenase from Bacillus cereus ATCC 14579
36% identity, 59% coverage
- Time dynamics of the Bacillus cereus exoproteome are shaped by cellular oxidation
Madeira, Frontiers in microbiology 2015 - “...(BC5380). The two proteins that specifically accumulated under low-ORP anaerobiosis are a putative D-3-phosphoglycerate dehydrogenase (BC3248) and a putative nucleoside-binding protein (BC3791). No protein was found to be specifically assigned to high-ORP anoxic conditions. Figure 2 Venn diagrambased comparison of the exoproteomes identified in the three...”
Psyr_4852 Amino acid-binding ACT:D-isomer specific 2-hydroxyacid dehydrogenase, catalytic region:D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Pseudomonas syringae pv. syringae B728a
33% identity, 56% coverage
PMI2031 D-3-phosphoglycerate dehydrogenase from Proteus mirabilis HI4320
34% identity, 56% coverage
DDB_G0281071 3-phosphoglycerate dehydrogenase from Dictyostelium discoideum AX4
34% identity, 56% coverage
- D-Serine Metabolism and Its Importance in Development of Dictyostelium discoideum
Ito, Frontiers in microbiology 2018 - “...ligase ( Cosloy and McFall, 1973 ). The D. discoideum genome encodes a 3-phosphoglycerate dehydrogenase (DDB_G0281071) and a pantoate--alanine ligase (DDB_G0288935). Indeed, we observed slightly decreased intracellular levels of L -Ser in dsd -null cells. The decrease in intracellular L -Ser concentration may reflect a weakened...”
A4VGK3 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Pseudomonas stutzeri (see paper)
35% identity, 56% coverage
Echvi_2777 fused D-3-phosphoglycerate dehydrogenase / phosphoserine phosphatase (EC 1.1.1.95; EC 3.1.3.3) from Echinicola vietnamensis KMM 6221, DSM 17526
33% identity, 52% coverage
- mutant phenotype: # Important for fitness in defined media, unless serine is added as a nitrogen source. The N-terminal part is distantly related to the phosphoserine phosphatase from Arabidopsis, and no other candidate was found for this step. The C-terminal part is 52% identical to E. coli phosphoglycerate dehydrogenase.
FTT_1230 D-3-phosphoglycerate dehydrogenase from Francisella tularensis subsp. tularensis SCHU S4
33% identity, 57% coverage
2p9eA / P0A9T0 Crystal structure of g336v mutant of e.Coli phosphoglycerate dehydrogenase (see paper)
33% identity, 56% coverage
- Ligand: 1,4-dihydronicotinamide adenine dinucleotide (2p9eA)
Pcar_0629 3-phosphoglycerate dehydrogenase from Pelobacter carbinolicus str. DSM 2380
35% identity, 54% coverage
Q81FZ7 Glyoxylate reductase (NADP+) from Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711)
39% identity, 56% coverage
OEOE_1672 Lactate dehydrogenase related enzyme from Oenococcus oeni PSU-1
39% identity, 45% coverage
Clo1313_0586 phosphoglycerate dehydrogenase from Acetivibrio thermocellus DSM 1313
38% identity, 49% coverage
- Genome-Wide Transcription Factor DNA Binding Sites and Gene Regulatory Networks in Clostridium thermocellum
Hebdon, Frontiers in microbiology 2021 - “...Clo1313_0020-23 Pyruvate ferredoxin oxidoreductase Athe_0874-77 + 1 Clo1313_0530 Energy-coupling factor transport protein + 1 b Clo1313_0586 2-hydroxyacid dehydrogenase Athe_2125 + 2 b Clo1313_1571 Hydrogenase maturation enzyme, hydG Athe_0169 + 1 b Clo1313_1572 Putative iron-only hydrogenase system transcriptional regulator Athe_0168 1 b Clo1313_1686 Acetyl-CoA synthetase 1 Clo1313_1875...”
- “...of the proteins encoded by these genes such as a PFOR complex (Clo1313_0020-Clo1313_0023), 3-phosphoglycerate dehydrogenase (Clo1313_0586) and isocitrate dehydrogenase (Clo1313_1944) would produce reducing equivalents (NADH or typically NADPH for the case of isocitrate dehydrogenase) during consumption of cellobiose, while others would consume reducing equivalents: lactate dehydrogenase...”
SerA / b2913 phosphoglycerate dehydrogenase (EC 1.1.1.95; EC 1.1.1.399) from Escherichia coli K-12 substr. MG1655 (see 36 papers)
serA / P0A9T0 phosphoglycerate dehydrogenase (EC 1.1.1.95; EC 1.1.1.399) from Escherichia coli (strain K12) (see 36 papers)
SERA_ECOLI / P0A9T0 D-3-phosphoglycerate dehydrogenase; PGDH; 2-oxoglutarate reductase; EC 1.1.1.95; EC 1.1.1.399 from Escherichia coli (strain K12) (see paper)
C3SVM7 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Escherichia coli (see paper)
P0A9T0 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Escherichia coli (see 7 papers)
serA / RF|NP_417388 D-3-phosphoglycerate dehydrogenase; EC 1.1.1.95 from Escherichia coli K12 (see 5 papers)
NP_417388 phosphoglycerate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
b2913 D-3-phosphoglycerate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
c3494 D-3-phosphoglycerate dehydrogenase from Escherichia coli CFT073
ECs3784 D-3-phosphoglycerate dehydrogenase from Escherichia coli O157:H7 str. Sakai
B21_RS14345, ETEC_3105 phosphoglycerate dehydrogenase from Escherichia coli ETEC H10407
33% identity, 56% coverage
- function: Catalyzes the reversible oxidation of 3-phospho-D-glycerate to 3-phosphonooxypyruvate, the first step of the phosphorylated L- serine biosynthesis pathway. Also catalyzes the reversible oxidation of 2-hydroxyglutarate to 2-oxoglutarate.
catalytic activity: (2R)-3-phosphoglycerate + NAD(+) = 3-phosphooxypyruvate + NADH + H(+) (RHEA:12641)
catalytic activity: (R)-2-hydroxyglutarate + NAD(+) = 2-oxoglutarate + NADH + H(+) (RHEA:49612)
subunit: Homotetramer - Inhibition of glycine cleavage system by pyridoxine 5'-phosphate causes synthetic lethality in glyA yggS and serA yggS in Escherichia coli.
Ito, Molecular microbiology 2020 - GeneRIF: Inhibition of glycine cleavage system by pyridoxine 5'-phosphate causes synthetic lethality in glyA yggS and serA yggS in Escherichia coli.
- Transient kinetic analysis of L-serine interaction with Escherichia coli D-3-phosphoglycerate dehydrogenase containing amino acid mutations in the hinge regions.
Grant, Biochemistry 2011 - GeneRIF: Data indicate that the cooperative transmission induced by serine binding is transmitted through the D-3-phosphoglycerate dehydrogenase Gly294-Gly295 hinge region to the opposite serine binding interface.
- Transient kinetic analysis of the interaction of L-serine with Escherichia coli D-3-phosphoglycerate dehydrogenase reveals the mechanism of V-type regulation and the order of effector binding.
Burton, Biochemistry 2009 - GeneRIF: L-serine, inhibitor of D-3-phosphoglycerate dehydrogenase, exerts its effect on at least two steps in the kinetic mechanism, but to very different degrees.
- A stopped flow transient kinetic analysis of substrate binding and catalysis in Escherichia coli D-3-phosphoglycerate dehydrogenase.
Burton, The Journal of biological chemistry 2008 - GeneRIF: the rate-limiting step in both directions is a conformational change in the Escherichia coli D-3-phosphoglycerate dehydrogenase enzyme that is not detected optically
- The effect of hinge mutations on effector binding and domain rotation in Escherichia coli D-3-phosphoglycerate dehydrogenase.
Dey, The Journal of biological chemistry 2007 (PubMed)- GeneRIF: analysis of mutation effects on effector binding and domain rotation in Escherichia coli D-3-phosphoglycerate dehydrogenase
- Vmax regulation through domain and subunit changes. The active form of phosphoglycerate dehydrogenase.
Thompson, Biochemistry 2005 (PubMed) - Identification of amino acid residues contributing to the mechanism of cooperativity in Escherichia coli D-3-phosphoglycerate dehydrogenase.
Grant, Biochemistry 2005 - GeneRIF: L-Serine inhibits the catalytic activity of D-3-phosphoglycerate dehydrogenase by binding to its regulatory domain.
- Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link, Electrophoresis 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on mature peptide
- Identification of YigL as a PLP/PNP phosphatase in <i>Escherichia coli</i>
Matsuo, Applied and environmental microbiology 2024 (secret) - A Multiplex Enzymatic Machinery for Cellular Protein S-nitrosylation
Seth, Molecular cell 2018 - “...Fold- change (N/F) hcp Fold- change (N/F) WT/ hcp Interact with Hcp SerA D-3phosphoglycerate dehydrogenase P0A9T0 4.7 1.1 4.3 FdnG Formate dehydrogenase, major subunit P24183 11.2 2.7 4.1 Y GlyA Serine hydroxymethyltransferase P0A825 3.8 0.9 4.2 EfG Elongation factor G P0A6M8 5.8 1.5 3.9 AceE Pyruvate...”
- Automated characterization and analysis of expression compatibility between regulatory sequences and metabolic genes in Escherichia coli
Wen, Synthetic and systems biotechnology 2024 - “...b1854 pykA Pyruvate kinase b2029 gnd 6-Phosphogluconate dehydrogenase b2296 ackA Acetate kinase b2388 glk Glucokinase b2913 serA Phosphoglycerate dehydrogenase b2914 rpiA Ribose-5-phosphate isomerase A b2935 tktA Transketolase b2943 galP Galactose/H+ symporter b3041 ribB 3,4-Dihydroxy-2-butanone-4-phosphate synthase b3916 pfkA 6-Phosphofructokinase 1 b3919 tpiA Triose-phosphate isomerase b4025 pgi Glucose-6-phosphate...”
- FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization
Hassani, Microbial cell factories 2024 - “...PFL, ACALD, THD2pp, THD2pp 0.19 23.49 b0351, b1241, b0903, b3951, b2579, b3952, b3114, b0902, b1602, b2913 OBTFL, 'ALCD2x', 'ALCD19' Table5 The maximum rates of succinate growth-coupled production in iJR904 in rich medium ( Strain0 in LB cultivation medium) Number of knocked out reactions Deleted reactions Biomass...”
- Towards creating an extended metabolic model (EMM) for E. coli using enzyme promiscuity prediction and metabolomics data
Amin, Microbial cell factories 2019 - “...3.2.2.10 (b2795) Cytosine+5-phospho-- d -ribose-1-diphosphateCMP+diphosphate Cytosine+ d -ribose-5-phosphateCMP+H 2 O Predicted iML1515 1.1.1.79 (b1033) 1.1.1.95 (b2913) 2-Oxoglutarate+NADPH+H + 2-hydroxyglutarate+NADP + 2-Oxoglutarate+NADH+H + 2-hydroxyglutarate+NAD + Predicted KEGG 3.6.1.7 (b0968) 6.3.5.5 (b0032 or b0033) Bicarbonate+orthophosphatecarboxyphosphate+H 2 O Bicarbonate+ATPcarboxyphosphate+ADP Predicted iML1515 2.8.3.10 (b0615) 2.8.3.8 (b2221and b2222 or b1694) or...”
- Genome-wide analysis of fitness data and its application to improve metabolic models
Vitkin, BMC bioinformatics 2018 - “...points in Fig. 2b are from uncharacterized promoters that reside in ilvC (b3774) and serA (b2913) coding sequence. Both ilvC and serA have correlated fitness values (Spearman R =0.66, p -value=3.3810 7 ) and regulate amino acid synthesis. Fig. 2 a First enriched motif in D-Glucose...”
- Improved Metabolic Models for E. coli and Mycoplasma genitalium from GlobalFit, an Algorithm That Simultaneously Matches Growth and Non-Growth Data Sets
Hartleb, PLoS computational biology 2016 - “...or Phosphatidylglycerophosphate (dioctadec-11-enoyl, n-C18:1) b2114 METTRS TRNA(Met) b2514 HISTRS L-Histidyl-tRNA(His) TRNA(His) b2551 GHMT2r, THFAT 5-Formyltetrahydrofolate b2913 PGCD 3-Phosphohydroxypyruvate b3288 FMETTRS N-Formylmethionyl-tRNA b3384 TRPTRS L-Tryptophanyl-tRNA(Trp) TRNA(Trp) b4258 VALTRS L-Valyl-tRNA(Val) TRNA(Val) Solving FPp: Removing reactions 25 FPp could be resolved by removing a total of 18 reactions from...”
- “...RNTR1c2 for ) or (GTHOr for and RNTR1c2 for ) b2508 IMPD HXAND or XPPT b2913 PGCD GHMT2r back b2926 PGK TPI for b3731 ATPS4rpp (F6PA back and PGK back ) or (G6PDH2r for and PGK back ) b3733 ATPS4rpp (F6PA back and PGK back )...”
- Reconstruction of novel transcription factor regulons through inference of their binding sites
Elmas, BMC bioinformatics 2015 - “...). Table 5 Novel binding sites for PurR regulon Locus Gene Position Score TFBS sequence b2913 serA -95 8.1 ATATGAACGTTTGCGT b3714 yieG -115 8.4 ACGGCAACGATTGCGT b4064 yjcD -76 7.6 AAGATAACGTTTCGCT GO annotationss for this putative regulon suggested a cluster of genes with significant functional enrichment. Among...”
- A system-level model for the microbial regulatory genome
Brooks, Molecular systems biology 2014 - “...Fitness correlation Regulon gene 1 Regulon gene 2 Corems b3774 b3959 0.959012 IlvY ArgR 512157 b2913 b3829 0.938764 PurR MetR 512157 b3829 b3959 0.934393 MetR ArgR 512157;554056 b2913 b3941 0.932025 PurR MetR 512157 b3957 b3941 0.931565 ArgR MetR 512157;554056 b3172 b3829 0.930382 ArgR MetR 512157;554056 b2913...”
- Global transcriptomic analysis of an engineered Escherichia coli strain lacking the phosphoenolpyruvate: carbohydrate phosphotransferase system during shikimic acid production in rich culture medium
Cortés-Tolalpa, Microbial cell factories 2014 - “...IlvM Amino acid metabolism 16.9332 metE b3829 Cobalamin-independent homocysteine transmethylase Amino acid metabolism 59.0097 serA b2913 -Ketoglutarate reductase/D-3-phosphoglycerate dehydrogenase Amino acid metabolism 15.4266 ybaS b0485 Glutaminase Amino acid metabolism 27.4637 fimC b4316 Periplasmic chaperone, required for type 1 fimbriae Cell envelope 20.5382 ydiQ b1697 Putative subunit...”
- More
- The Role of Long Polar Fimbriae in Escherichia coli O104:H4 Adhesion and Colonization
Ross, PloS one 2015 - “...form a patient with HUS during the 2011 outbreak Obtained from CDC BRL1-17B O104:H4 2011 c3494 lpfA1 ::Cm This study JHU-1 O104:H4 2011 c3494 lpfA2 ::Gm This study BRL12-17B O104:H4 2011 c3494 lpfA1 ::Cm lpfA2 ::Gm created by conjugating SM10 (pCVD442 lpfA1 ::Cm) with JHU-1 This...”
- “...of the lpfA1 gene, we determined their ability to adhere to Caco-2 cells. Wild-type O104:H4 c3494 strain and the lpfA2 adhered to the Caco-2 monolayer to numbers higher than the input, (MOI 100), yielding 348.1 198.1% and 265.4 159.0% of the input respectively ( Fig 2...”
- Fitness of Escherichia coli during urinary tract infection requires gluconeogenesis and the TCA cycle
Alteri, PLoS pathogens 2009 - “...5.66 0.00021 XylA c4385 xylose isomerase 5.25 6.90E-07 TpiA c4871 triosephosphate isomerase 4.58 1.30E-07 SerA c3494 D-3-phosphoglycerate dehydrogenase 4.44 3.40E-09 SpeB c3522 agmantinase 4.06 3.90E-07 UxuA c5402 mannonate dehydratase 3.76 7.20E-03 NanA c3979 N-acetylneuraminate lyase subunit 3.64 4.50E-06 ArgG c3929 argininosuccinate dehydrogenase 3.41 5.80E-03 FklB c5306...”
- “...OppA c1707 oligopeptide substrate-binding protein 2.39 7.80E-03 OppA c1707 oligopeptide substrate-binding protein 2.34 2.10E-04 SerA c3494 D-3-phosphoglycerate dehydrogenase 2.28 1.90E-05 YghU c3726 hypothetical GST-like protein 2.27 1.10E-05 YbhE c0844 6-phosphogluconolactonase 2.2 9.90E-03 SucC c0805 succinyl-CoA synthetase beta chain 2.14 1.50E-04 GlpA c2782 anaerobic glycerol-3-phosphate dehydrogenase 2.13...”
- The attachment process and physiological properties of Escherichia coli O157:H7 on quartz
Wang, BMC microbiology 2020 - “...upregulated, indicating that glycolysis/glycogenesis was enhanced in attached cells. In addition, the genes Ecs2523 (1.4), Ecs3784 (1.9) and Ecs0990 (1.3) involved in the biosynthesis and degradation of L-serine were upregulated, indicating that the metabolic activity of L-serine was enhanced in attached cells. We confirmed through RT-qPCR...”
- “...fermentation metabolism-related genes pstC , Ecs4664 , Ecs2907 , Ecs2846 , pgk , Ecs2523 , Ecs3784 , Ecs0990 , and yodB (Fig. 3 b and c). Tolerance of environmental stress after E. coli O157:H7 attachment As shown in Table S 6 , the expression levels of...”
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...- 3.52 2 ECs3224 fadJ 4.26 2 ECs3772 yqfB -2.02 1 ECs3225 fadI 4.50 2 ECs3784 serA -3.66 1 ECs3227 fadL 5.39 2 ECs3810 tktA -4.16 1 ECs3230 yfdC 2.55 2 ECs3815 yqgB -2.40 1 ECs3259 yfdZ 3.57 2 ECs3833 ansB -2.31 4 ECs3271 - 3.06...”
- Cross-Kingdom Comparative Transcriptomics Reveals Conserved Genetic Modules in Response to Cadmium Stress
Chen, mSystems 2021 - “...ATPase YDR039C 0.57 <0.001 K/Na ion transmembrane transport CHLRE_16g682369v5 1.91 <0.001 Cu ion transmembrane transporter B21_RS14345 0.28 0.03 d -3-Phosphoglycerate dehydrogenase YIL074C 0.90 <0.001 Phosphoglycerate dehydrogenase SER33 CHLRE_16g689700v5 1.52 <0.001 Intracellular trafficking, secretion, and vesicular transport B21_RS10695 0.60 <0.001 Lactate dehydrogenase B21_RS13605 4.28 <0.001 Assimilatory sulfite...”
- The molecular basis for control of ETEC enterotoxin expression in response to environment and host
Haycocks, PLoS pathogens 2015 - “...CCTGGG TCAC G ETEC_3017 rppH 3324543 TGTG GGCTACG T A ACA (ETEC_3075) (ydhD) 3361162 n.d. ETEC_3105 serA 3368992 T T TGA TGCACCG CACA ( ETEC_3113 ) ( ygfI ) 3382158 TGTGA TCTACAA CAC G ETEC_3126 cmtB 3390811 TGTGA TTTGCT TCACA ETEC_3133 galP 3408173 TGTGA TGTGGA T...”
Q5HLU4 Putative 2-hydroxyacid dehydrogenase SERP1888 from Staphylococcus epidermidis (strain ATCC 35984 / DSM 28319 / BCRC 17069 / CCUG 31568 / BM 3577 / RP62A)
39% identity, 52% coverage
BMEII0813 D-3-PHOSPHOGLYCERATE DEHYDROGENASE from Brucella melitensis 16M
35% identity, 56% coverage
DSY4020 hypothetical protein from Desulfitobacterium hafniense Y51
Dhaf_1344 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Desulfitobacterium hafniense DCB-2
34% identity, 56% coverage
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...Previously, four genes have been proposed as potential vanH -encoding genes (DSY0996, DSY1673, DSY3442 and DSY4020) in the genome of D. hafniense Y51 (Kalan et al ., 2009 ). The homologues of these four genes were also found in the genomes of D. hafniense DCB-2 (Dhaf_1344,...”
- Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51
Kalan, Antimicrobial agents and chemotherapy 2009 - “...2-hydroxyacid dehydrogenase genes (DSY0996, DSY1673, DSY3442, and DSY4020) are present in the genome of D. hafniense Y51. The organism exhibits high-level...”
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...homologues of these four genes were also found in the genomes of D. hafniense DCB-2 (Dhaf_1344, Dhaf_1980, Dhaf_2079 and Dhaf_2820) and D. hafniense DP7 (data not shown). The complete genomes of D. hafniense Y51 and DCB-2 (Nonaka et al ., 2006 ; Kim et al .,...”
Q8CNB8 Putative 2-hydroxyacid dehydrogenase SE_1879 from Staphylococcus epidermidis (strain ATCC 12228 / FDA PCI 1200)
39% identity, 52% coverage
slcC / Q1QWN6 S-sulfolactate dehydrogenase subunit (EC 1.1.1.310) from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11) (see paper)
SLCC_CHRSD / Q1QWN6 (S)-sulfolactate dehydrogenase; (2S)-3-sulfolactate dehydrogenase; (S)-sulfolactate oxidoreductase; EC 1.1.1.310 from Chromohalobacter salexigens (strain ATCC BAA-138 / DSM 3043 / CIP 106854 / NCIMB 13768 / 1H11) (see paper)
33% identity, 54% coverage
- function: Dehydrogenase of the (R,S)-sulfolactate degradation pathway that only acts on the (S)-enantiomer of 3-sulfolactate. Together with ComC, provides a racemase system that converts (2S)-3-sulfolactate to (2R)-3-sulfolactate, which is degraded further by (2R)-sulfolactate sulfo-lyase. Specific for NAD. Also able to form sulfolactate from sulfopyruvate.
catalytic activity: (2S)-3-sulfolactate + NAD(+) = 3-sulfopyruvate + NADH + H(+) (RHEA:28194)
PA14_04110 D-3-phosphoglycerate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
34% identity, 56% coverage
Q9I6H5 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Pseudomonas aeruginosa (see paper)
PA0316 D-3-phosphoglycerate dehydrogenase from Pseudomonas aeruginosa PAO1
NP_249007 D-3-phosphoglycerate dehydrogenase from Pseudomonas aeruginosa PAO1
34% identity, 56% coverage
- Massively parallel mutant selection identifies genetic determinants of <i>Pseudomonas aeruginosa</i> colonization of <i>Drosophila melanogaster</i>
Miles, mSystems 2024 - “...leuC Amino acids [E] PA5495 thrB Amino acids [E] PA3736 hom Amino acids [E] + PA0316 serA Amino acids [E] PA4565 proB Amino acids [E] + PA0381 thiG Coenzyme metabolism [H] PA5118 thiI Coenzyme metabolism [H] + PA3975 thiD Coenzyme metabolism [H] + PA0501 bioF Coenzyme...”
- Quantitative proteomics analysis of proteins involved in alkane uptake comparing the profiling of Pseudomonas aeruginosa SJTD-1 in response to n-octadecane and n-hexadecane
Zhou, PloS one 2017 - “...membrane protein PA4589 fadL 2.51 1.60 gi|15596964 Uncharacterized protein PA1767 2.26 1.77 gi|15595513 D-3-phosphoglycerate dehydrogenase PA0316 serA 2.11 1.5 gi|15598528 Uncharacterized PhzA/B-like protein PA3332 2.02 2.23 gi|15598222 Uncharacterized protein PA3026 0.5 0.57 Note: a Proteins with fold changes of 2 or 0.5 (label free) and 1.5...”
- Pseudomonas aeruginosa serA Gene Is Required for Bacterial Translocation through Caco-2 Cell Monolayers
Yasuda, PloS one 2017 - “...Table 3 ). Among these 21 genes, we focused our attention on the serA gene (PA0316), as it is not known how PGDH contributes to the ability of P . aeruginosa to penetrate the intestinal epithelial cell barrier. There was no significant difference in the growth...”
- “...heat shock protein DnaK dnaK NP_253449.1 1 PA3818 extragenic suppressor protein SuhB suhB NP_252507.1 1 PA0316 D-3-phosphoglycerate dehydrogenase serA NP_249007.1 1 PA3164 still frameshift 3-phosphoshikimate 1-carboxyvinyltransferase aroA AE_004091.2 2 PA3763 phosphoribosylformylglycinamidine synthase purL NP_252452.1 1 PA5015 pyruvate dehydrogenase aceE NP_253702.1 3 PA0413 component of chemotactic signal...”
- The Pseudomonas aeruginosa PAO1 Two-Component Regulator CarSR Regulates Calcium Homeostasis and Calcium-Induced Virulence Factor Production through Its Regulatory Targets CarO and CarP
Guragain, Journal of bacteriology 2016 - “...0.99 Downregulated by high Ca during biofilm growth PA0316 PA0890 PA1053 PA1927 PA4453 PA4455 PA4773 PA4774 PA4775 PA4776 PA4777 PA4781 PA4782 PA4826 serA aotM...”
- Genomewide identification of genetic determinants of antimicrobial drug resistance in Pseudomonas aeruginosa
Dötsch, Antimicrobial agents and chemotherapy 2009 - “...PA14_31820 PA0089 PA0090 PA0140 PA0227 PA0247 PA0287 PA0316 PA0339 PA0381 PA0387 PA0407 PA0415 PA0432 PA0460 PA0479 PA0533 PA0545 PA0596 PA0597 PA0610...”
- Proteomic, microarray, and signature-tagged mutagenesis analyses of anaerobic Pseudomonas aeruginosa at pH 6.5, likely representing chronic, late-stage cystic fibrosis airway conditions
Platt, Journal of bacteriology 2008 - “...PA0519 PA4273 PA1596 PA3914 PA0520 PA0519 PA2945 PA1927 PA0316 PA0519 PA1562 PA0519 PA3915 PA0519 PA5497 PA3875 PA2846 PA5034 PA2445 PA0139 PA0519 PA0519 PA5427...”
- “...expressed proteins Protein PA0040 PA0139 (ahpC) PA0265 (gabD) PA0316 (serA) PA0519 (nirS) PA0520 (nirQ) PA0548 (tktA) PA0588 PA0595 (ostA) PA0895 (aruC) PA0962...”
- Pseudomonas aeruginosa serA Gene Is Required for Bacterial Translocation through Caco-2 Cell Monolayers.
Yasuda, PloS one 2017 - GeneRIF: serA is associated with bacterial motility and adherence, which are mediated by flagella that play a key role in the penetration of P. aeruginosa through Caco-2 cell monolayers.
E9AG23 D-3-phosphoglycerate dehydrogenase-like protein from Leishmania infantum
33% identity, 61% coverage
BAB2_0783 Amino acid-binding ACT:D-isomer specific 2-hydroxyacid dehydrogenase, catalytic domain:D-isomer specific 2-hydroxyacid dehydr... from Brucella melitensis biovar Abortus 2308
34% identity, 56% coverage
STM14_3699 phosphoglycerate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhimurium str. 14028S
STM3062 D-3-phosphoglycerate dehydrogenase from Salmonella typhimurium LT2
33% identity, 56% coverage
SAR2389 putative D-isomer specific 2-hydroxyacid dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
Q6GEC9 Putative 2-hydroxyacid dehydrogenase SAR2389 from Staphylococcus aureus (strain MRSA252)
38% identity, 52% coverage
DSVG11_0961 phosphoglycerate dehydrogenase from Desulfovibrio sp. G11
35% identity, 54% coverage
- The reductive glycine pathway allows autotrophic growth of Desulfovibrio desulfuricans
Sánchez-Andrea, Nature communications 2020 - “...or other transaminases), subsequent reduction of hydroxypyruvate to glycerate (potentially by 2-hydroxyacid dehydrogenases DSVG11_0256 or DSVG11_0961) and finally the generation of phospho-glycerate by glycerate kinase (DSVG11_0656 or DSVG11_1884). During autotrophic growth, assimilation probably proceeds primarily via the glycine reduction route rather than the serine route, as...”
SAUSA300_2254 glycerate dehydrogenase-like protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
MW2224 ORFID:MW2224~hypothetical protein, similar to glycerate dehydrogenase from Staphylococcus aureus subsp. aureus MW2
38% identity, 52% coverage
SAOV_2344 2-hydroxyacid dehydrogenase family protein from Staphylococcus aureus subsp. aureus ED133
38% identity, 52% coverage
- Staphylococcus aureus seroproteomes discriminate ruminant isolates causing mild or severe mastitis
Le, Veterinary research 2011 - “...046_0709 SAOV_0095 5,68 94945 2090,64 45,45 33 2,26 CW C D-3-phosphoglycerate dehydrogenase 100 011_0585 046_1131 SAOV_2344 5,32 34652 717,85 43,53 11 1,72 CW C atpD F0F1 ATP synthase subunit beta 62, 90 011_2064 046_0898 SAOV_2144c 4,68 51368 631,03 30,21 10 0,98 S,CW C [ 83 ]...”
BIF_01365 phosphoglycerate dehydrogenase from Bifidobacterium animalis subsp. lactis BB-12
33% identity, 57% coverage
- Updated Genome Sequence for the Probiotic Bacterium Bifidobacterium animalis subsp. lactis BB-12
Jensen, Microbiology resource announcements 2021 - “...4bp18bp Intergenic(+47/26) BIF_00002 / BIF_02140 45995 + TGGAATTCCACGGGCCT Intergenic(+95/+86) BIF_01763 / BIF_01079 93265 +CG Intergenic(+43/+6) BIF_01365 / BIF_02171 93267 +AACC Intergenic(+45/+4) BIF_01365 / BIF_02171 93268 TA Intergenic(+46/+3) BIF_01365 / BIF_02171 93270 +AT Intergenic(+48/+1) BIF_01365 / BIF_02171 103949 4bp22bp Intergenic(+18/+56) BIF_01186 / BIF_02012 103961 CA Intergenic(+30/+47) BIF_01186...”
Q608T2 hydroxypyruvate reductase (EC 1.1.1.81) from Methylococcus capsulatus (see paper)
34% identity, 51% coverage
DSY1673 hypothetical protein from Desulfitobacterium hafniense Y51
31% identity, 57% coverage
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...., 2008 ). Previously, four genes have been proposed as potential vanH -encoding genes (DSY0996, DSY1673, DSY3442 and DSY4020) in the genome of D. hafniense Y51 (Kalan et al ., 2009 ). The homologues of these four genes were also found in the genomes of D....”
- Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51
Kalan, Antimicrobial agents and chemotherapy 2009 - “...four annotated D-isomer-specific 2-hydroxyacid dehydrogenase genes (DSY0996, DSY1673, DSY3442, and DSY4020) are present in the genome of D. hafniense Y51. The...”
Dhaf_2820 Glyoxylate reductase from Desulfitobacterium hafniense DCB-2
31% identity, 57% coverage
SAV2305 glycerate dehydrogenase from Staphylococcus aureus subsp. aureus Mu50
SA2098 glycerate dehydrogenase from Staphylococcus aureus subsp. aureus N315
38% identity, 52% coverage
- Inhibition of Staphylococcus aureus biofilm formation by gurmarin, a plant-derived cyclic peptide
Chang, Frontiers in cellular and infection microbiology 2022 - “...protein homolog 0.02 SACOL2119 4.74 CTP synthase pyrG 0.03 SAV2029 4.67 GroEL protein groEL 0.03 SAV2305 4.64 Glycerate dehydrogenase 0.03 SACOL1245 4.54 3-oxoacyl-(acyl-carrier-protein) reductase fabG1 0.04 SACOL1437 4.42 Cold shock protein, CSD family cspA 0.02 MW2014 4.23 Thiamin phosphate synthase (chain B) thiE 0.03 SAV1766 4.17...”
- The effect of skin fatty acids on Staphylococcus aureus
Neumann, Archives of microbiology 2015 - “...13.54 SA1984 Asp23 Alkaline shock protein 23 10.13 SA1984 Asp23 Alkaline shock protein 23 8.04 SA2098 Putative 2-hydroxyacid dehydrogenase SA2098 2.25 SA2125 Formimidoylglutamase 2.12 SA2240 Hypothetical protein, similar to para-nitrobenzyl esterase chain A 8.60 SA2317 Hypothetical protein 0.44 SA2336 ClpL ATP-dependent Clp proteinase chain clpL 2.57...”
- “...14.42 SA2085 UreE Urease accessory protein UreE 5.85 SA2085 UreE Urease accessory protein UreE 3.28 SA2098 Putative 2-hydroxyacid dehydrogenase SA2098 2.09 SA2311 Putative NAD(P)H nitroreductase SA2311 2.62 SA2312 Ddh d -lactate dehydrogenase 2.44 SA2336 ClpL ATP-dependent Clp proteinase chain clpL 2.26 SA2336 ClpL ATP-dependent Clp proteinase...”
- Characterizing the effects of inorganic acid and alkaline shock on the Staphylococcus aureus transcriptome and messenger RNA turnover
Anderson, FEMS immunology and medical microbiology 2010 - “...3.3 15 stable atpG SA2096 F0F1 ATP synthase subunit sa_c4422s3769_a_at * 3.1 15 30 atpH SA2098 F0F1 ATP synthase subunit sa_c6417s5584_a_at * 2.9 2.5 30 betB SA2628 betaine aldehyde dehydrogenase sa_c736s544_a_at 22.7 2.5 15 cydA SA1094 cytochrome d ubiquinol oxidase, subunit I sa_c740s548_a_at 29.2 2.5 30...”
- “...* 2.2 15 15 atpG SA2096 F0F1 ATP synthase sa_c4422s3769_a_at * 2.3 15 15 atpH SA2098 F0F1 ATP synthase sa_c6417s5584_a_at * 2.9 2.5 15 betB SA2628 betaine aldehyde dehydrogenase sa_c5252s4546_a_at 2.1 2.5 2.5 fni SA2341 isopentenyl diphosphate isomerase sa_c6467s5637_a_at 3.3 5 ND gpxA2 SA2641 glutathione peroxidase...”
- Identification and phenotypic characterization of a beta-lactam-dependent, methicillin-resistant Staphylococcus aureus strain
Goldstein, Antimicrobial agents and chemotherapy 2007 - “...synthase II SA1557 COL, catabolite control protein SA2098 N315, "ORFID:SA2098, hypothetical protein, similar to glycerate dehydrogenase" SAV1002 Mu50, conserved...”
- Identification of novel adhesins from Group B streptococci by use of phage display reveals that C5a peptidase mediates fibronectin binding
Beckmann, Infection and immunity 2002 - “...Conserved hypothetical protein (S. pyogenes M1) ORFID (SA2098 hypothetical protein similar to glycerate dehydrogenase) (S. aureus) Putative integral membrane...”
SSU0623 D-isomer specific 2-hydroxyacid dehydrogenase from Streptococcus suis P1/7
ZY05719_03245 phosphoglycerate dehydrogenase from Streptococcus suis
33% identity, 64% coverage
- Identification of conditionally essential genes for Streptococcus suis infection in pigs
Arenas, Virulence 2020 - “...]. Accordingly, mutations in genes encoding enzymes participating in the synthesis of serine from glycerate-3-phosphate (SSU0623, serC , SSU1325), alanine (SSU0319), cysteine ( cysE ), glutamine (g lnA ), proline ( proA, proC ) and homocysteine ( hoM ), a precursor of methionine and threonine appeared...”
- Establishment of Streptococcus suis Biofilm Infection Model In Vivo and Comparative Analysis of Gene Expression Profiles between In Vivo and In Vitro Biofilms
Yi, Microbiology spectrum 2023 - “...II secretory pathway, pullulanase PulA and related glycosidases ZY05719_01910 AKG39782.1 4--Glucanotransferase ZY05719_09285 AKG41167.1 Dihydroxyacetone kinase ZY05719_03245 AKG40024.1 Phosphoglycerate dehydrogenase ZY05719_05855 AKG40512.1 Ribokinase family sugar kinase Amino acid metabolism ZY05719_09250 AKG41160.1 Leucyl aminopeptidase (aminopeptidase T) ZY05719_08880 AKG41090.1 Selenocysteine lyase Nucleotide metabolism ZY05719_10310 AKG41365.1 Inosine 5-monophosphate dehydrogenase ZY05719_02630...”
lpg0242 D-3-phosphoglycerate dehydrogenase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
39% identity, 46% coverage
BMEI1952 gluconate 2-dehydrogenase from Brucella melitensis 16M
36% identity, 49% coverage
- Integrated Bioinformatics-Based Subtractive Genomics Approach to Decipher the Therapeutic Drug Target and Its Possible Intervention against Brucellosis
Khan, Bioengineering (Basel, Switzerland) 2022 - “...nearby like: malate synthase G, involved in the glycolate utilization (glcB); aconitate hydratase (BMEI1855), (BMEII0009), (BMEI1952), (BMEII1061), (BMEI1939), (BMEII1060), (BMEII1062), (BMEII1064); and ureidoglycolate lyase (allA) and (BMEI0799). The PPI results showed that isocitrate lyase had a total number of nodes 11, average node numbers 7.09, average...”
BPHYT_RS11290 2-ketogluconate 6-phosphate reductase (EC 1.1.1.43) from Burkholderia phytofirmans PsJN
34% identity, 56% coverage
- mutant phenotype: Specifically important for: D-Gluconic Acid sodium salt. Gluconate is probably primarily catabolized via gluconate kinase (BPHYT_RS16720) and the Entner-Doudoroff pathway (starting with phosphogluconate dehydratase, BPHYT_RS16735). However it appears that there is a side pathway involving gluconate 2-dehydrogenase (BPHYT_RS14520, which has no phenotype because this side path is not beneficial), 2-ketogluconate kinase (BPHYT_RS11300, no fitness data), and 2-ketogluconate-6-P reductase (this gene). A similar side path is known in P. putida (PMCID:PMC4646247) and this gene is similar to the P. putida 2-ketoglutarate-6-phosphate reductase (PP3376).
SMa2137 probable glycerate from Sinorhizobium meliloti 1021
36% identity, 49% coverage
- In silico insights into the symbiotic nitrogen fixation in Sinorhizobium meliloti via metabolic reconstruction
Zhao, PloS one 2012 - “...3-hydroxybutyryl-CoA dehydrogenase Glutamyl-tRNA reductase B6KJQ6 8.00E-63 1.1.1.169 SM_b20362 Inositol-phosphate phosphatase 2-dehydropantoate 2-reductase A8TQC8 3.00E-46 1.1.1.290 SMa2137 dehydrogenase 4-phosphoerythronate dehydrogenase D4HBH5 3.00E-65 2.7.4.16 SMa0028 Selenophosphate synthase Thiamine-phosphate kinase E6PJ50 2.00E-13 3.1.3.15 SMa0483 Phosphatase Histidinol-phosphatase C5B1H3 6.00E-55 3.1.3.73 SMc04281 Probable threonine-phosphate decarboxylase Cobalamin biosynthesis (CobC) D4Z875 2.00E-37 3.1.3.74...”
- The Sinorhizobium meliloti fur gene regulates, with dependence on Mn(II), transcription of the sitABCD operon, encoding a metal-type transporter
Chao, Journal of bacteriology 2004 - “...(smc01664), five probable enzymatic proteins (mdeA, glnD, sma2137, smc01821, and smc02416), and seven proteins which have been annotated as hypothetical...”
- “...smc01664 smc01637 smc01124 (glnD) smb21403 smb20532 smb20335 sma2137 sma1413 sma1016 sma0875 (nolG) 2.38() 3.00() 2.15() 11.62() 7.22() 2.35() 2.64() 4.69()...”
- Nucleotide sequence and predicted functions of the entire Sinorhizobium meliloti pSymA megaplasmid
Barnett, Proceedings of the National Academy of Sciences of the United States of America 2001 - “...(GlyA2; SMA2135; Fig. 1), glycerate dehydrogenase (SMA2137), hydroxypyruvate reductase (SMA1406), a serine glycine transaminase similar to eukaryotic enzymes...”
BPSL1577 2-ketogluconate reductase from Burkholderia pseudomallei K96243
37% identity, 49% coverage
PITG_10264 D-3-phosphoglycerate dehydrogenase from Phytophthora infestans T30-4
39% identity, 45% coverage
PH0597 glyoxylate reductase from Pyrococcus horikoshii OT3
O58320 Glyoxylate reductase from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
36% identity, 53% coverage
2dbqA / O58320 Crystal structure of glyoxylate reductase (ph0597) from pyrococcus horikoshii ot3, complexed with NADP (i41) (see paper)
36% identity, 53% coverage
- Ligand: nadp nicotinamide-adenine-dinucleotide phosphate (2dbqA)
Mchl_2132 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Methylobacterium chloromethanicum CM4
40% identity, 44% coverage
YPO1288 putative D-isomer specific 2-hydroxyacid dehydrogenase family protein from Yersinia pestis CO92
35% identity, 45% coverage
BP1026B_I0581 2-hydroxyacid dehydrogenase from Burkholderia pseudomallei 1026b
36% identity, 46% coverage
C645_RS00700, WP_005672300 2-hydroxyacid dehydrogenase from Haemophilus influenzae
38% identity, 44% coverage
- Access to highly specialized growth substrates and production of epithelial immunomodulatory metabolites determine survival of Haemophilus influenzae in human airway epithelial cells
Hosmer, PLoS pathogens 2022 - “...lldD , C645_RS09865, WP_005657875.1) or two gene fragment ( dld , C645_RS09380, WP_046067851.1; ldhA , C645_RS00700, WP_005672300; guaB , C645_RS01605, WP_005660592.1) were cloned into pGEMT-Easy (Promega) or pBluescriptIISK (Stratagene), respectively, yielding pGEM-Hi lldD , pBlu-Hi ldhA , pBlu-Hi dld , and pBlu-Hi ImpDH . Suitable restriction...”
- “..., C645_RS09865, WP_005657875.1) or two gene fragment ( dld , C645_RS09380, WP_046067851.1; ldhA , C645_RS00700, WP_005672300; guaB , C645_RS01605, WP_005660592.1) were cloned into pGEMT-Easy (Promega) or pBluescriptIISK (Stratagene), respectively, yielding pGEM-Hi lldD , pBlu-Hi ldhA , pBlu-Hi dld , and pBlu-Hi ImpDH . Suitable restriction enzyme...”
BLJ_1306 phosphoglycerate dehydrogenase from Bifidobacterium longum subsp. longum JDM301
32% identity, 57% coverage
STM3646 2-keto-D-gluconate reductase from Salmonella typhimurium LT2
35% identity, 48% coverage
- CTAG-containing cleavage site profiling to delineate Salmonella into natural clusters
Tang, PloS one 2014 - “...3619357 3559340 XbaI 18 STM3594STM3595 3765983 3766163 3766042 3779743 3788912 3787367 3787368 3727350 XbaI 19 STM3646 3833687 3834661 3834463 3848154 3857340 3855778 3855779 3795761 XbaI 20 STM3714STM3715 3910705 3910806 3910806 3924498 3933683 3932120 3932121 3872105 XbaI 21 STM3785 3984439 3985182 3984523 3998215 4007398 4005836 4005837 3945822...”
Blon_0845 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Bifidobacterium longum subsp. infantis ATCC 15697
33% identity, 52% coverage
Ssal_00539 3-phosphoglycerate dehydrogenase family protein from Streptococcus salivarius 57.I
34% identity, 56% coverage
slr2123 D-isomer specific 2-hydroxyacid dehydrogenase family from Synechocystis sp. PCC 6803
36% identity, 47% coverage
hprA / Q59516 hydroxypyruvate reductase subunit (EC 1.1.1.81) from Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1) (see 2 papers)
39% identity, 44% coverage
D3F4F1 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein from Conexibacter woesei (strain DSM 14684 / CCUG 47730 / CIP 108061 / JCM 11494 / NBRC 100937 / ID131577)
37% identity, 57% coverage
- Detection and differentiation of fowl adenovirus serotype 4 and duck adenovirus 3 using high resolution melting curve assay.
Chen, Poultry science 2024 - “...on the 100 K genetic comparison of DAdV-3 and FAdV-4, a pair of qPCR-HRM primers (D3F4F1 and D3F4R1; Table 1 ) was designed with 116-nt target amplification fragments. The variation of the target amplified region (116-nt) between FAdV-4 and DAdV-3 are listed in Table 2 ....”
- “...here means the position of the 100 K gene of FAdV-4. B, the forward primer (D3F4F1) and reverse primer (D3F4R1) shared100 % matched with DAdV-3 and FAdV-4. Table 2 Variations in the target region between 100 K of FAdV-4 and DAdV-3. Table 2 Position 1-58 DAdV-3...”
L0084 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) from Lactococcus lactis subsp. lactis Il1403
33% identity, 58% coverage
WP_124144079 phosphonate dehydrogenase from Okeania hirsuta
31% identity, 56% coverage
- A novel salt- and organic solvent-tolerant phosphite dehydrogenase from Cyanothece sp. ATCC 51142
Abdel-Hady, Frontiers in bioengineering and biotechnology 2023 - “...(EJK14408), Cupriavidus basilensis KF708 (WP_026485313), Cyanothece sp. ATCC51142 (WP_009544749), Trichodesmium erythraeum GBRTRLIN201 (MBS9771025), Okeania hirsute (WP_124144079), Anabaena sp. PCC 7120(WP_010994144), Nostoc sp. KVJ3 (WP_265276617), Burkholderia vietnamiensis G4 (ABO60092), and Acinetobacter sp. SH024 (EFF86760). To characterize its enzymatic properties, the Ct-PtxD gene fragment was inserted into the...”
Dhaf_2079 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Desulfitobacterium hafniense DCB-2
34% identity, 47% coverage
Q0W9V5 Glyoxylate/hydroxypyruvate reductase B from Yersinia pestis
34% identity, 48% coverage
- Metaproteomics reveals major microbial players and their biodegradation functions in a large-scale aerobic composting plant
Liu, Microbial biotechnology 2015 - “...sp. Actinobacteria Fructose-1,6-bisphosphatase class 1 C0QTP7 Glycolysis / Gluconeogenesis Persephonella marina Aquificae Glyoxylate/hydroxypyruvate reductase B Q0W9V5 Pyruvate metabolism Yersinia pestis Gammaproteobacteria Acetyl-coenzyme A synthetase Q9F7R5 Pyruvate metabolism uncultured marine gamma proteobacterium Gammaproteobacteria Acetyl-coenzyme A synthetase 1 Q9Z3R3 Pyruvate metabolism Sinorhizobium meliloti Alphaproteobacteria Pyruvate, phosphate dikinase Q59754...”
- “...Bacilli; Bacillales Pyruvate dehydrogenase E1 component Q59637 Pyruvate metabolism Pseudomonas aeruginosa Gammaproteobacteria Glyoxylate/hydroxypyruvate reductase B Q0W9V5 Pyruvate metabolism Yersinia pestis Gammaproteobacteria Acetyl-coenzyme A synthetase Q9F7R5 Pyruvate metabolism uncultured marine Gammaproteobacterium Gammaproteobacteria Acetyl-coenzyme A synthetase 1 Q9Z3R3 Pyruvate metabolism Sinorhizobium meliloti Alphaproteobacteria Malate dehydrogenase A5WGM2 TCA Psychrobacter...”
SEET0819_01960 glyoxylate/hydroxypyruvate reductase GhrB from Salmonella enterica subsp. enterica serovar Tennessee str.
34% identity, 48% coverage
DVU0339 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Desulfovibrio vulgaris Hildenborough
35% identity, 49% coverage
DvMF_1902 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding from Desulfovibrio vulgaris str. Miyazaki F
35% identity, 46% coverage
lp_0203 phosphoglycerate dehydrogenase from Lactobacillus plantarum WCFS1
34% identity, 54% coverage
- Tannic acid-dependent modulation of selected Lactobacillus plantarum traits linked to gastrointestinal survival
Reverón, PloS one 2013 - “...Transpeptidase (penicillin binding protein 2B2) 1.39 n.d. Other lp_2790 (serA) 2-hydroxyacid dehydrogenase 1.75 g n.d. lp_0203 (serA) C-terminal ACT (regulatory) 1.98 e n.d. lp_2956 ( tanLp1 ) tannin acylhydrolase 4.31 12.00 e a Designated gene number for the annotated L. plantarum WCFS1 genome. b Mean of...”
- “...an abundant amino acid in the L. plantarum cell-envelope proteins. We observed that lp_2790 and lp_0203 (another serA paralog overexpressed upon p -coumaric acid stress [31] ) were significantly induced by tannic acid. We also examined the expression of the tannin acylhydrolase (tannase) encoded by tanLp1...”
YPO2329 D-lactate dehydrogenase from Yersinia pestis CO92
YPTB2248 D-lactate dehydrogenase from Yersinia pseudotuberculosis IP 32953
35% identity, 45% coverage
NMB1685 D-lactate dehydrogenase from Neisseria meningitidis MC58
37% identity, 45% coverage
HPR_BLAHS / C0CMQ8 Hydroxypyruvate reductase; EC 1.1.1.81 from Blautia hydrogenotrophica (strain DSM 10507 / JCM 14656 / S5a33) (Ruminococcus hydrogenotrophicus) (see paper)
31% identity, 53% coverage
- function: Involved in catabolism of D-apiose. Catalyzes the reduction of 3-hydroxypyruvate to glycerate.
catalytic activity: (R)-glycerate + NAD(+) = 3-hydroxypyruvate + NADH + H(+) (RHEA:17905) - Functional assignment of multiple catabolic pathways for D-apiose
Carter, Nature chemical biology 2018 - “...dehydrogenase), B9JN19 (D-erythrulose 4-phosphate isomerase), B9JN20 (L-eythrulose 1-phosphate isomerase), C0CMQ5/C0CMQ6 (3-oxo-isoapionate transketolase), C0CMQ7 (D-apionate oxidoisomerase), C0CMQ8 (hydroxypyruvate reductase), F8GV06 (D-apionate oxidoisomerase), Q2JZQ0 (3-oxo-isoapionate 4-phosphate decarboxylase), Q2JZQ5 (D-apiose binding SBP), Q6D5T7 (D-apiose isomerase), Q6D5T8 (D-apulose kinase), Q6D8V3 (D-apionate oxidoisomerase), Q6D8V4 (3-oxo-isoapionate decarboxylase), Q6D8V5 (L-erythrulose 1-phosphate isomerase), Q6D8V6...”
- “...(pH 8.0), 2 mM MgCl 2 , 0.16 mM NADH, and 3.65 10 8 M C0CMQ8 in a final volume of 200 L. Data were fit to the Michaelis-Menten equation (kinetic constants are shown in Supplementary Table 4 ). 1 H NMR Assay for Lactonase Activity...”
NSP_RS15555 phosphonate dehydrogenase from Nodularia spumigena CCY9414
31% identity, 56% coverage
F8A9V0 D-lactate dehydrogenase (EC 1.1.1.28) from Thermodesulfatator indicus (see paper)
39% identity, 41% coverage
gbs1619 Unknown from Streptococcus agalactiae NEM316
32% identity, 64% coverage
PA3896 probable 2-hydroxyacid dehydrogenase from Pseudomonas aeruginosa PAO1
35% identity, 45% coverage
TkrA / b3553 glyoxylate reductase (EC 1.1.1.79; EC 1.1.1.215) from Escherichia coli K-12 substr. MG1655 (see 3 papers)
ghrB / P37666 glyoxylate reductase (EC 1.1.1.79; EC 1.1.1.215) from Escherichia coli (strain K12) (see 4 papers)
GHRB_ECOLI / P37666 Glyoxylate/hydroxypyruvate reductase B; 2-ketoaldonate reductase; 2-ketogluconate reductase; 2KR; EC 1.1.1.79; EC 1.1.1.81; EC 1.1.1.215 from Escherichia coli (strain K12) (see 2 papers)
ghrB / GB|AAC76577.2 glyoxylate/hydroxypyruvate reductase B; EC 1.1.1.215; EC 1.1.1.79; EC 1.1.1.81 from Escherichia coli K12 (see 6 papers)
NP_418009 glyoxylate reductase from Escherichia coli str. K-12 substr. MG1655
34% identity, 48% coverage
- function: Catalyzes the NADPH-dependent reduction of glyoxylate and hydroxypyruvate into glycolate and glycerate, respectively. Can also reduce 2,5-diketo-D-gluconate (25DKG) to 5-keto-D-gluconate (5KDG), 2- keto-D-gluconate (2KDG) to D-gluconate, and 2-keto-L-gulonate (2KLG) to L-idonate (IA), but it is not its physiological function. Inactive towards 2-oxoglutarate, oxaloacetate, pyruvate, 5-keto-D-gluconate, D- fructose and L-sorbose. Activity with NAD is very low
catalytic activity: glycolate + NADP(+) = glyoxylate + NADPH + H(+) (RHEA:10992)
catalytic activity: (R)-glycerate + NAD(+) = 3-hydroxypyruvate + NADH + H(+) (RHEA:17905)
catalytic activity: (R)-glycerate + NADP(+) = 3-hydroxypyruvate + NADPH + H(+) (RHEA:18657)
catalytic activity: D-gluconate + NADP(+) = 2-dehydro-D-gluconate + NADPH + H(+) (RHEA:16653)
subunit: Homodimer. - Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12.
Link, Electrophoresis 1997 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- An aldo-keto reductase with 2-keto-l-gulonate reductase activity functions in l-tartaric acid biosynthesis from vitamin C in Vitis vinifera
Jia, The Journal of biological chemistry 2019 - “...Fig. 1 ) in grapevine, the previously characterized E. coli 2-ketoaldonate reductase (yiaE, UniProt number P37666) ( 28 ) was used for homology searches. A consensus sequence (accession number TC59682) encoding a putative enzyme highly homologous (39% identity) to E. coli yiaE was identified by tBLASTn...”
- “...reductase gene from grapevine The amino acid sequence of the E. coli yiaE (UniProt number P37666) ( 28 ) was used as a query to tBLASTn ( E -value = 0) against the NCBI Gene Index Project: Gene Indices: Grape EST database. The encoded amino acid...”
- Identification of enzymes and regulatory proteins in Escherichia coli that are oxidized under nitrogen, carbon, or phosphate starvation
Noda, Proceedings of the National Academy of Sciences of the United States of America 2007 - “...P0A6M9 P0A6N2 P09373 P0AB71 Q8FBT4 P0A9C6 P25553 P08200 P37666 P05793 P0AD97 Q59346 P76558 Q8FB98 P0A7A0 Q8FCA6 P23721 P0AFG8 P0A826 P0A837 P0AC42 P0A9P4 P27302...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...Tig P0A850 Trigger factor 4.83/48,192.67 TkrA P37666 2-Ketogluconate reductase 5.5/35,395.5 TldD P0AGG8 Protein 4.93/51,364.09 TnaA P0A853 Tryptophanase...”
- Isolation of a chromosomal region of Klebsiella pneumoniae associated with allantoin metabolism and liver infection
Chou, Infection and immunity 2004 - “...4 Putative 2-ketogluconate transporter (NP_745517) 2-Ketoaldonate reductase (P37666) 246 (69) 322 (81) 8.8 5 Fimbrial chaperone protein (BAC55513) Fimbrial...”
- Biochemical characterization of the 2-ketoacid reductases encoded by ycdW and yiaE genes in Escherichia coli
Nuñez, The Biochemical journal 2001 (secret)
PG_2171 2-hydroxyacid dehydrogenase family protein from Porphyromonas gingivalis W83
34% identity, 56% coverage
ECs4438 2-hydroxyacid dehydrogenase from Escherichia coli O157:H7 str. Sakai
34% identity, 48% coverage
TON_0569 D-isomer specific 2-hydroxyacid dehydrogenase from Thermococcus onnurineus NA1
32% identity, 58% coverage
NGO1336 putative dehydrogenase, lactate from Neisseria gonorrhoeae FA 1090
36% identity, 45% coverage
- Dinner date: Neisseria gonorrhoeae central carbon metabolism and pathogenesis
Potter, Emerging topics in life sciences 2024 - “...truncated pseudo-protein NEIS1468, NEIS1469 lctP Lactate Permease NGO1449 NEIS0482 ldhA D-lactate Dehydrogenase, NAD + -Dependent NGO1336 NEIS1603 ldhD D-Lactate Dehydrogenase, Quinone-Dependent NGO0890 NEIS0984 lldD L-Lactate Dehydrogenase, Quinone-Dependent NGO0639 NEIS1312 lutACB L-Lactate Dehydrogenase, Quinone-Dependent NGO0904-0906 NEIS1371-NEIS1373 mqo Malate: Quinone Oxidoreductase NGO1980 NEIS2076 mtrCDE Multi-Drug Efflux Pump NGO1365-1363...”
- A role for lactate dehydrogenases in the survival of Neisseria gonorrhoeae in human polymorphonuclear leukocytes and cervical epithelial cells
Atack, The Journal of infectious diseases 2014 - “...FA1090 reveals that 3 genes (NGO0639, NGO0890, and NGO1336) are annotated as potential LDHs. The first 2 genes are predicted to be membrane-bound respiratory...”
- “...Neisseria meningitidis D-LDH [5]. The third predicted LDH (NGO1336, ldhA) is homologous to the soluble, D-lactate-specific, NAD+-linked LDH from E. coli, LdhA...”
sS8_1475 2-hydroxyacid dehydrogenase from Methylocaldum marinum
33% identity, 51% coverage
WP_265276617 phosphonate dehydrogenase from Nostoc sp. KVJ3
31% identity, 52% coverage
- A novel salt- and organic solvent-tolerant phosphite dehydrogenase from Cyanothece sp. ATCC 51142
Abdel-Hady, Frontiers in bioengineering and biotechnology 2023 - “...(WP_009544749), Trichodesmium erythraeum GBRTRLIN201 (MBS9771025), Okeania hirsute (WP_124144079), Anabaena sp. PCC 7120(WP_010994144), Nostoc sp. KVJ3 (WP_265276617), Burkholderia vietnamiensis G4 (ABO60092), and Acinetobacter sp. SH024 (EFF86760). To characterize its enzymatic properties, the Ct-PtxD gene fragment was inserted into the expression vector pET-21b (+), and the recombinant Ct-PtxD...”
EIP97_RS14860 2-hydroxyacid dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
36% identity, 47% coverage
PG1279 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Porphyromonas gingivalis W83
32% identity, 56% coverage
BL02138 2-hydroxyacid dehydrogenase from Bacillus licheniformis DSM 13 = ATCC 14580
34% identity, 47% coverage
- Metabolic engineering of Bacillus subtilis for growth on overflow metabolites
Kabisch, Microbial cell factories 2013 - “...much smaller extent (data not shown). B. licheniformis DSM13 possesses a putative glyoxylate reductase (ORF BL02138) which exhibits a 70% identity to a similar enzyme ( gyaR ) of Bacillus pumilus ATCC 7061. This putative glyoxylate reductase (ORF BL02138) could catalyze the reduction of glyoxylate to...”
EC958_3959 glyoxylate/hydroxypyruvate reductase GhrB from Escherichia coli O25b:H4-ST131
34% identity, 48% coverage
4zgsA / B0LUZ5 Identification of the pyruvate reductase of chlamydomonas reinhardtii (see paper)
34% identity, 48% coverage
- Ligand: nicotinamide-adenine-dinucleotide (4zgsA)
PP3376 2-ketogluconate 6-phosphate reductase from Pseudomonas putida KT2440
PP_3376 2-hydroxyacid dehydrogenase from Pseudomonas putida KT2440
35% identity, 49% coverage
- Integrated analysis of gene expression and metabolic fluxes in PHA-producing Pseudomonas putida grown on glycerol
Beckers, Microbial cell factories 2016 - “...PP3416 Carbohydrate kinase 0.06 0.52 0.10 0.7 kguK PP3378 Dehydroglucokinase 0.02 0.63 0.10 0.21 kguD PP3376 2-Ketogluconate 6-phosphate reductase 0.15 0.17 0.10 0.2 rpiA PP5150 Ribose-5-phosphate isomerase A 0.09 0.06 0.10 0.06 rpe PP0415 Ribulose-phosphate 3-epimerase 0.04 0.20 0.74 0.5 tktA PP4965 Transketolase 0.28 0.29 0.10...”
- Pseudomonas putida KT2440 Strain Metabolizes Glucose through a Cycle Formed by Enzymes of the Entner-Doudoroff, Embden-Meyerhof-Parnas, and Pentose Phosphate Pathways
Nikel, The Journal of biological chemistry 2015 - “...Gnd (PP4043) Icd (PP4011) PP4012 Mdh (PP0654) PP5391 KguD (PP3376) Gap-1 (PP1009) Gap-2 (PP2149) PP0665 PP3443 MaeB (PP5085) 32.9 8.7 67.1 10.8 6.2 0.1 93.8 0.7...”
- Production of medium chain length polyhydroxyalkanoate in metabolic flux optimized Pseudomonas putida
Borrero-de, Microbial cell factories 2014 - “...dehydrogenase -0.6 -0.1 gnuK PP3416 Carbohydrate kinase -1.1 -0.6 kguK PP3378 Dehydroglucokinase 0.45 -0.4 kguD PP3376 2-Ketogluconate 6-phosphate reductase -0.7 -0.5 rpiA PP5150 Ribose-5-phosphate isomerase A 0.3 0.0 rpe PP0415 Ribulose-phosphate 3-epimerase -0.5 -0.1 tktA PP4965 Transketolase 0.3 0.7 tal PP2168 Transaldolase B 0.4 0.3 Entner-Doudoroff...”
- “...dehydrogenase 0.2 -0.3 gnuK PP3416 Carbohydrate kinase -0.1 0.3 kguK PP3378 Dehydroglucokinase 0.6 0.5 kguD PP3376 2-Ketogluconate 6-phosphate reductase 0.1 -0.1 rpiA PP5150 Ribose-5-phosphate isomerase A 0.3 -0.4 rpe PP0415 Ribulose-phosphate 3-epimerase 0.2 -0.1 tktA PP4965 Transketolase 0.7 0.3 tal PP2168 Transaldolase B 0.2 0.1 Entner-Doudoroff...”
- Microbial responses to xenobiotic compounds. Identification of genes that allow Pseudomonas putida KT2440 to cope with 2,4,6-trinitrotoluene
Fernández, Microbial biotechnology 2009 - “...subunit 2.3 PP3761 Sensor histidine kinase/response regulator 2.2 M 4. Metabolism PP1081 Glutaredoxinrelated protein 2.1 PP3376 kguD 2ketogluconate 6phosphate reductase 2.7 M PP3781 Oxygenindependent Coproporphyrinogen III oxidase fam 4.7 5. Unknown /uncharacterized proteins 5.A. Membrane proteins PP2322 oprI outer membrane lipoprotein OprI 2.2 PP2595 ABC transporter...”
- A set of activators and repressors control peripheral glucose pathways in Pseudomonas putida to yield a common central intermediate
del, Journal of bacteriology 2008 - “...within a cluster in the chromosome that covers from PP3376 to PP3384. A regulator of the Pseudomonas putida mt-2 was isolated from soils in Japan and identified...”
- “...2KG transport (PP3377) and its metabolism (PP3379, PP3378, and PP3376) form another operon that is transcribed from its own promoter. The ptxS gene is located...”
- Convergent peripheral pathways catalyze initial glucose catabolism in Pseudomonas putida: genomic and flux analysis
del, Journal of bacteriology 2007 - “...gluconokinase (gnuK; PP3416), and 2-ketogluconate-6-phosphate reductase (kguD; PP3376), we hypothesized that the inability to obtain mutants in a step above...”
- “...genes (not shown). We found that the set of genes from PP3376 to PP3384 is organized in two operons, one that included the kgu genes (kguE to kguT) and the ptxS...”
- Genetic evidence that catabolites of the Entner-Doudoroff pathway signal C source repression of the sigma54 Pu promoter of Pseudomonas putida
Velázquez, Journal of bacteriology 2004 - “...key enzymes of the kgu cluster (encoded by PP3376 and PP3378 in P. putida), 2KG can originate 2-dehydrogluconate phosphate and 2-dehydro-3-deoxygluconate, which...”
- Phosphite synthetic auxotrophy as an effective biocontainment strategy for the industrial chassis Pseudomonas putida
Asin-Garcia, Microbial cell factories 2022 - “...is relevant due to the existence of a native PtxD from P. putida encoded by PP_3376 , which was inferred from homology. Since the native PtxD does not seem to mediate our function of interest, we do not consider it in this study and refer to...”
- Nitrogen Metabolism in Pseudomonas putida: Functional Analysis Using Random Barcode Transposon Sequencing
Schmidt, Applied and environmental microbiology 2022 (secret)
TK0551 D-isomer specific 2-hydroxyacid dehydrogenase from Thermococcus kodakaraensis KOD1
30% identity, 56% coverage
- Removal of phosphoglycolate in hyperthermophilic archaea
Michimori, Proceedings of the National Academy of Sciences of the United States of America 2024 - “...respectively. ( B ) GLDH activity from glycolate to glyoxylate in cell extracts from KU216, TK0551, and TK0683 strains. Gray or white bars indicate the specific activities in extracts from cells grown under anaerobic or microaerobic conditions, respectively. ( C ) GLDH activity from glyoxylate to...”
- “...( B ) proteins were measured toward various phosphorylated metabolites. Dehydrogenase activities of the purified TK0551 ( C ) and TK0683 ( D ) proteins were examined toward various 2-hydroxyacids. Aminotransferase activities of the purified TK0186/TK1094 proteins with various amino donor compounds in the presence of...”
- An archaeal ADP-dependent serine kinase involved in cysteine biosynthesis and serine metabolism
Makino, Nature communications 2016 - “...with relatively high similarity, annotated as lactate dehydrogenases (LDHs), were also present ( Tk-ldhA1 : TK0551 (29% identical), Tk-ldhA2 : TK0683 (31% identical)), we constructed a triple gene disruption strain of these genes to ensure the complete shutdown of pathway Cys2. As a result, growth without...”
- “...construct disruption vectors for tk1449 (TK1449, metC ), Tk - serA (TK1966), Tk - ldhA1 (TK0551), Tk - ldhA2 (TK0683), Tk-cysK (TK1687), Tk-serK (TK0378), Tk-glyA (TK0528) and Tk-tdh (TK0916), their coding regions along with about 1,000bps of 5- and 3-flanking regions were amplified by PCR using...”
DSY0996 hypothetical protein from Desulfitobacterium hafniense Y51
33% identity, 47% coverage
- vanI: a novel D-Ala-D-Lac vancomycin resistance gene cluster found in Desulfitobacterium hafniense
Kruse, Microbial biotechnology 2014 - “...al ., 2008 ). Previously, four genes have been proposed as potential vanH -encoding genes (DSY0996, DSY1673, DSY3442 and DSY4020) in the genome of D. hafniense Y51 (Kalan et al ., 2009 ). The homologues of these four genes were also found in the genomes of...”
- Noncanonical vancomycin resistance cluster from Desulfitobacterium hafniense Y51
Kalan, Antimicrobial agents and chemotherapy 2009 - “...cluster, four annotated D-isomer-specific 2-hydroxyacid dehydrogenase genes (DSY0996, DSY1673, DSY3442, and DSY4020) are present in the genome of D. hafniense...”
PA2263 probable 2-hydroxyacid dehydrogenase from Pseudomonas aeruginosa PAO1
35% identity, 47% coverage
BCAL3179 probable D-lactate dehydrogenase from Burkholderia cenocepacia J2315
37% identity, 43% coverage
- Identification of functions linking quorum sensing with biofilm formation in Burkholderia cenocepacia H111
Inhülsen, MicrobiologyOpen 2012 - “...n.d. BCAM2142 5.3 n.d. n.d. BCAM2143 ( bapA ) 5.1 2.6 Energy production and conversion BCAL3179 ( ldhA ) 3.4 2.6 n.d. BCAL3285 ( hmpA ) 25.8 n.d. n.d. Defense mechanisms BCAM0200 9.2 15.0 n.d. BCAM0393 4.1 5.6 n.d. BCAS0293 ( aidA ) 167.2 24.0 BCAS0292...”
- “...were found to be QS-regulated only in strain H111: BCAL0121, BCAL0510, BCAL1678BCAL1681, BCAL1813, BCAL1921, BCAL3178, BCAL3179, BCAL3285, BCAM0028, BCAM0030, BCAM0393, BCAM0835, BCAM2140BCAM2143, BCAM2308, BCAM2720, BCAS0236, and BCAS0498 ( Table 1 ). We found that a large proportion of the QS-regulated proteins was not among the QS-regulated...”
- Burkholderia cenocepacia differential gene expression during host-pathogen interactions and adaptation to the host environment
O'Grady, Frontiers in cellular and infection microbiology 2011 - “...Conserved hypothetical protein 2.19 BCAL3109 Urease accessory protein 1.69 BCAL3178 LysR family regulatory protein 1.72 BCAL3179 Probable d -lactate dehydrogenase 1.91 BCAL3211 Conserved hypothetical protein 1.66 BCAL3227 Conserved hypothetical protein 2.10 BCAL3231 Hypothetical protein 1.63 BCAL3234 Glycosyltransferase 1.69 BCAL3239 Glucosyltransferase 1.84 BCAL3368 Putative regulatory protein 1.85...”
AO353_26885 phosphogluconate 2-dehydrogenase KguD (EC 1.1.1.43) from Pseudomonas fluorescens FW300-N2E3
33% identity, 54% coverage
- mutant phenotype: Specific phenotype: utilization of D-Gluconic Acid and of glucose with alternate N sources. See PMC1951859
PF0370 phosphoglycerate dehydrogenase from Pyrococcus furiosus DSM 3638
30% identity, 56% coverage
SMc01622 PUTATIVE OXIDOREDUCTASE PROTEIN from Sinorhizobium meliloti 1021
34% identity, 49% coverage
- Genetic characterization of a complex locus necessary for the transport and catabolism of erythritol, adonitol and L-arabitol in Sinorhizobium meliloti
Geddes, Microbiology (Reading, England) 2012 (PubMed)- “...necessary for both polyols (SMc01617, rbtC; SMc01618, rbtB; SMc01622, rbtA). Genetic and biochemical data show that in addition to utilizing erythritol as a...”
- “...was used to construct deletions of SMc01619, SMc01618, SMc01622 and SMc01617 to yield strains SRmD208, SRmD209, SRmD247 and SRmD249, respectively (House et al.,...”
kguD / Q5TM04 2-dehydro-6-phosphogluconate reductase (EC 1.1.1.43) from Pseudomonas fluorescens (strain ATCC BAA-477 / NRRL B-23932 / Pf-5) (see 2 papers)
32% identity, 54% coverage
PHYSODRAFT_503916 hypothetical protein from Phytophthora sojae
37% identity, 44% coverage
- Insights into the adaptive response of the plant-pathogenic oomycete Phytophthora capsici to the fungicide flumorph
Pang, Scientific reports 2016 - “...protein PHYSODRAFT_284882 Nucleobase-containing compound metabolism 348677381 Hypothetical protein PHYSODRAFT_354553 Nucleobase-containing compound metabolism 348677150 hypothetical protein PHYSODRAFT_503916 Nucleobase-containing compound metabolism 348673952 Hypothetical protein PHYSODRAFT_286691 Nucleobase-containing compound metabolism 348672301 hypothetical protein PHYSODRAFT_547952 Nucleobase-containing compound metabolism 348671618 Hypothetical protein PHYSODRAFT_435859 Nucleobase-containing compound metabolism 348670008 hypothetical protein PHYSODRAFT_347790 Nucleobase-containing compound...”
ETAE_1771 D-lactate dehydrogenase from Edwardsiella tarda EIB202
34% identity, 45% coverage
lmo2824 similar to D-3-phosphoglycerate dehydrogenase from Listeria monocytogenes EGD-e
LMON_2843 phosphoglycerate dehydrogenase from Listeria monocytogenes EGD
33% identity, 55% coverage
- Survival of Listeria monocytogenes in Soil Requires AgrA-Mediated Regulation
Vivant, Applied and environmental microbiology 2015 - “...phosphate isomerase), lmo0347 (dihydroxyacetone kinase), and lmo2824 (D-3phosphoglycerate dehydrogenase), or functions related to the transport of proteins,...”
- The transcriptional response of Listeria monocytogenes during adaptation to growth on lactate and diacetate includes synergistic changes that increase fermentative acetoin production
Stasiewicz, Applied and environmental microbiology 2011 - “...biosynthesis enzymes; lmo2647, encoding a putative creatininase; lmo2824 (serA), encoding a serine biosynthesis enzyme; lmo0689 (cheV), encoding a chemotaxis...”
- Proteomic analyses of a Listeria monocytogenes mutant lacking sigmaB identify new components of the sigmaB regulon and highlight a role for sigmaB in the utilization of glycerol
Abram, Applied and environmental microbiology 2008 - “...serine protease (100/100) Lmo1601 Lmo1602 Lmo0956 Lmo0398 Lmo0292 Lmo2824 PyrF ProS TcsA Lmo0344 Lmo0443 DaaA Lmo0342 DeoD Lmo1699 Lmo1681 DltD Lmo0560 Lmo1057...”
- “...13 proteins were negatively influenced by B (Lmo2824, Lmo0344, Lmo0342, Lmo1057, Lmo2258, Lmo1867, Lmo0521, Lmo0536, PyrF, DeoD, Lmo0560, DaaA, and Lmo1681)....”
- Genome-wide analyses reveal lineage specific contributions of positive selection and recombination to the evolution of Listeria monocytogenes
Orsi, BMC evolutionary biology 2008 - “...- Lmo2804 conserved hypothetical protein NCOG GCV; MAX; NSS; PHI Overall 6.5E-17 16.53 0.044 - Lmo2824 D-isomer specific 2- hydroxyacid dehydrogenase family protein E; H GCV; MAX; NSS LM2A 0.160 229.62 0.003 - (1) NCOG: Not in COGs; K: Transcription; G: Carbohydrate transport and metabolism; T:...”
- Glycerol metabolism and PrfA activity in Listeria monocytogenes
Joseph, Journal of bacteriology 2008 - “...hom fbaA lmo2601 lmo2684 lmo2720 serS guaB lmo2769 lmo2824 serC Similar to transport system permease protein Similar to amino acid ABC transporter, permease...”
- Microarray-based characterization of the Listeria monocytogenes cold regulon in log- and stationary-phase cells
Chan, Applied and environmental microbiology 2007 - “...genes flaA, which encodes a flagellin protein, and lmo2824, which encodes a D-3-phosphoglycerate dehydrogenase, were also found to have higher transcript levels...”
- Strand specific RNA-sequencing and membrane lipid profiling reveals growth phase-dependent cold stress response mechanisms in Listeria monocytogenes
Hingston, PloS one 2017 - “...the shared upregulated genes encoded reductases ( LMON_1496 , LMON_2403 , LMON_0798 , LMON_0643 , LMON_2843 ) with known or putative roles in maintaining redox balance within the cell and managing oxidative stress. Core set of genes suppressed under cold stress A total of 42 genes...”
Tery_0368 D-isomer specific 2-hydroxyacid dehydrogenase, NAD-binding from Trichodesmium erythraeum IMS101
30% identity, 56% coverage
Thicy_1457 2-hydroxyacid dehydrogenase from Thiomicrospira cyclica ALM1
36% identity, 41% coverage
- Complete genome sequence of the haloalkaliphilic, obligately chemolithoautotrophic thiosulfate and sulfide-oxidizing γ-proteobacterium Thioalkalimicrobium cyclicum type strain ALM 1 (DSM 14477(T))
Kappler, Standards in genomic sciences 2016 - “...oxaloacetate (PEP synthase, Thicy_1283, EC 2.7.9.2; PEP carboxylase, Thicy_1240, EC 4.1.1.31) or lactate (D-lactate dehydrogenase, Thicy_1457, 1.1.1.28) The TCA cycle of T. cyclicum is incomplete, with genes encoding the 2-oxoglutarate dehydrogenase or homologous enzymes (e.g. 2-oxoglutarate:ferredoxin oxidoreductase, KorAB) not having been identified in the genome. This...”
PGDH1 / A2DLU8 phosphoglycerate dehydrogenase (EC 1.1.1.95) from Trichomonas vaginalis (strain ATCC PRA-98 / G3) (see paper)
33% identity, 56% coverage
ZMO_RS05565 2-hydroxyacid dehydrogenase from Zymomonas mobilis subsp. mobilis ZM4 = ATCC 31821
ZMO1237 D-isomer specific 2-hydroxyacid dehydrogenase NAD-binding protein from Zymomonas mobilis subsp. mobilis ZM4
34% identity, 44% coverage
- Molecular mechanism of engineered Zymomonas mobilis to furfural and acetic acid stress
Shabbir, Microbial cell factories 2023 - “...in both strains (Additional file 1 : Tables S7, 8, S9, S10). ZMO_RS03395 (hydroxyacylglutathione hydrolase), ZMO_RS05565 (2-hydroxy acid dehydrogenase), ZMO_RS05445 (glucose-6-phosphate isomerase), ZMO_RS03970 (galactose-1-epimerase), and ZMO_RS05445 (glucose-6-phosphate isomerase) were up-regulated in ZM532 (Additional file 1 : Tables S7, S10). These genes may partly account for the...”
- Engineering Zymomonas mobilis for the Production of Xylonic Acid from Sugarcane Bagasse Hydrolysate
Herrera, Microorganisms 2021 - “...by homologous recombination. Target genes were ZMO_RS04375 (old locus tag ZMO0976, an aldo/keto reductase) and ZMO_RS05565 (old locus tag ZMO1237, a D-lactate dehydrogenase). Primers used for construction of gene deletion cassettes and to confirm events of integration and marker excision are listed in Table S1 ....”
- Improvement of Acetaldehyde Production in Zymomonas mobilis by Engineering of Its Aerobic Metabolism
Kalnenieks, Frontiers in microbiology 2019 - “...II respiratory NADH dehydrogenase CAGATGGCCGATACAGTTTTTGA AATGCAGGCGATAGAGCGAGTTA ldh (ZMO_RS01110) FAD-dependent respiratory lactate dehydrogenase TTGCGGCGAAATACGGAAAAGAT ATAACGCGGCAAGAAACTGACACG ldh (ZMO_RS05565) NAD-dependent lactate dehydrogenase ACTTCGGCATTGGCTTCGTC CGCGTCGCAATATTCAGTTCC ald (Zmob_1390) Aldehyde dehydrogenase CGTATCGCGGGACCGTATCTGA GCGCCCGCTTCTTCCAAAAC cat (ZMO_RS04105) Catalase TCGCCCTTTGAAAACGCATCCTA AACGGGCTTTTTCATCCTCTTTCA gap (ZMO_RS00775) Glyceraldehyde 3 P dehydrogenase ACCCCGGATGTCAGCCTTGTTG GGAGCTGTGCGGATCGGAGTAGAA glk (ZMO_RS01580) Glucokinase GCCGCTTTGGATCGCTTCTGCT ACCGACACCACCGCCAATAACAAC zwf...”
- Characterization and Application of the Sugar Transporter Zmo0293 from Zymomonas mobilis
Zhang, International journal of molecular sciences 2023 - “...ED pathway genes possess the same expression level, ZMO1236 ( adhA , encoding alcohol dehydrogenase), ZMO1237 ( ldhA , encoding D-lactate dehydrogenase), ZMO1570 ( pflB , encoding formate acetyltransferase), ZMO0178 ( pgk , encoding phosphoglycerate kinase), ZMO1240 ( gpmA , encoding 2,3-diphosphoglycerate-dependent phosphoglycerate mutase), and ZMO1496...”
- “...0.22 0.09 1.01 0.45 1.68 ZMO1236 adhA alcohol dehydrogenase 1 0.96 0.59 1 0.23 1.32 ZMO1237 ldhA D-Lactate dehydrogenase 1.06 0.9 0.51 1 0.97 6.14 ZM01754 ssdA aldehyde dehydrogenase (NAD + ) 1.05 1.14 0.73 1 1.53 4.85 ZMO1722 adhC class III alcohol dehydrogenase 0.91 0.39...”
- Metabolic engineering of Zymomonas mobilis for co-production of D-lactic acid and ethanol using waste feedstocks of molasses and corncob residue hydrolysate
Hu, Frontiers in bioengineering and biotechnology 2023 - “...al., 2019 ). Z. mobilis ZM4 has two homologous proteins encoding lactate dehydrogenase (ZMO0256 and ZMO1237) and can produce less than 1g/L lactate ( Yang et al., 2016 ; Martien et al., 2019 ). Lactate production can be further increased when heterologous lactate dehydrogenase genes were...”
- Engineering Zymomonas mobilis for the Production of Xylonic Acid from Sugarcane Bagasse Hydrolysate
Herrera, Microorganisms 2021 - “...genes were ZMO_RS04375 (old locus tag ZMO0976, an aldo/keto reductase) and ZMO_RS05565 (old locus tag ZMO1237, a D-lactate dehydrogenase). Primers used for construction of gene deletion cassettes and to confirm events of integration and marker excision are listed in Table S1 . Briefly, upstream and downstream...”
- “...by-product which is toxic to the cells [ 54 ]. To reduce other by-products formation, ZMO1237 was also deleted. This gene codes for a lactate dehydrogenase which produces lactate from pyruvate mainly under aerobioses [ 55 ], a condition that would benefit xylonic acid formation due...”
- Investigation of the impact of a broad range of temperatures on the physiological and transcriptional profiles of Zymomonas mobilis ZM4 for high-temperature-tolerant recombinant strain development
Li, Biotechnology for biofuels 2021 - “...8.5 ZMO0740 General stress protein CsbD 3.06 8.03 ZMO1113 FAD-dependent pyridine nucleotide-disulfide oxidoreductase 1.62 8.34 ZMO1237 Lactate dehydrogenase 2.82 9.39 ZMO1522 TonB-dependent receptor 1.01 3.88 ZMO1533 Hypothetical protein 3.01 12.07 ZMO1754 Succinate-semialdehyde dehydrogenase SSADH 3.95 11.33 ZMO1776 Aminopeptidase N 1.97 9.64 ZMO1940 Hypothetical protein 4.87 7.45...”
- The Magnesium Concentration in Yeast Extracts Is a Major Determinant Affecting Ethanol Fermentation Performance of Zymomonas mobilis
Li, Frontiers in bioengineering and biotechnology 2020 - “...protein 1.30 2.21 ZMO0740 General stress protein CsbD 1.44 2.56 ZMO1521 Hypothetical protein 1.70 2.41 ZMO1237 Lactate dehydrogenase 1.70 2.19 ZMO1289 Putative transglycosylase-associated protein 2.06 3.23 ZMO1522 TonB-dependent receptor 2.75 3.88 Down-regulated gene in ZM4 cultured in RM OXOID compared with RM BD ZMO0934 Secretion-related protein...”
- Establishment and application of a CRISPR-Cas12a assisted genome-editing system in Zymomonas mobilis
Shen, Microbial cell factories 2019 - “...target a sequence on the coding or noncoding strand of a lactate dehydrogenase encoding gene ZMO1237 ( ldh ). We next assayed the DNA cleavage activity of the exogenously introduced CRISPRCas12a system. To this end, the self-targeting plasmids were individually introduced into either ZM4 or ZM4-Cas12a...”
- “...Identification of edited genes To identify positive clones with nucleotide substitutions of the ldh ( ZMO1237 ) open reading frame, colony PCR was conducted using primers Ldh-check-F/R. PCR products were digested with Pst I. To confirm the deletion (or the replacement) of native gene, colonies with...”
- Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032
Yang, Biotechnology for biofuels 2018 - “...- wecH - tetA cassette was found to be inserted at the 3 end of ZMO1237 ( ldhA ). Interestingly in 2032, integration of P gap_xylA - xylB - yiaB - yiaA - wecH - tetA led to a duplication of xylA and partial duplication of...”
- “...to 708bp (in both 2032 and 8b) 10155321015532 Promoter of ZMO0998 C to T 12639841265916 ZMO1237 ( ldhA ) 11bp (CATGGGTCATA) deletion and 2881-bp duplicated Pgap-xylA xylB inserted into ZMO1237 (ldhA) 3-end, with ZMO1237 shorten from 996bp to 498bp 12659171266864 ZMO1237 ( ldhA ) Duplicated downstream...”
- Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars
Yang, Biotechnology for biofuels 2016 - “...5 d). We had previously shown that the expression levels of the lactate dehydrogenase gene ZMO1237 were more abundant under aerobic conditions [ 63 ], and the expression of another d -lactate dehydrogenase gene, ZMO0256, was upregulated in the ethanol-treated cells during stationary phase [ 57...”
- “...9C, used in this study, is a derivative of Z. mobilis 8b in which the ZMO1237 gene was inactivated [ 37 ]. Therefore, ZMO1237 may play the major role in lactate production under aerobic conditions. However, another lactate dehydrogenase gene, ZMO0256, could also be activated under...”
- More
O66939 D-lactate dehydrogenase (EC 1.1.1.28) from Aquifex aeolicus (see paper)
3kb6B / O66939 Crystal structure of d-lactate dehydrogenase from aquifex aeolicus complexed with NAD and lactic acid (see paper)
aq_727 D-lactate dehydrogenase from Aquifex aeolicus VF5
33% identity, 46% coverage
1sc6D / P0A9T0 Crystal structure of w139g d-3-phosphoglycerate dehydrogenase complexed with NAD+ (see paper)
32% identity, 56% coverage
- Ligand: nicotinamide-adenine-dinucleotide (1sc6D)
alr0058 D-lactate dehydrogenase from Nostoc sp. PCC 7120
34% identity, 45% coverage
PS417_12555 phosphogluconate 2-dehydrogenase KguD (EC 1.1.1.43) from Pseudomonas simiae WCS417
33% identity, 51% coverage
- mutant phenotype: Variably important for glucose utilization, especially with nitrogen sources other than ammonia. 72% identical to the characterized KguD from P.putida (PP3376, see PMC4646247)
DVU1412 D-isomer specific 2-hydroxyacid dehydrogenase family protein from Desulfovibrio vulgaris Hildenborough
33% identity, 47% coverage
- The primary pathway for lactate oxidation in Desulfovibrio vulgaris
Vita, Frontiers in microbiology 2015 - “...essential residue for enzymatic catalysis ( Dong et al., 1993 ). In addition, DVU0600 and DVU1412 were found to exhibit approximately 40 and 50% sequence identity with fermentative LDHs from Clostridium cellulolyticum ( Li et al., 2012 ) and S. oneidensis ( Pinchuk et al., 2009...”
- “...(1783) L -LdD DVU2784 Dehydrogenase, FMN-dependent family Fermentative LDHs DVU0600 L -lactate dehydrogenase D -LdhA DVU1412 D -isomer specific 2-hydroxyacid dehydrogenase family protein To obtain information on the functional role of LDH orthologs, expression of the corresponding encoding genes was measured in Dv H WT cells...”
- Metabolic modeling of a mutualistic microbial community
Stolyar, Molecular systems biology 2007 - “...annotated as a NAD + -dependent L -lactate dehydrogenase by TIGR (COG39, EC 1.1.1.27), and DVU1412, which was annotated as a NAD + -dependent D -isomer-specific 2-hydroxyacid dehydrogenase family protein by TIGR (COG1052, EC 1.1.1.29). To assess the potential importance of these putative reactions to the...”
BRADO4794 putative D-3-phosphoglycerate dehydrogenase from Bradyrhizobium sp. ORS278
34% identity, 49% coverage
WP_049588155 2-hydroxyacid dehydrogenase from Pseudomonas alloputida
35% identity, 46% coverage
PP1649, PP_1649 D-lactate dehydrogenase from Pseudomonas putida KT2440
35% identity, 46% coverage
PG1190 glycerate dehydrogenase from Porphyromonas gingivalis W83
HMPREF1322_RS05995 D-2-hydroxyacid dehydrogenase from Porphyromonas gingivalis W50
34% identity, 47% coverage
- Porphyromonas gingivalis Sphingolipid Synthesis Limits the Host Inflammatory Response
Rocha, Journal of dental research 2020 (secret) - Protein Analysis of Sapienic Acid-Treated Porphyromonas gingivalis Suggests Differential Regulation of Multiple Metabolic Pathways
Fischer, Journal of bacteriology 2016 - “...pathway Carbon metabolism 1200 PG2124, PG1278, PG1417, PG1190, PG0548, PG1755, PG1812, PG1809 PG1417, PG1278, PG1190, PG2124, PG1755, PG0429, PG1809, PG1812...”
- “...PG1417, PG0429, PG1809, PG1812 PG1417, PG1232, PG1278, PG1190, PG1803, PG2124, PG1755, PG1764, PG2141, PG0669, PG0429, PG1809, PG1912 PG1764, PG2141 PG1190,...”
- A putative TetR regulator is involved in nitric oxide stress resistance in Porphyromonas gingivalis
Boutrin, Molecular oral microbiology 2016 - “...up regulated (e.g. PG0045 , PG1208 , PG1118 , PG0010 , PG0520-01 , PG1775-79 , PG1190 , PG0195 , PG0421 and PG1546 ) and down regulated (e.g. PG0214-18 , PG0419 , PG0914 , PG1718 and PG1320 ) for both mutants in comparison to the wild-type. Transcriptome...”
- Role of sodium in the RprY-dependent stress response in Porphyromonas gingivalis
Krishnan, PloS one 2013 - “...1.12 0.4240 12 2.02 0.0000 12 PG1134 Thioredoxin reductase 1.27 0.0248 12 1.93 0.0075 12 PG1190 Glycerate dehydrogenase 1.56 0.1968 12 4.20 0.0000 10 PG1286 Ferritin 2.03 0.0005 12 4.00 0.0000 12 PG1321 Formatetetrahydrofolate ligase 4.79 0.0001 12 6.78 0.0000 12 PG1545 Superoxide dismutase, Fe-Mn 1.96...”
- Role of the Porphyromonas gingivalis extracytoplasmic function sigma factor, SigH
Yanamandra, Molecular oral microbiology 2012 - “...the presence of oxygen in the wild-type strain, such as superoxide dismutase (PG1545), glycerate dehydrogenase (PG1190), thioredoxins (PG0034, PG0275, PG1134, and PG1638), are significantly downregulated in the V2948 strain. Superoxide dismutase is required for protection of P. gingivalis from atmospheric oxygen ( Nakayama, 1994 ). Glycerate...”
- “...0.112295 19.001963 0.000000 (9.2E-10) 12 PG1641 phosphotyrosine protein phosphatase 2.918043 0.132307 110.35678 0.000000 (4.2E-18) 12 PG1190 Glycerate dehydrogenase 2.843835 0.139290 26.540702 0.000000 (2.5E-11) 12 PG1729 thiol peroxidase 2.837745 0.139879 34.986562 0.000000 (1.2E-12) 12 PG1841 conserved hypothetical protein 2.792744 0.144311 14.702032 0.000000 (1.4E-08) 12 PG1842 acetyltransferase, GNAT...”
- Differential response of Porphyromonas gingivalis to varying levels and duration of hydrogen peroxide-induced oxidative stress
McKenzie, Microbiology (Reading, England) 2012 - “...cation-transporting ATPase, EI-E2 family, authentic frameshift pg1190 glycerate dehydrogenase pg0520 chaperonin, 60 kDa pg1124 DUF80 domain protein pg1837...”
- Adaptation of Porphyromonas gingivalis to microaerophilic conditions involves increased consumption of formate and reduced utilization of lactate
Lewis, Microbiology (Reading, England) 2009 - “...al., 2006). In addition, this study showed that PG1190, which encodes glycerate dehydrogenase (HprA), was significantly upregulated (Table 1, Fig. 2). This...”
- “...P value Repeat PG0619 PG1827 PG0900 PG0618 PG2213 PG1190 PG1868 PG1729 PG0275 PG1842 PG0433 PG0209 PG1642 PG0899 PG1321 PG1545 PG1286 PG0432 PG1043 PG0047...”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, mSystems 2023 - “...12.62% 8.66E-06 HMPREF1322_RS00725 Lactate utilization protein Yes HMPREF1322_RS00725,HMPREF1322_RS00730, HMPREF1322_RS00735 NZ_AJZS01000063.1 3841 5.37% 0.00% 5.37% 8.67E-06 HMPREF1322_RS05995 NZ_AJZS01000101.1 9445 50.00% 75.93% 25.93% 9.71E-06 HMPREF1322_RS09650,HMPREF1322_RS09490, HMPREF1322_RS09495 NZ_AJZS01000091.1 663 5.19% 0.00% 5.19% 9.98E-06 HMPREF1322_RS08515 8-Amino-7-oxono-noate synthase No HMPREF1322_RS08515 NZ_AJZS01000068.1 5296 24.60% 41.90% 17.30% 1.10E-05 HMPREF1322_RS06440 Glycine--tRNA-ligase Yes HMPREF1322_RS06440,HMPREF1322_RS06445 NZ_AJZS01000011.1...”
- Hemin availability induces coordinated DNA methylation and gene expression changes in Porphyromonas gingivalis
Costeira, 2022
HtpH / b1380 D-lactate dehydrogenase (EC 1.1.1.28) from Escherichia coli K-12 substr. MG1655 (see 4 papers)
ldhA / P52643 D-lactate dehydrogenase (EC 1.1.1.28) from Escherichia coli (strain K12) (see 22 papers)
ldhA D-lactate dehydrogenase; EC 1.1.1.28 from Escherichia coli K12 (see 7 papers)
NP_415898 D-lactate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
P52643 D-lactate dehydrogenase from Escherichia coli (strain K12)
b1380 D-lactate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
36% identity, 43% coverage
- ldhA-induced persister in Escherichia coli is formed through accidental SOS response via intracellular metabolic perturbation.
Yamamoto, Microbiology and immunology 2022 (PubMed)- GeneRIF: ldhA-induced persister in Escherichia coli is formed through accidental SOS response via intracellular metabolic perturbation.
- Stochastic expression of lactate dehydrogenase A induces Escherichia coli persister formation.
Yamamoto, Journal of bioscience and bioengineering 2018 (PubMed)- GeneRIF: LdhA-mediated persister formation pathway is different from previously reported persister formation via repression of aerobic metabolism.
- Production of succinate by a pflB ldhA double mutant of Escherichia coli overexpressing malate dehydrogenase.
Wang, Bioprocess and biosystems engineering 2009 (PubMed)- GeneRIF: The gene encoding malate dehydrogenase (MDH) was overexpressed in a pflB ldhA double mutant, NZN111, for succinic acid production.
- Eliminating side products and increasing succinate yields in engineered strains of Escherichia coli C.
Jantama, Biotechnology and bioengineering 2008 (PubMed)- GeneRIF: Deletion of the E. coli ldhA gene (together with deletions of other ferementation disruption genes) increased production of succinate
- Systems biology approach for enhancing limonene yield by re-engineering Escherichia coli
Khanijou, NPJ systems biology and applications 2024 - “...study. CRISPR Cas9-assisted recombineering method as described previously 106 was used to delete ldhA (UniProt P52643) and adhE (UniProt P0A9Q7) genes from the E. coli MG1655 strain, resulting in LDH and ALDH-ADH knockouts, respectively. The ldhA and adhE regions of three successfully knockout strains were PCR...”
- Comparative genomics of the closely related fungal genera Cryptococcus and Kwoniella reveals karyotype dynamics and suggests evolutionary mechanisms of pathogenesis
Coelho, PLoS biology 2024 - “...proteins from C . neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) showing structural similarity. Pairwise structure alignments were performed and visualized in the Protein Data Bank (PDB) website ( https://www.rcsb.org/alignment ) using the JjFATCAT-rigid algorithm. The phylogenetic tree file is provided...”
- “...AlphaFold-predicted structures of Cryptococcus neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) are individually displayed at the top. Pairwise structure alignments with the C . neoformans protein were conducted with the JjFATCAT-rigid algorithm on the Protein Data Bank website ( https://www.rcsb.org/alignment )....”
- Comparative genomics of Cryptococcus and Kwoniella reveals pathogenesis evolution and contrasting karyotype dynamics via intercentromeric recombination or chromosome fusion.
Coelho, bioRxiv : the preprint server for biology 2024 - “...dehydrogenease proteins from C. neoformans (UniProt J9VFV7), Aspergillus fischeri (UniProt A1D163), and Escherichia coli (UniProt P52643) showing structural similarity. Pairwise structure alignments were performed and visualized in the Protein Data Bank (PDB) website ( https://www.rcsb.org/alignment ) using the JjFATCAT-rigid algorithm. Fig 9. Proposed model of chromosome...”
- A global analysis of function and conservation of catalytic residues in enzymes
Ribeiro, The Journal of biological chemistry 2020 (secret) - The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...5.11/44,335 5.15/44,053 4.70/22,351 5.15/43,951 5.00/74,518 IdhA P52643 D-Lactate IlvA P04968 IlvB P08142 IlvC dehydrogenase (DIGE 4.5-6.5) (DIGE 4.5-6.5)...”
- “...11, 2017 by University of California, Berkeley P52643 P04816 5.29/36,534.79 Experimentald LdhA LivK dehydrogenase pI/MW Theoreticalc ESCHERICHIA COLI PROTEOME...”
- FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization
Hassani, Microbial cell factories 2024 - “...0.16 5.11 9.50 1.41E-2 b1241 LCADi_copy2 Double ADHEr, LDH_D 0.15 8.08 9.51 1.43E-2 b1241, b2133, b1380 LCADi_copy2 Triple ADHEr, LDH_D, PFL 0.12 11.08 12.73 1.53E-2 b1241, b2133, b1380, b3114, b0902, b3951 LCADi_copy, OBTFL Quadruple ADHEr, LDH_D, PFL, THD2 0.11 12.29 13.01 2.58E-2 b1241, b2133, b1380, b3114,...”
- “...b1602 LCADi_copy, OBTFL Quintuple ADHEr, LDH_D, GLUDy, PFL, THD2 0.10 12.34 13.06 2.61E-2 b1241, b2133, b1380, b1761, b3114, b0902, b3951, b1602 LCADi_copy, OBTFL Fig.2 Production envelopes for the best solutions presented in Table 3 regarding succinate production from single to quintuple reaction deletions in iJR904. Knocking...”
- Genetic tools for the redirection of the central carbon flow towards the production of lactate in the human gut bacterium Phocaeicola (Bacteroides) vulgatus
Lück, Applied microbiology and biotechnology 2022 - “...VA, USA). BLASTp analysis ( https://www.ncbi.nlm.nih.gov/ ) using the biochemically characterized D-LDH from E. coli (b1380) was performed resulting in the identification of protein BVU_2499 as a potential D-LDH in P. vulgatus. The corresponding gene ( ldh ) was amplified including 250 bp of the upstream...”
- NtrBC and Nac contribute to efficient Shigella flexneri intracellular replication
Waddell, Journal of bacteriology 2014 - “...flexneri genes regulated by Naca Annotationc b1380 Fermentative d-lactate dehydrogenase, NAD dependent Predicted protein potentially involved in detoxification...”
- “...involved in cellular respiration, such as ldhA (b1380), which encodes the NADdependent lactate dehydrogenase, and cybB (b1418), which encodes cytochrome b561....”
- 18th Congress of the European Hematology Association, Stockholm, Sweden, June 13–16, 2013
, Haematologica 2013 - Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655
Portnoy, Applied and environmental microbiology 2010 - “...b2925 b2097 b3919 b1779 b2926 b2779 b1380 b3713 b1004 b4151-b4154 b0721-b0724 b2288-b2276 Phosphoglucose isomerase 6-Phosphofructose kinase Fructose...”
- Differential gene expression for investigation of Escherichia coli biofilm inhibition by plant extract ursolic acid
Ren, Applied and environmental microbiology 2005 - “...0.0055 1.8 hycI b2717 1.3 0.0434 1.7 0.0103 1.2 ldhA narZ b1380 b1468 1.0 1.0 0.7186 0.8904 1.7 0.0008 1.4 0.0057 1.1 1.8 miaA b4171 1.4 0.0002 1.7 0.0189 1.1...”
- DNA microarray analyses of the long-term adaptive response of Escherichia coli to acetate and propionate
Polen, Applied and environmental microbiology 2003 - “...0.91 b1370 yi52_5 1 IS5 transposase 0.57* 0.47* 0.96 b1380 IdhA 1 Fermentative D-lactate dehydrogenase, NAD 3.27* 1.78 1.80* b1480 rpsV 1 30S ribosomal subunit...”
A9762_00050 NAD(P)-dependent oxidoreductase from Pandoraea sp. ISTKB
35% identity, 47% coverage
- Genomic and proteomic analysis of lignin degrading and polyhydroxyalkanoate accumulating β-proteobacterium Pandoraea sp. ISTKB
Kumar, Biotechnology for biofuels 2018 - “...20 73.6 30.685 1.63E183 A0A1E3LG16 A9762_22220 Glyoxylate/hydroxypyruvate reductase A 1.99991 14 69.4 33.941 4.47E124 A0A1E3LQJ8 A9762_00050 Bifunctional glyoxylate/hydroxypyruvate reductase B 0.601011 20 82.2 34.525 1.34E204 A0A1E3LI17 A9762_19295 Alkene reductase 0.075801 28 92 40.61 0 A0A1E3LIA9 A9762_18295 2-Alkenal reductase 0.117504 12 46.4 42.805 2.10E74 A0A1E3LDX7 A9762_24675 FerredoxinNADP(+)...”
- “...0.973988 9 69.1 19.818 1.98E77 A0A1E3LAB2 A9762_08440 NADPH:quinone reductase 1.850827 14 71.9 36.075 3.86E109 A0A1E3LQJ8 A9762_00050 Hydroxypyruvate reductase B 0.601011 20 82.2 34.525 1.34E204 A0A1E3LLZ7 A9762_13130 Fumarate reductase 1.805886 2 7.4 52.225 7.89E05 Dehydrogenases A0A1E3LDJ7 A9762_25850 Formate dehydrogenase subunit beta 1.664541 6 23.2 34.213 1.25E22 A0A1E3LDC4...”
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The PaperBLAST database links 793,807 different protein sequences to 1,259,118 scientific articles. Searches against EuropePMC were last performed on March 13 2025.
PaperBLAST builds a database of protein sequences that are linked
to scientific articles. These links come from automated text searches
against the articles in EuropePMC
and from manually-curated information from GeneRIF, UniProtKB/Swiss-Prot,
BRENDA,
CAZy (as made available by dbCAN),
BioLiP,
CharProtDB,
MetaCyc,
EcoCyc,
TCDB,
REBASE,
the Fitness Browser,
and a subset of the European Nucleotide Archive with the /experiment tag.
Given this database and a protein sequence query,
PaperBLAST uses protein-protein BLAST
to find similar sequences with E < 0.001.
To build the database, we query EuropePMC with locus tags, with RefSeq protein
identifiers, and with UniProt
accessions. We obtain the locus tags from RefSeq or from MicrobesOnline. We use
queries of the form "locus_tag AND genus_name" to try to ensure that
the paper is actually discussing that gene. Because EuropePMC indexes
most recent biomedical papers, even if they are not open access, some
of the links may be to papers that you cannot read or that our
computers cannot read. We query each of these identifiers that
appears in the open access part of EuropePMC, as well as every locus
tag that appears in the 500 most-referenced genomes, so that a gene
may appear in the PaperBLAST results even though none of the papers
that mention it are open access. We also incorporate text-mined links
from EuropePMC that link open access articles to UniProt or RefSeq
identifiers. (This yields some additional links because EuropePMC
uses different heuristics for their text mining than we do.)
For every article that mentions a locus tag, a RefSeq protein
identifier, or a UniProt accession, we try to select one or two
snippets of text that refer to the protein. If we cannot get access to
the full text, we try to select a snippet from the abstract, but
unfortunately, unique identifiers such as locus tags are rarely
provided in abstracts.
PaperBLAST also incorporates manually-curated protein functions:
- Proteins from NCBI's RefSeq are included if a
GeneRIF
entry links the gene to an article in
PubMed®.
GeneRIF also provides a short summary of the article's claim about the
protein, which is shown instead of a snippet.
- Proteins from Swiss-Prot (the curated part of UniProt)
are included if the curators
identified experimental evidence for the protein's function (evidence
code ECO:0000269). For these proteins, the fields of the Swiss-Prot entry that
describe the protein's function are shown (with bold headings).
- Proteins from BRENDA,
a curated database of enzymes, are included if they are linked to a paper in PubMed
and their full sequence is known.
- Every protein from the non-redundant subset of
BioLiP,
a database
of ligand-binding sites and catalytic residues in protein structures, is included. Since BioLiP itself
does not include descriptions of the proteins, those are taken from the
Protein Data Bank.
Descriptions from PDB rely on the original submitter of the
structure and cannot be updated by others, so they may be less reliable.
(For SitesBLAST and Sites on a Tree, we use a larger subset of BioLiP so that every
ligand is represented among a group of structures with similar sequences, but for
PaperBLAST, we use the non-redundant set provided by BioLiP.)
- Every protein from EcoCyc, a curated
database of the proteins in Escherichia coli K-12, is included, regardless
of whether they are characterized or not.
- Proteins from the MetaCyc metabolic pathway database
are included if they are linked to a paper in PubMed and their full sequence is known.
- Proteins from the Transport Classification Database (TCDB)
are included if they have known substrate(s), have reference(s),
and are not described as uncharacterized or putative.
(Some of the references are not visible on the PaperBLAST web site.)
- Every protein from CharProtDB,
a database of experimentally characterized protein annotations, is included.
- Proteins from the CAZy database of carbohydrate-active enzymes
are included if they are associated with an Enzyme Classification number.
Even though CAZy does not provide links from individual protein sequences to papers,
these should all be experimentally-characterized proteins.
- Proteins from the REBASE database
of restriction enzymes are included if they have known specificity.
- Every protein with an evidence-based reannotation (based on mutant phenotypes)
in the Fitness Browser is included.
- Sequence-specific transcription factors (including sigma factors and DNA-binding response regulators)
with experimentally-determined DNA binding sites from the
PRODORIC database of gene regulation in prokaryotes.
- Putative transcription factors from RegPrecise
that have manually-curated predictions for their binding sites. These predictions are based on
conserved putative regulatory sites across genomes that contain similar transcription factors,
so PaperBLAST clusters the TFs at 70% identity and retains just one member of each cluster.
- Coding sequence (CDS) features from the
European Nucleotide Archive (ENA)
are included if the /experiment tag is set (implying that there is experimental evidence for the annotation),
the nucleotide entry links to paper(s) in PubMed,
and the nucleotide entry is from the STD data class
(implying that these are targeted annotated sequences, not from shotgun sequencing).
Also, to filter out genes whose transcription or translation was detected, but whose function
was not studied, nucleotide entries or papers with more than 25 such proteins are excluded.
Descriptions from ENA rely on the original submitter of the
sequence and cannot be updated by others, so they may be less reliable.
Except for GeneRIF and ENA,
the curated entries include a short curated
description of the protein's function.
For entries from BioLiP, the protein's function may not be known beyond binding to the ligand.
Many of these entries also link to articles in PubMed.
For more information see the
PaperBLAST paper (mSystems 2017)
or the code.
You can download PaperBLAST's database here.
Changes to PaperBLAST since the paper was written:
- November 2023: incorporated PRODORIC and RegPrecise. Many PRODORIC entries were not linked to a protein sequence (no UniProt identifier), so we added this information.
- February 2023: BioLiP changed their download format. PaperBLAST now includes their non-redundant subset. SitesBLAST and Sites on a Tree use a larger non-redundant subset that ensures that every ligand is represented within each cluster. This should ensure that every binding site is represented.
- June 2022: incorporated some coding sequences from ENA with the /experiment tag.
- March 2022: incorporated BioLiP.
- April 2020: incorporated TCDB.
- April 2019: EuropePMC now returns table entries in their search results. This has expanded PaperBLAST's database, but most of the new entries are of low relevance, and the resulting snippets are often just lists of locus tags with annotations.
- February 2018: the alignment page reports the conservation of the hit's functional sites (if available from from Swiss-Prot or UniProt)
- January 2018: incorporated BRENDA.
- December 2017: incorporated MetaCyc, CharProtDB, CAZy, REBASE, and the reannotations from the Fitness Browser.
- September 2017: EuropePMC no longer returns some table entries in their search results. This has shrunk PaperBLAST's database, but has also reduced the number of low-relevance hits.
Many of these changes are described in Interactive tools for functional annotation of bacterial genomes.
PaperBLAST cannot provide snippets for many of the papers that are
published in non-open-access journals. This limitation applies even if
the paper is marked as "free" on the publisher's web site and is
available in PubmedCentral or EuropePMC. If a journal that you publish
in is marked as "secret," please consider publishing elsewhere.
Many important articles are missing from PaperBLAST, either because
the article's full text is not in EuropePMC (as for many older
articles), or because the paper does not mention a protein identifier such as a locus tag, or because of PaperBLAST's heuristics. If you notice an
article that characterizes a protein's function but is missing from
PaperBLAST, please notify the curators at UniProt
or add an entry to GeneRIF.
Entries in either of these databases will eventually be incorporated
into PaperBLAST. Note that to add an entry to UniProt, you will need
to find the UniProt identifier for the protein. If the protein is not
already in UniProt, you can ask them to create an entry. To add an
entry to GeneRIF, you will need an NCBI Gene identifier, but
unfortunately many prokaryotic proteins in RefSeq do not have
corresponding Gene identifers.
References
PaperBLAST: Text-mining papers for information about homologs.
M. N. Price and A. P. Arkin (2017). mSystems, 10.1128/mSystems.00039-17.
Europe PMC in 2017.
M. Levchenko et al (2017). Nucleic Acids Research, 10.1093/nar/gkx1005.
Gene indexing: characterization and analysis of NLM's GeneRIFs.
J. A. Mitchell et al (2003). AMIA Annu Symp Proc 2003:460-464.
UniProt: the universal protein knowledgebase.
The UniProt Consortium (2016). Nucleic Acids Research, 10.1093/nar/gkw1099.
BRENDA in 2017: new perspectives and new tools in BRENDA.
S. Placzek et al (2017). Nucleic Acids Research, 10.1093/nar/gkw952.
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.
I. M. Keeseler et al (2016). Nucleic Acids Research, 10.1093/nar/gkw1003.
The MetaCyc database of metabolic pathways and enzymes.
R. Caspi et al (2018). Nucleic Acids Research, 10.1093/nar/gkx935.
CharProtDB: a database of experimentally characterized protein annotations.
R. Madupu et al (2012). Nucleic Acids Research, 10.1093/nar/gkr1133.
The carbohydrate-active enzymes database (CAZy) in 2013.
V. Lombard et al (2014). Nucleic Acids Research, 10.1093/nar/gkt1178.
The Transporter Classification Database (TCDB): recent advances
M. H. Saier, Jr. et al (2016). Nucleic Acids Research, 10.1093/nar/gkv1103.
REBASE - a database for DNA restriction and modification: enzymes, genes and genomes.
R. J. Roberts et al (2015). Nucleic Acids Research, 10.1093/nar/gku1046.
Deep annotation of protein function across diverse bacteria from mutant phenotypes.
M. N. Price et al (2016). bioRxiv, 10.1101/072470.
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory