PaperBLAST
PaperBLAST Hits for sp|Q9HZF8|PYRD_PSEAE Dihydroorotate dehydrogenase (quinone) OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=pyrD PE=3 SV=1 (342 a.a., MYTLARQLLF...)
Show query sequence
>sp|Q9HZF8|PYRD_PSEAE Dihydroorotate dehydrogenase (quinone) OS=Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1) OX=208964 GN=pyrD PE=3 SV=1
MYTLARQLLFKLSPETSHELSIDLIGAGGRLGLNRLLTPKPASLPVSVLGLEFPNPVGLA
AGLDKNGDAIDGFGQLGFGFIEIGTVTPRPQPGNPRPRLFRLPQANAIINRMGFNNHGVD
HLLARVRAAKYRGVLGINIGKNFDTPVERAVDDYLICLDKVYADASYVTVNVSSPNTPGL
RSLQFGDSLKQLLEALRQRQEALALRHGRRVPLAIKIAPDMTDEETALVAAALVEAGMDA
VIATNTTLGREGVEGLPHGDEAGGLSGAPVREKSTHTVKVLAGELGGRLPIIAAGGITEG
AHAAEKIAAGASLVQIYSGFIYKGPALIREAVDAIAALPRRN
Running BLASTp...
Found 153 similar proteins in the literature:
PA3050 dihydroorotate dehydrogenase from Pseudomonas aeruginosa PAO1
100% identity, 100% coverage
- Toward a Comprehensive Analysis of Posttranscriptional Regulatory Networks: a New Tool for the Identification of Small RNA Regulators of Specific mRNAs
Han, mBio 2021 - “...ReaL 15 sRNA PA3535 PA3536 55 3 sRmf 9 3 RNA of rmf mRNA PA3049 PA3050 4 sAdhC 7 3 RNA of adhC mRNA PA3628 PA3630 5 s3661 6 3 RNA of PA3661 mRNA PA3661 PA3665 C. rpoS Vc Rank Name Max coverage a Mapping location...”
- Pyrimidine Biosynthesis Regulates the Small-Colony Variant and Mucoidy in Pseudomonas aeruginosa through Sigma Factor Competition
Al, Journal of bacteriology 2019 - “...pEX100T, sacB oriT Cbr 1.2-kb fragment flanking pyrD (PA3050) gene ligated into pEX100T-NotI with in-frame deletion of pyrD 8.3 kb, promoterless lacZ, Apr,...”
- Identification of a small molecule that simultaneously suppresses virulence and antibiotic resistance of Pseudomonas aeruginosa
Guo, Scientific reports 2016 - “...may affect cytotoxicity through decreased attachment of the bacteria to the HeLa cells 22 . PA3050, PA0871, PA1195 and PA0770 encode enzyme for pyrimidine, nucleotide and energy metabolism, respectively. PA4781 encodes a cyclic di-GMP phosphodiesterase and PA5288 encodes a nitrogen regulatory protein which responds to cellular...”
- “...2b ), confirming the role of PyrD in the observed phenotypes. As we grew the PA3050 ( pyrD ) mutant in LB, we noticed that the culture remained yellowish even at the stationary growth phase, whereas the culture of wild type PA14 turned green. This phenotype...”
- Effect of Shear Stress on Pseudomonas aeruginosa Isolated from the Cystic Fibrosis Lung
Dingemans, mBio 2016 - “...(RNA-Seq) sRNA10 d 202 IR PA3964PA3965 No 2.35 SPA0117 201 IR PA3049 ( rmf ) PA3050 ( pyrD ); overlapping both genes Yes 1.94 P8 78 IR PA1030PA1031 Yes 1.85 SPA0003 137 IR PA2729PA2730 Yes 1.58 a Downregulated 1.50-fold; P < 0.05, FDR < 0.05. b...”
- Characterization of the polymyxin B resistome of Pseudomonas aeruginosa
Fernández, Antimicrobial agents and chemotherapy 2013 - “...PA0401 PA0402 PA1180 PA1375 PA1588 PA1799 PA2023 PA3050 PA4020 PA4069 PA4109 PA4459 PA4748 PA4776 PA5000 PA5001 PA5038 PA5199 Noncatalytic dihydroorotase-like...”
- “...B concn of: PAO1 ortholog PA0401 PA1375 PA1558 PA2023 PA3050 PA3552d PA4020 PA4069 PA4109 PA4459 PA4748 PA5000 PA4776 PA5001 PA5038 PA5199 Gene pdxB sucC galU...”
- Genetic determinants involved in the susceptibility of Pseudomonas aeruginosa to beta-lactam antibiotics
Alvarez-Ortega, Antimicrobial agents and chemotherapy 2010 - “...PA14_07490/07510 PA14_59780 PA1483 PA2128 PA2615 PA2963 PA2970 PA3050 PA3262 PA3433 PA3649 PA3800 PA3818 PA3978 PA4005 PA4007 PA4069 PA4088 PA4269 PA4393 PA4745...”
- ClpXP proteases positively regulate alginate overexpression and mucoid conversion in Pseudomonas aeruginosa
Qiu, Microbiology (Reading, England) 2008 - “...purF (PA5426, encoding the glutamine phosphoribosylpyrophosphate amidotransferase), purM (PA0945, encoding the phosphoribosylformyglycinamidine cycloligase), and pyrD (PA3050, encoding dihydroorotate dehydrogenase). However, the role of these metabolic genes in the mucoid phenotype was not investigated further. Of greater interest were the transposon insertions in the non-mucoid mutants mapped...”
PA14_24640 dihydroorotate dehydrogenase from Pseudomonas aeruginosa UCBPP-PA14
99% identity, 100% coverage
ACA40_10035 quinone-dependent dihydroorotate dehydrogenase from Pseudomonas syringae pv. lapsa
88% identity, 99% coverage
- Complete Genome Sequence of Pseudomonas syringae pv. lapsa Strain ATCC 10859, Isolated from Infected Wheat
Kong, Genome announcements 2016 - “...several secondary metabolism associated gene clusters, such as genes associated with pyrimidine synthesis (ACA40_02470, ACA40_02475, ACA40_10035, ACA40_01095, ACA40_19310, ACA40_20760) and genes associated with benzoate synthesis (ACA40_09900, ACA40_10125, ACA40_24870), were identified in this strain. Meanwhile, 6 fimbrial gene clusters (cup) (ACA40_01475, ACA40_07220, ACA40_09125, ACA40_13630, ACA40_15640, ACA40_22320), which...”
PSPPH_2077 dihydroorotate dehydrogenase from Pseudomonas syringae pv. phaseolicola 1448A
88% identity, 92% coverage
PsgB076_10315 quinone-dependent dihydroorotate dehydrogenase from Pseudomonas savastanoi pv. glycinea str. B076
87% identity, 99% coverage
BTH_I2511 dihydroorotate oxidase from Burkholderia thailandensis E264
61% identity, 97% coverage
B0V824 Dihydroorotate dehydrogenase (quinone) from Acinetobacter baumannii (strain AYE)
ABBFA_001187 dihydroorotate oxidase from Acinetobacter baumannii AB307-0294
59% identity, 98% coverage
VF_1285 dihydroorotate dehydrogenase 2 from Vibrio fischeri ES114
56% identity, 98% coverage
A6T739 Dihydroorotate dehydrogenase (quinone) from Klebsiella pneumoniae subsp. pneumoniae (strain ATCC 700721 / MGH 78578)
57% identity, 98% coverage
- Disruption of KPC-producing Klebsiella pneumoniae membrane via induction of oxidative stress by cinnamon bark (Cinnamomum verum J. Presl) essential oil
Yang, PloS one 2019 - “...Protein biosynthesis Control 72 Dihydroorotase pyrC A6T7D6 Pyrimidine biosynthesis Control 73 Dihydroorotate dehydrogenase (quinone) pyrD A6T739 Pyrimidine biosynthesis Control 74 Dihydroxy-acid dehydratase ilvD A6TGF8 Protein biosynthesis Control 75 DNA gyrase inhibitor YacG yacG A6T4P3 DNA processing Control 76 DNA mismatch repair protein MutS mutS A6TD24 Stress...”
- “...protein DnaA Lost A6TDC6 Cobalamin biosynthesis protein CobD Upregulated * A6TAW4 D-amino acid dehydrogenase Lost A6T739 Dihydroorotate dehydrogenase (quinone) Lost B5XWP9 Electron transport complex subunit C Lost B5XWS2 Glucans biosynthesis protein D Lost A6TGV0 Glycerol-3-phosphate acyltransferase Lost A6TDR6 Glycine cleavage system H protein Lost B5XNC0 Large-conductance...”
7ut5A / B7GZW7 Acinetobacter baumannii dihydroorotate dehydrogenase bound with inhibitor dsm186 (see paper)
57% identity, 98% coverage
- Ligands: (4r)-7-methyl-n-[4-(pentafluoro-lambda~6~-sulfanyl)phenyl]imidazo[1,2-a]pyrimidin-5-amine; flavin mononucleotide (7ut5A)
VC1491 dihydroorotate dehydrogenase from Vibrio cholerae O1 biovar eltor str. N16961
55% identity, 97% coverage
c1081 Dihydroorotate dehydrogenase from Escherichia coli CFT073
UTI89_C1010 dihydroorotate dehydrogenase from Escherichia coli UTI89
57% identity, 97% coverage
- Transcriptional responses of uropathogenic Escherichia coli to increased environmental osmolality caused by salt or urea
Withman, Infection and immunity 2013 - “...(purEK, c0637-c0636, 0.2, 1.1; pyrC, c1329, 0.3, 0.7; pyrD, c1081, 0.3, 0.7) showed low mRNA expression in medium with salt. A significant number of genes of...”
- F1C fimbriae play an important role in biofilm formation and intestinal colonization by the Escherichia coli commensal strain Nissle 1917
Lasaro, Applied and environmental microbiology 2009 - “...ilvI (c0095) ybiW (c0908) cmk (c1048) pyrD (c1081) Aspartate ammonia-lyase Acetolactate synthase 3 catalytic subunit Formate acetyltransferase Cytidylate kinase...”
- Genetic requirements for uropathogenic <i>E. coli</i> proliferation in the bladder cell infection cycle
Mediati, mSystems 2024 - “...biosynthesis) 8.21 4.37E-04 2.12E-02 UTI89_C2298 hisF Imidazole glycerol phosphate synthase (histidine biosynthesis) 7.29 4.26E-04 2.06E-02 UTI89_C1010 pyrD Dihydroorotate dehydrogenase (pyrimidine biosynthesis) 6.72 1.74E-02 1.63E-01 UTI89_C3926 glpD Glycerol-3-phosphate dehydrogenase (aerobic growth on glycerol) 6.57 5.53E-04 1.91E-02 UTI89_C0736 tolB Periplasmic Tol-Pal system protein (cell envelope function and integrity)...”
YPTB1439 dihydroorotate dehydrogenase from Yersinia pseudotuberculosis IP 32953
YPO1415 dihydroorotate dehydrogenase from Yersinia pestis CO92
55% identity, 98% coverage
A1S_2253 dihydroorotate dehydrogenase 2 from Acinetobacter baumannii ATCC 17978
63% identity, 85% coverage
PyrD / b0945 dihydroorotate dehydrogenase, type 2 (EC 1.3.5.2) from Escherichia coli K-12 substr. MG1655 (see 12 papers)
pyrD / P0A7E1 dihydroorotate dehydrogenase, type 2 (EC 1.3.5.2) from Escherichia coli (strain K12) (see 11 papers)
PYRD_ECOLI / P0A7E1 Dihydroorotate dehydrogenase (quinone); DHOdehase; DHOD; DHODase; Dihydroorotate oxidase; EC 1.3.5.2 from Escherichia coli (strain K12) (see 2 papers)
B1X8P9 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Escherichia coli (see paper)
1f76A / P0A7E1 Escherichia coli dihydroorotate dehydrogenase (see paper)
NP_415465 dihydroorotate dehydrogenase, type 2 from Escherichia coli str. K-12 substr. MG1655
b0945 dihydroorotate dehydrogenase from Escherichia coli str. K-12 substr. MG1655
ECs1029 dihydro-orotate dehydrogenase from Escherichia coli O157:H7 str. Sakai
57% identity, 98% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor.
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Monomer. - Ligand: flavin mononucleotide (1f76A)
- New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition.
Orozco, International journal of molecular sciences 2022 - GeneRIF: New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition.
- Nucleotide sequence of the pyrD gene of Escherichia coli and characterization of the flavoprotein dihydroorotate dehydrogenase.
Larsen, European journal of biochemistry 1985 (PubMed)- GeneRIF: N-terminus verified by Edman degradation on complete protein
- Biodistribution of 89Zr-DFO-labeled avian pathogenic Escherichia coli outer membrane vesicles by PET imaging in chickens
Li, Poultry science 2023 - “...ECNB Function unknown Cell membrane 312 P0AAJ5 FDOH Energy production and conversion Cell membrane 313 P0A7E1 PYRD Nucleotide transport and metabolism Cell membrane 314 P09152 NARG Energy production and conversion Cell membrane 315 P11349 NARH Energy production and conversion Cell membrane Cell inner membrane 316 P0ABA0...”
- New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition
Orozco, International journal of molecular sciences 2022 - “...of interest. Accession Numbers Full-length HsDHODH sequence (Uniprot Q02127, PYRD_HUMAN) and E. coli DHODH (Uniprot P0A7E1, PYRD_ECOLI). Abbreviations Proteins Hs DHODH human dihydroorotate dehydrogenase Hs 29DHODH human N-terminal truncated dihydroorotate dehydrogenase Ec DHODH dihydroorotate dehydrogenase from Escherichia coli Phospholipid classes PC phosphatidylcholine CL cardiolipin PE phosphatidylethanolamine...”
- “...DHODH sequence (Uniprot Q02127, PYRD_HUMAN), and indicates the shorter C-terminal length of Ec DHODH (Uniprot P0A7E1, PYRD_ECOLI). ( B ) Crystal structures for N-terminal truncated Hs DHODH (PDB ID: 2PRM) and Ec DHODH (PDB ID: 1F76). The 1-2 microdomain is shown in red, the catalytic domain...”
- Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis
Bouwknegt, Fungal biology and biotechnology 2021 - “...L. kluyveri (LkUra9; Q6V3W9), O. parapolymorpha (OpUra9; W1QJ07), K. marxianus (KmUra9; Q6SZS6), E. coli (EcUra9; P0A7E1), D. bruxellensis (DbUra9; I2JUI3), Sch. japonicus (SjUra9; B6JXQ5), A. robustus (ArUra9; A0A1Y1XN91), N. californiae (NcUra9; A0A1Y2ELQ6) and P. finnis (PfUra9; A0A1Y1VDI5) and C. reversa (CmUra9; A0A2G5BHD4), Sm. culicis (ScuUra9; A0A1R1YI62)...”
- The Escherichia coli proteome: past, present, and future prospects
Han, Microbiology and molecular biology reviews : MMBR 2006 - “...6.13/35,321 PyrC PyrD PyrF P05020 P0A7E1 P08244 5.77/38,696.19 7.66/36,774.52 5.81/26,350.24 PyrG P0A7E5 Aspartate carbamoyltransferase catalytic chain...”
- Transcriptomic Response Analysis of Escherichia coli to Palladium Stress
Joudeh, Frontiers in microbiology 2021 - “...110 12 b1520 yneE Predicted inner membrane protein, bestrophin family; possible chloride channel 109 27 b0945 pyrD Dihydroorotate dehydrogenase, UMP biosynthesis 106 21 b3622 waaL LPS core biosynthesis; O-antigen ligase 85 13 b0991 ymcE Cold shock protein, function unknown 80 64 b2352 gtrS Serotype-specific glucosyl transferase,...”
- 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 - “...DADK NDPK1 for or PRPPS back or R1PK for or PPM back or R15BPK for b0945 DHORD2, DHORD5 DHORDfum for b0954 T2DECAI (CTECOAI6 back and CTRCOAI7 back ) or (CTECOAI6 back and AACPS4 for ) b1207 PRPPS R1PK for or PPM back or R15BPK for b1638...”
- EcoliNet: a database of cofunctional gene network for Escherichia coli
Kim, Database : the journal of biological databases and curation 2015 - “...pattern (IEP), traceable author statement (TAS). ( b ) Top 10 inferred GO-BP terms for b0945, a genes for tobramycin resistance. EcoliNet freely distributes edge information, not only for the integrated network but also for all individual component networks, including those for individual data sets at...”
- Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding
Myers, PLoS genetics 2013 - “...Evidence of FNR Regulated Expression j Operons directly activated by FNR (Category 1) 1,003,976 pyrD b0945 Dihydroorotate Dehydrogenase 1 38.5 + o [29] [17] 1,656,036 ynfEFGH- dmsD b1587 Putative Selenate Reductase ( ynfEFGH ); DMS Reductase Maturation Protein ( dmsD ) 1 40.5 + + None...”
- Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions
Orth, BMC systems biology 2012 - “...folD (b0529) 5fthf[c] and methf[c] may be essential entD (b0583) enter[c] may be essential pyrD (b0945) alternate pathway ( DHORDfum ) is an orphan reaction pdxH (b1638) pydx5p[c] may be essential pgsA (b1912) pgp120[p] - pgp181[p] may be essential nrdA (b2234) alternate pathway ( RNDR1b RNDR4b...”
- Genome-scale analysis to the impact of gene deletion on the metabolism of E. coli: constraint-based simulation approach
Xu, BMC bioinformatics 2009 - “...APM GM MLM PPB genes b0159 b0159 b0175 b0185 b0522, b0523 b2687 b0386 b2585 b1092 b0945, b1062 b2942 b2818 b3018 b1094 b1131, b1281 b3939 b3172 b4041 b2316 b2312, b2476 b4013 b3957 b4160 b2323 b2499, b2507 s0001 b3958 b3255 b2557, b2780 b3959 b3256 b3642, b4005 b3960 b4006,...”
- Experimental and computational assessment of conditionally essential genes in Escherichia coli
Joyce, Journal of bacteriology 2006 - “...pyrB (b4245) pyrC (b1062) pyrD (b0945) pyrE (b3642) pyrF (b1281) thyA (b2827) Cofactor production..................................................... folB...”
- Genome-wide transcriptional profiling of the Escherichia coli responses to superoxide stress and sodium salicylate
Pomposiello, Journal of bacteriology 2001 - “...b2323 b1925 b2025 b3580 b0923 b1224 b3480 b0929 b4245 b0945 b4387 b1656 b1646 b2497 b0193 b0315 b1347 b2597 b3087 b3088 b3112 b3516 b3582 b3879 b3888 b4048...”
- More
- Global transcriptional response of Escherichia coli O157:H7 to growth transitions in glucose minimal medium
Bergholz, BMC microbiology 2007 - “...pflB -2.61 6 ECs2840 wbdP -2.14 1 ECs1008 ycbB 2.15 2 ECs2847 O157 -2.25 1 ECs1029 pyrD -2.88 1 ECs3038 yeiT 2.14 3 ECs1037 rmf 2.24 2 ECs3060 fruK -2.13 1 ECs1072 O157 -2.13 5 ECs3061 fruB -2.38 1 ECs1091 O157 3.24 2 ECs3136 yfaX -2.04...”
ETAE_1248 dihydroorotate dehydrogenase 2 from Edwardsiella tarda EIB202
56% identity, 98% coverage
S1011 dihydro-orotate dehydrogenase from Shigella flexneri 2a str. 2457T
56% identity, 98% coverage
PMI_RS03790 quinone-dependent dihydroorotate dehydrogenase from Proteus mirabilis HI4320
55% identity, 98% coverage
- Decreased biofilm formation in Proteus mirabilis after short-term exposure to a simulated microgravity environment
Wang, Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology] 2021 - “...XRE family transcriptional regulator, master regulator for biofilm formation PMI_RS15440 1353 1.70558100358398 Up 0.00032 No PMI_RS03790 pyrD 1011 1.10139831452801 Up 8.69E-05 Type VI secretion system secreted protein Hcp PMI_RS06685 gstA 612 1.51757779099496 Down 0.00028 Lglutathione S-transferase PMI_RS09365 grcA 384 1.7488696118053 Down 6.98E-05 Autonomous glycyl radical cofactor...”
t1862 dihydroorotate dehydrogenase from Salmonella enterica subsp. enterica serovar Typhi Ty2
55% identity, 98% coverage
STM1058 dihydro-orotate oxidase from Salmonella typhimurium LT2
55% identity, 98% coverage
- De novo pyrimidine synthesis is necessary for intestinal colonization of Salmonella Typhimurium in chicks
Yang, PloS one 2017 - “...encoded by six unlinked genes, pyrA (STM0067) , pyrB (STM4460) , pyrC (STM1163) , pyrD (STM1058) , pyrE (STM3733) and pyrF (STM1707) respectively ( Fig 1 ) [ 5 ]. Several studies of the regulation of expression of the pyr genes and their role in virulence...”
- “...used instead (Figs 3 and 4 ). Consistent with our findings, Salmonella mutants lacking pyrD (STM1058) , the fourth enzyme in the pyrimidine biosynthetic pathway encoding dihydroorotate dehydrogenase (DHOdehase; EC 1.3.3.1), also grow poorly in pyrimidine limited conditions [ 31 ], and appear to be under...”
BB3975 dihydroorotate dehydrogenase from Bordetella bronchiseptica RB50
56% identity, 96% coverage
NP_881968 dihydroorotate dehydrogenase from Bordetella pertussis Tohama I
BP3442 quinone-dependent dihydroorotate dehydrogenase from Bordetella pertussis Tohama I
55% identity, 96% coverage
Asuc_1385 Dihydroorotate oxidase from Actinobacillus succinogenes 130Z
53% identity, 98% coverage
HI1401 dihydroorotate dehydrogenase (pyrD) from Haemophilus influenzae Rd KW20
51% identity, 98% coverage
lpg1821 dihydroorotate oxidase from Legionella pneumophila subsp. pneumophila str. Philadelphia 1
51% identity, 87% coverage
- Small Regulatory RNA and Legionella pneumophila
Faucher, Frontiers in microbiology 2011 - “...lpr0037 1425122 1425478 356 lpg1297 Weissenmayer et al. ( 2011 ) lpr0043 2040383 2040499 116 lpg1821 Weissenmayer et al. ( 2011 ) lpr0044 2122994 2122901 93 lpg1903 Weissenmayer et al. ( 2011 ) lpr0049 2389440 2389117 323 lpg2142 Weissenmayer et al. ( 2011 ) lpr0050 2418574...”
BMEI1611 DIHYDROOROTATE DEHYDROGENASE from Brucella melitensis 16M
47% identity, 89% coverage
Caur_3923 Dihydroorotate oxidase from Chloroflexus aurantiacus J-10-fl
47% identity, 91% coverage
BOV_RS01655 quinone-dependent dihydroorotate dehydrogenase from Brucella ovis ATCC 25840
45% identity, 93% coverage
- Mining the Flavoproteome of Brucella ovis, the Brucellosis Causing Agent in Ovis aries
Minjárez-Sáenz, Microbiology spectrum 2022 - “..._A (63) Succ_DH_flav_C (PF02910) 474-613 11 1.3.5.2 PyrD dihydroorotate dehydrogenase 2 (quinone) DHO_dh (PF01180) 44-336 BOV_RS01655 (pyrD) ABQ61413.1 FMN Quinone 4ORI (48) 12 1.3.8.1 Short Chain Acyl-CoA dehydrogenase Acyl-CoA_dh_N (PF02771) 37-155 BOV_RS02120 ABQ60180.1 FAD 1BUC (29) Acyl-CoA_dh_M (PF02770) 160-268 Acyl-CoA_dh_1 (PF00441) 288-457 Acyl-CoA_dh_C (PF12806) 470-585 13...”
BAB1_0341 Dihydroorotate dehydrogenase:FMN/related compound-binding core:Dihydroorotate dehydrogenase 2 from Brucella melitensis biovar Abortus 2308
46% identity, 89% coverage
SCO1482 dihydroorotate dehydrogenase from Streptomyces coelicolor A3(2)
45% identity, 93% coverage
NP_001008608 dihydroorotate dehydrogenase (quinone), mitochondrial from Danio rerio
43% identity, 79% coverage
PYRD_RAT / Q63707 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Rattus norvegicus (Rat) (see 2 papers)
45% identity, 83% coverage
Q8NQC0 Dihydroorotate dehydrogenase (quinone) from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)
cg1713 dihydroorotate dehydrogenase 2 from Corynebacterium glutamicum ATCC 13032
44% identity, 89% coverage
- Diverse protein regulations on PHA formation in Ralstonia eutropha on short chain organic acids
Lee, International journal of biological sciences 2009 - “...2 20 (17) P16246 Streptomyces coelicolor Purine and pyrimidine biosynthesis Dihydroorotate dehydrogease 2 27 (25) Q8NQC0 Corynebacterium glutamicum Nucleotide biosynthesis Quinolinate synthetase A 5 22 (17) Q9F364 Streptomyces coelicolor NAD biosynthesis Bifunctional purine biosynthesis protein purH 4 30 (27) Q8FB68 Escherichia coli Nucleotide biosynthesis Nicotinate phosphoribosyltransferase...”
- Functional Genomics Uncovers Pleiotropic Role of Rhomboids in Corynebacterium glutamicum
Luenenschloss, Frontiers in microbiology 2022 - “...the MF at 40C, Uridylate kinase (Cg2218) in the MF at 30C, and dihydroorotate dehydrogenase (Cg1713) in the CF at 40C. Lower amounts of nucleoside diphosphate kinase (Cg2603) at 30C and the nucleotide-salvage enzyme hypoxanthine-guanine phosphoribosyltransferase (Cg2985) at 30 and 40C corroborate the aforementioned hypothesis. Carbohydrate...”
Q75XR0 dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) from Euglena gracilis (see paper)
44% identity, 74% coverage
I7EMP0 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Phytophthora infestans (see paper)
PITG_01913 dihydroorotate dehydrogenase, mitochondrial precursor from Phytophthora infestans T30-4
43% identity, 78% coverage
- A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi
Garrett, Frontiers in microbiology 2023 - “...previously expressed and purified DHODHs from Solanum tuberosum DHODH (UniProtID: M1BCR0), Phytophthora infestans DHODH (UniProtID: I7EMP0), Arabidopsis thaliana DHODH (UniProtID: P32746), Plasmodium falciparum DHODH (UniProtID: Q08210), and Homo sapiens DHODH (UniProtID: Q02127) ( Supplementary Figure S1 ), yielding residue 21 from EhDHODH as an appropriate start...”
- Phytophthora infestans Dihydroorotate Dehydrogenase Is a Potential Target for Chemical Control - A Comparison With the Enzyme From Solanum tuberosum
Garavito, Frontiers in microbiology 2019 - “...Homo sapiens , 1D3G NP_001352; Pfal, P. falciparum , 1TV5 XP_966023; Pinf, P. infestans , PITG_01913; Stub, S. tuberosum , PGSC0003DMG401016396; Zmay, Zea mays , NP_001152058; Atha, A. thaliana , AAN64025. Expression Constructs Solanum tuberosum cDNA was prepared from commercially available potato plants (Sabanera variety). Total...”
- “...Primers for PCR amplification were designed based on the sequences Gene ID PGSC0003DMG401016396 (StDHODH) and PITG_01913 (PiDHODH) ( Supplementary Table 1 ). PCR products were adenylated and ligated in the pGMT-Easy vector (Promega, United States), prior to transforming in E. coli DH5- electro-competent cells (Agilent, United...”
PYRD_BOVIN / Q5E9W3 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Bos taurus (Bovine) (see 2 papers)
45% identity, 80% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. Required for UMP biosynthesis via de novo pathway.
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Monomer.
PYRD_HUMAN / Q02127 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Homo sapiens (Human) (see 5 papers)
Q02127 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Homo sapiens (see 11 papers)
NP_001352 dihydroorotate dehydrogenase (quinone), mitochondrial from Homo sapiens
44% identity, 83% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor. Required for UMP biosynthesis via de novo pathway.
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Monomer. - Pivotal role of dihydroorotate dehydrogenase as a therapeutic target in adult T-cell leukemia.
Ishikawa, European journal of haematology 2024 (PubMed)- GeneRIF: Pivotal role of dihydroorotate dehydrogenase as a therapeutic target in adult T-cell leukemia.
- Bioinformatics analysis and experimental verification of the cancer-promoting effect of DHODH in clear cell renal cell carcinoma.
Wang, Scientific reports 2024 - GeneRIF: Bioinformatics analysis and experimental verification of the cancer-promoting effect of DHODH in clear cell renal cell carcinoma.
- Screening for DAX1/EWS-FLI1 functional inhibitors identified dihydroorotate dehydrogenase as a therapeutic target for Ewing's sarcoma.
Watanabe, Cancer medicine 2023 - GeneRIF: Screening for DAX1/EWS-FLI1 functional inhibitors identified dihydroorotate dehydrogenase as a therapeutic target for Ewing's sarcoma.
- Exploiting Cancer Vulnerabilities by Blocking of the DHODH and GPX4 Pathways: A Multifunctional Bodipy/PROTAC Nanoplatform for the Efficient Synergistic Ferroptosis Therapy.
Yao, Advanced healthcare materials 2023 (PubMed)- GeneRIF: Exploiting Cancer Vulnerabilities by Blocking of the DHODH and GPX4 Pathways: A Multifunctional Bodipy/PROTAC Nanoplatform for the Efficient Synergistic Ferroptosis Therapy.
- Protein production, kinetic and biophysical characterization of three human dihydroorotate dehydrogenase mutants associated with Miller syndrome.
Orozco, Nucleosides, nucleotides & nucleic acids 2022 (PubMed)- GeneRIF: Protein production, kinetic and biophysical characterization of three human dihydroorotate dehydrogenase mutants associated with Miller syndrome.
- Protein-lipid interactions of human dihydroorotate dehydrogenase and three mutants associated with Miller syndrome.
Orozco, Nucleosides, nucleotides & nucleic acids 2022 (PubMed)- GeneRIF: Protein-lipid interactions of human dihydroorotate dehydrogenase and three mutants associated with Miller syndrome.
- New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition.
Orozco, International journal of molecular sciences 2022 - GeneRIF: New Insights into the Interaction of Class II Dihydroorotate Dehydrogenases with Ubiquinone in Lipid Bilayers as a Function of Lipid Composition.
- DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma.
Olsen, JCI insight 2022 - GeneRIF: DHODH is an independent prognostic marker and potent therapeutic target in neuroblastoma.
- More
- Vidofludimus inhibits porcine reproductive and respiratory syndrome virus infection by targeting dihydroorotate dehydrogenase
Yang, Veterinary research 2023 - “...are listed). Target Common name Uniprot ID ChEMBL ID Target class Probability* Dihydroorotate dehydrogenase DHODH Q02127 CHEMBL1966 Oxidoreductase 1.000 Epidermal growth factor receptor erbB1 EGFR P00533 CHEMBL203 Kinase 0.109 Fibroblast growth factor receptor 1 FGFR1 P11362 CHEMBL3650 Kinase 0.109 Peroxisome proliferator-activated receptor gamma PPARG P37231 CHEMBL235...”
- A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi
Garrett, Frontiers in microbiology 2023 - “...Arabidopsis thaliana DHODH (UniProtID: P32746), Plasmodium falciparum DHODH (UniProtID: Q08210), and Homo sapiens DHODH (UniProtID: Q02127) ( Supplementary Figure S1 ), yielding residue 21 from EhDHODH as an appropriate start site. Classification of the excluded 20-residue sequence as a mitochondrial signal peptide was performed using DeepLoc...”
- A Novel mechanism of herbicide action through disruption of pyrimidine biosynthesis
Kang, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...a C-terminal TEV-cleavable decahistidine affinity tag was included. Coding sequences for H. sapiens (Uniprot accession Q02127), Z. mays (B6U892), A. thaliana (P32746), S. italica (A0A368QCC1), and O. sativa (Q7XKC8) DHODH were initiated at sequence positions M29, D82, A72, E82, and G88, respectively. For the O. sativa...”
- Identifying Potential Molecular Targets in Fungi Based on (Dis)Similarities in Binding Site Architecture with Proteins of the Human Pharmacolome.
Bedoya-Cardona, Molecules (Basel, Switzerland) 2023 - “...beta P49841 F0UQX6 87 Q4WDL1 93 A0A2H0ZU47 83 G8BDX2 80 Q5KMR8 90 A0A0D2XCF2 87 DHOdehase Q02127 F0UDX1 87 Q4X169 87 Q874I4 100 G8BA68 100 Q5KK62 100 Histone deacetylase 7 Q8WUI4 F0UVW7 85 Q4WE71 75 Q5A960 80 G8BBK1 80 Q5KL48 80 A0A0D2YC83 72.7 Thymidylate synthase P04818 F0URV8...”
- “...Histone deacetylase 6 Q9UBN7 F0UVW7 81.2 Q5A960 75 G8BBK1 75 Q5KL48 86.7 A0A0D2YC83 87.5 DHOdehase Q02127 F0UDX1 80 Q4X169 88 Histone deacetylase 8 Q9BY41 F0UKC3 80 Q4WHY0 80 A0A2H0ZKW1 80 G8BBB0 76 Q5KF65 76.2 A0A0D2X821 80 PPIase FKBP1A P62942 F0URT3 78 P28870 74 P0CP94 78 HMG-CoA...”
- Mitochondria-derived vesicles and their potential roles in kidney stone disease.
Chaiyarit, Journal of translational medicine 2023 - “...dehydrogenase complex component E2) (OGDC-E2) (Dihydrolipoamide succinyltransferase component of 2-oxoglutarate dehydrogenase complex) (E2K) 73 DHODH Q02127 Dihydroorotate dehydrogenase (quinone), mitochondrial (DHOdehase) (EC 1.3.5.2) (Dihydroorotate oxidase) 74 DNAJA3 Q96EY1 DnaJ homolog subfamily A member 3, mitochondrial (DnaJ protein Tid-1) (hTid-1) (Hepatocellular carcinoma-associated antigen 57) (Tumorous imaginal discs...”
- Uncovering the molecular mechanism of Gynostemma pentaphyllum (Thunb.) Makino against breast cancer using network pharmacology and molecular docking
Wang, Medicine 2022 - “...Closeness centrality Degree Albumin ALB O60674 1HK4 0.377607 0.806452 19 Epidermal growth factor receptor EGFR Q02127 3POZ 0.172591 0.735294 16 Estrogen receptor ESR1 P28482 1XPC 0.159369 0.735294 16 Androgen receptor AR P60568 1T65 0.052421 0.675676 13 Progesterone receptor PGR P01375 1SQN 0.020849 0.641026 11 Heat shock...”
- The Pharmacological Mechanism of Xiyanping Injection for the Treatment of Novel Coronavirus Pneumonia (COVID-19): Based on Network Pharmacology Strategy
Xia, Evidence-based complementary and alternative medicine : eCAM 2022 - “...ADAM17 P31749 AKT1 P51636 CAV2 P53779 MAPK10 P30530 AXL Q9H2X3 CLEC4M O76074 PDE5A P68104 EEF1A1 Q02127 DHODH P45983 MAPK8 P05121 SERPINE1 P06400 RB1 P26447 S100A4 P48506 GCLC Q16236 NFE2L2 P40763 STAT3 P08670 VIM P04040 CAT P12830 CDH1 Q15910 EZH2 P35968 KDR P28482 MAPK1 P27361 MAPK3 P04637...”
- DCZ19931, a novel multi-targeting kinase inhibitor, inhibits ocular neovascularization
Zhang, Scientific reports 2022 - “...CHEMBL2094128 Other cytosolic protein 0.095623787 GRM1 Q13255 CHEMBL3772 Family C G protein-coupled receptor 0.095623787 DHODH Q02127 CHEMBL1966 Oxidoreductase 0.095623787 ATM Q13315 CHEMBL3797 Kinase 0.095623787 RORC P51449 CHEMBL1741186 Nuclear receptor 0.095623787 GRIN2A/GRIN1 Q12879/Q05586 CHEMBL1907604 Ligand-gated ion channel 0.095623787 SLC6A9 P48067 CHEMBL2337 Electrochemical transporter 0.095623787 NR1H3 Q13133 CHEMBL2808...”
- More
9dhhA / Q02127 9dhhA (see paper)
44% identity, 89% coverage
- Ligands: flavin mononucleotide; (3s,7p)-7-[4-ethyl-3-(hydroxymethyl)-5-oxo-4,5-dihydro-1h-1,2,4-triazol-1-yl]-6-fluoro-3-(2-methylphenyl)-1-(propan-2-yl)-2,3-dihydroquinolin-4(1h)-one (9dhhA)
LIC13433 dihydroorotate dehydrogenase from Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130
40% identity, 84% coverage
- Global transcriptomic response of Leptospira interrogans serovar Copenhageni upon exposure to serum
Patarakul, BMC microbiology 2010 - “...- LIC12184 (LA1598) - nucleotide transport and metabolism (F) pyrD 2.01 dihydroorotate dehydrogenase - - LIC13433 (LA4290) dgt 1.54 deoxyguanosinetriphosphate - - LIC11663 (LA2274) triphosphohydrolase - coenzyme transport and metabolism (H) 1.82 pyrimidine reductase - LIC13208 (LA4019) 1.58 methylase/methyl transferase - - LIC20082 (LB105) coaE 1.55...”
- “...cycle [ 79 ]. The transition of Leptospira to serum resulted in up-regulation of pyrD (LIC13433), predicted to encode a dihydroorotate dehydrogenase which catalyzes the fourth step in the de novo pyrimidine nucleotide biosynthetic pathway [ 80 ], possibly due to limited availability of pyrimidine in...”
NP_064430 dihydroorotate dehydrogenase (quinone), mitochondrial precursor from Mus musculus
O35435 Dihydroorotate dehydrogenase (quinone), mitochondrial from Mus musculus
44% identity, 83% coverage
- Targeting DHODH reveals therapeutic opportunities in ATRA-resistant acute promyelocytic leukemia.
Yang, Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie 2023 (PubMed)- GeneRIF: Targeting DHODH reveals therapeutic opportunities in ATRA-resistant acute promyelocytic leukemia.
- Mitochondrial Regulation of the Hippocampal Firing Rate Set Point and Seizure Susceptibility.
Styr, Neuron 2019 - GeneRIF: Knockdown of Dhodh reduced hippocampus mean firing rate.
- DHODH modulates transcriptional elongation in the neural crest and melanoma.
White, Nature 2011 - GeneRIF: DHODH inhibition led to a marked decrease in melanoma growth both in vitro and in mouse xenograft studies
- Dihydroorotate dehydrogenase mRNA and protein expression analysis in normal and drug-resistant cells.
Löffler, Nucleosides, nucleotides & nucleic acids 2004 (PubMed)- GeneRIF: Dihydroorotate dehydrogenase mRNA and protein expression analysis in normal and drug-resistant cells of different species
- In vitro and in Vivo inhibition of immunoglobulin secretion by the immunosuppressive compound HR325 is reversed by exogenous uridine.
Thomson, Scandinavian journal of immunology 2002 (PubMed)- GeneRIF: immunosuppressive agent HR325 (an inhibitor of dihydroorotate dehydrogenase, DHODH) inhibits immunoglobulin (Ig) secretion both in vitro and in vivo and that this effect can be reverse with exogenous uridine
- Modulation of Proteome Profile in AβPP/PS1 Mice Hippocampus, Medial Prefrontal Cortex, and Striatum by Palm Oil Derived Tocotrienol-Rich Fraction
Hamezah, Journal of Alzheimer's disease : JAD 2019 - “...3 NDUFB3 Q8K183 Pyridoxal kinase PDXK P54071 Isocitrate dehydrogenase [NADP] IDH2 P05202 Aspartate aminotransferase GOT2 O35435 Dihydroorotate dehydrogenase (quinone) DHODH P16858 Glyceraldehyde-3-phosphate dehydrogenase GAPDH Biosynthesis of amino acids 3 0.0002 0.0132 P05202 Aspartate aminotransferase GOT2 P54071 Isocitrate dehydrogenase [NADP] IDH2 P16858 Glyceraldehyde-3-phosphate dehydrogenase GAPDH Carbon metabolism...”
- A new non-canonical pathway of Gα(q) protein regulating mitochondrial dynamics and bioenergetics
Benincá, Cellular signalling 2014 - “...9 373 42.1 8.48 32.70 Lipoyltransferase 1, mitochondrial OS=Mus musculus GN=Lipt1 PE=2 SV=1 - [LIPT_MOUSE] O35435 53.42 13 13 395 42.7 9.55 32.01 Dihydroorotate dehydrogenase, mitochondrial OS=Mus musculus GN=Dhodh PE=2 SV=2 - [PYRD_MOUSE] Q91WK2 26.99 9 8 352 39.8 6.67 29.85 Eukaryotic translation initiation factor 3...”
D2S350 Dihydroorotate dehydrogenase (quinone) from Haloterrigena turkmenica (strain ATCC 51198 / DSM 5511 / JCM 9101 / NCIMB 13204 / VKM B-1734 / 4k)
42% identity, 92% coverage
A8HZX8 Dihydroorotate dehydrogenase (quinone) from Azorhizobium caulinodans (strain ATCC 43989 / DSM 5975 / JCM 20966 / LMG 6465 / NBRC 14845 / NCIMB 13405 / ORS 571)
45% identity, 92% coverage
SYNPCC7002_A2195 dihydroorotate dehydrogenase from Synechococcus sp. PCC 7002
42% identity, 84% coverage
- Transcription Profiling of the Model Cyanobacterium Synechococcus sp. Strain PCC 7002 by Next-Gen (SOLiD™) Sequencing of cDNA
Ludwig, Frontiers in microbiology 2011 - “...1.37 0.00 0.30 n.d. 32.59 isiB Flavodoxin SYNPCC7002_A1442 0.84 31.80 49.22 1.55 0.86 Dihydroorotate dehydrogenase SYNPCC7002_A2195 0.88 0.76 0.20 0.26 0.78 pyrD Dihydroorotate dehydrogenase SYNPCC7002_A2286 2.29 0.33 0.12 0.36 1.01 pstA Phosphate ABC transporter, permease protein SYNPCC7002_A1895 1.66 0.76 0.33 0.44 0.97 pstB Phosphate import ATP-binding...”
- “...an operon under a common regulatory mechanism. The transcript level for a second pyrD gene (SYNPCC7002_A2195) did not change much upon dark oxic treatment, but was about five-fold lower after 1h under dark anoxic incubation when compared to cells grown under standard conditions. The transcript levels...”
4oriA / Q63707 Rat dihydroorotate dehydrogenase bound with dsm338 (n-[3,5-difluoro-4- (trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2, 4]triazolo[1,5-a]pyrimidin-7-amine) (see paper)
43% identity, 92% coverage
- Ligands: flavin mononucleotide; n-[3,5-difluoro-4-(trifluoromethyl)phenyl]-5-methyl-2-(trifluoromethyl)[1,2,4]triazolo[1,5-a]pyrimidin-7-amine (4oriA)
B7PXW4 Dihydroorotate dehydrogenase (quinone), mitochondrial (Fragment) from Ixodes scapularis
41% identity, 88% coverage
XP_004924203 dihydroorotate dehydrogenase (quinone), mitochondrial isoform X2 from Bombyx mori
40% identity, 85% coverage
Rv2139 dihydroorotate dehydrogenase from Mycobacterium tuberculosis H37Rv
43% identity, 94% coverage
- Characteristic SNPs defining the major multidrug-resistant Mycobacterium tuberculosis clusters identified by EuSeqMyTB to support routine surveillance, EU/EEA, 2017 to 2019
de, Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin 2024 - “...polymerase III subunit epsilon Rv3711c Val251Val (gtc/gtT) 7 7 Beijing (2.2.1) 2399093_A 15 Dihydroorotate dehydrogenase Rv2139 Arg125Gln (cgg/cAg) 7 7 Beijing (2.2.1) 1008074_A 16 Acetyl-CoA carboxylase carboxyl transferase beta Rv0904c Ala36Val (gcg/gTg) 7 8 Beijing (2.2.1) 4284172_T 17 Hypothetical protein Rv3819 Asp59Asp (gac/gaT) 5 9 LAM...”
- Fluorescence Imaging-Based Discovery of Membrane Domain-Associated Proteins in Mycobacterium smegmatis
Rokicki, Journal of bacteriology 2021 (secret) - Correlation of drug resistance with single nucleotide variations through genome analysis and experimental validation in a multi-drug resistant clinical isolate of M. tuberculosis
Bhattacharyya, BMC microbiology 2020 - “...identified in 18 genes including ABC transporter pstA1 ( Rv0930 ), dihydroorotate dehydrogenase pyrD ( Rv2139 ), fatty-acid-CoA synthase fadD15 ( Rv2187 ), NADPH: adrenodoxin oxidoreductase fprA ( Rv3106 ) and NAD(P) H quinone reductase lpdA ( Rv3303c ) (Table 1 ). In these cases we...”
- “...protein 1,037,911 Rv0930 pstA1 C913T R305X 3 Probable phosphate-transport integral membrane ABC transporter PstA1 2,399,782 Rv2139 pyrD C1063T Q355X 2 Probable dihydroorotate dehydrogenase 2,448,288 Rv2187 fadD15 G129A W43X 558 Actelyco asynthetase like AMP synthetase ligase 2,882,317 Rv2563 Rv2563 C28T Q10X 340 Probable glutamine-transport transmembrane ABC transporter...”
- Integration of Metabolic Modeling with Gene Co-expression Reveals Transcriptionally Programmed Reactions Explaining Robustness in Mycobacterium tuberculosis
Puniya, Scientific reports 2016 - “...(2-amino-4-hydroxy-6-hydroxymethyldihydropteridine di-phosphokinase) ( Rv3606c ) Folate Metabolism (DHNPA2, DHPS2) DHORD2 (dihydoorotic acid dehydrogenase quinone8) ( Rv2139 ) Glycolysis(PGK), Histidine Metabolism (IG3PS) DESAT18 (stearoyl-CoA desaturase) ( Rv1094 or Rv0824c ) Fatty Acid Metabolism (FACOAL181, FAS181) GCCa (glycine cleavage complex) ( Rv1832 ) Pyrimidine Metabolism ( DHORTS )...”
- Target prediction for an open access set of compounds active against Mycobacterium tuberculosis
Martínez-Jiménez, PLoS computational biology 2013 - “...Approach Targets Compound families mtu00240 STR Rv1381 255 Pyrimidine metabolism Rv3048c 86 Rv3314c 255 CHEM Rv2139 Several Rv2764c Several Rv3247c 497 HIST Rv2139 2 mtu00260 STR Rv0489 551 Glycine, serine and threonine metabolism Rv1296 551 Rv3708c 551 CHEM Rv1905c 5,252,497 Rv3170 Several HIST Rv3170 5 mtu00330...”
- “...Pathway GSK975842A Rv2182c Glycerolipid metabolism (mtu00561) Glycerophospholipid metabolism (mtu00564) Rv2483c No Pathway Rv2045c No Pathway Rv2139 Pyrimidine metabolism (mtu00240) Rv2299c No Pathway Rv2483c No Pathway 3 GSK547481A Rv0194 ABC transporters (mtu02010) GSK547490A Rv0194 ABC transporters (mtu02010) GSK547491A Rv0194 ABC transporters (mtu02010) GSK547499A Rv0194 ABC transporters (mtu02010)...”
- Individual Mycobacterium tuberculosis universal stress protein homologues are dispensable in vitro
Hingley-Wilson, Tuberculosis (Edinburgh, Scotland) 2010 - “...site 29,30 and a conserved D (in a DGS motif) in USPA domain 1, except Rv2139 which has only a partially conserved motif (G12xGS). Four of the USPs also have these features fully conserved in UspA domain 2 (Rv2005c, Rv2623, Rv2026c and Rv1996). So all of...”
- Development and analysis of an in vivo-compatible metabolic network of Mycobacterium tuberculosis
Fang, BMC systems biology 2010 - “...FP Nucleotide metabolism Functions as orotidine-5'-phosphate decarboxylase (1) Allowed the uptake of cytidine 31 38 Rv2139 pyrD FP Nucleotide metabolism Functions as dihydroorotic acid dehydrogenase (1) Allowed the uptake of cytidine 32 39 Rv3393 iunH FP Nucleotide metabolism Hydrolysis of inosine (1) Let the reaction catalyzed...”
CSUI_008592 dihydroorotate dehydrogenase from Cystoisospora suis
39% identity, 51% coverage
- Unravelling the sexual developmental biology of Cystoisospora suis, a model for comparative coccidian parasite studies
Cruz-Bustos, Frontiers in cellular and infection microbiology 2023 - “...Citrate synthase TCA 1.287 2.215 1.262 -1.530 CSUI_010097 malate dehydrogenase TCA 0.485 1.075 1.041 -0.876 CSUI_008592 Dihydroorotate dehydrogenase Complex I/pyrimidine/folate metabolism 1.018 2.653 1.450 -0.970 CSUI_001762 Short chain dehydrogenase reductase family protein Fatty acid biosynthetic process 0.261 0.844 2.481 0.982 CSUI_010330 Acyl carrier protein Fatty acid...”
- “...levels during asexual and immature sexual stages and decreased levels in unsporulated oocysts except for CSUI_008592. 3.4 Processing of genetic information The category of genetic information processing, encompassing core processes like DNA replication, transcription, and translation, is well represented in the C. suis proteome, comprising 213...”
XP_794275 dihydroorotate dehydrogenase (quinone), mitochondrial from Strongylocentrotus purpuratus
41% identity, 80% coverage
MSMEG_4198 dihydroorotate oxidase from Mycobacterium smegmatis str. MC2 155
45% identity, 83% coverage
- Compartmentalization of galactan biosynthesis in mycobacteria
Savková, The Journal of biological chemistry 2024 - “...Psd (MSMEG_0861), polyprenol-monophosphomannose synthase Ppm1 (MSMEG_3859), glycosyltransferase Gtf1 (MSMEG_0389), geranylgeranyl reductase (MSMEG_2308), dihydroorotate dehydrogenase PyrD (MSMEG_4198), and a putative membrane protein (MSMEG_1944) ( 18 ). For five of these proteins (GlfT2, Gtf1, MSMEG_2308, PyrD, and MSMEG_1944), their localization to PMf was also confirmed by the construction...”
- Fluorescence Imaging-Based Discovery of Membrane Domain-Associated Proteins in Mycobacterium smegmatis
Rokicki, Journal of bacteriology 2021 (secret) - Spatially distinct and metabolically active membrane domain in mycobacteria
Hayashi, Proceedings of the National Academy of Sciences of the United States of America 2016 - “...a geranylgeranyl reductase (MSMEG_2308), PyrD (MSMEG_4198, dihydroorotate dehydrogenase), and a putative membrane protein (MSMEG_1944), of which...”
slr1418 dihydroorotate dehydrogenase from Synechocystis sp. PCC 6803
41% identity, 80% coverage
- C-ferroptosis is an iron-dependent form of regulated cell death in cyanobacteria
Aguilera, The Journal of cell biology 2022 - “...( Gaber et al., 2001 ). FSP1ubiquinol Synechocystis sp. PCC 6803 encodes one dihydroorotate dehydrogenase (slr1418) that catalyzes the conversion of dihydroorotate to orotate with quinone or plastoquinone as electron acceptor ( Nara et al., 2000 ; Baers et al., 2019 ). Dihydroorotate dehydrogenaseubiquinol SLC7A11 transmembrane...”
- “...cyanobacteria. On the other hand, the genome of Synechocystis encodes one membrane-bound dihydroorotate dehydrogenase (pyrD, slr1418 ) that catalyzes the conversion of dihydroorotate to orotate with quinone or plastoquinone as the electron acceptor ( Baers et al., 2019 ; Nara et al., 2000 ; Table 2...”
- RNA-seq based identification and mutant validation of gene targets related to ethanol resistance in cyanobacterial Synechocystis sp. PCC 6803
Wang, Biotechnology for biofuels 2012 - “...hydroxylase 1.59 1.59 slr1350 acyl-lipid desaturase 1.72 1.57 slr1379 quinol oxidase subunit I 1.56 1.70 slr1418 dihydroorotate dehydrogenase 2.50 2.63 slr1452 sulfate transport system substrate-binding protein 1.83 2.00 slr1596 a protein in the cytoplasmic membrane 2.31 2.08 slr1626 dihydroneopterin aldolase 1.80 3.30 slr1805 two-component sensor histidine...”
6ajeA / U6KL66 Crystal structure of dhodh in complex with ferulenol from eimeria tenella (see paper)
41% identity, 85% coverage
- Ligands: flavin mononucleotide; 4-oxidanyl-3-[(2~{e},6~{e})-3,7,11-trimethyldodeca-2,6,10-trienyl]chromen-2-one (6ajeA)
M1BCR0 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Solanum tuberosum (see paper)
40% identity, 69% coverage
SAUSA300_2526 dihydroorotate dehydrogenase from Staphylococcus aureus subsp. aureus USA300_FPR3757
SACOL2606 dihydroorotate dehydrogenase from Staphylococcus aureus subsp. aureus COL
38% identity, 95% coverage
- Transposon sequencing identifies genes impacting Staphylococcus aureus invasion in a human macrophage model
Lo, Infection and immunity 2023 (secret) - Impact of the pentose phosphate pathway on metabolism and pathogenesis of Staphylococcus aureus
Kim, PLoS pathogens 2023 (no snippet) - Novel Regulation of Alpha-Toxin and the Phenol-Soluble Modulins by Peptidyl-Prolyl cis/trans Isomerase Enzymes in Staphylococcus aureus
Keogh, Toxins 2019 - “...UvrB 0.29 DNA metabolism SAUSA300_0692 SaeQ 0.27 Conserved hypothetical protein SAUSA300_1523 0.27 Conserved hypothetical protein SAUSA300_2526 PyrD 0.26 Purines, pyrimidines, nucleosides, and nucleotides SAUSA300_0364 YchF 0.26 Unknown function SAUSA300_1144 TrmFO 0.24 Unknown function SAUSA300_1861 0.24 Conserved hypothetical protein SAUSA300_1007 0.24 Unknown function SAUSA300_0329 0.24 Unknown function...”
- Cigarette Smoke Extract-Exposed Methicillin-Resistant Staphylococcus aureus Regulates Leukocyte Function for Pulmonary Persistence
Kulkarni, American journal of respiratory cell and molecular biology 2016 - “...SAUSA300_0057 SAUSA300_1238 SAUSA300_0490 SAUSA300_0146 SAUSA300_2526 SAUSA300_1570 SAUSA300_0256 SAUSA300_2532 SAUSA300_2172 hisZ SAUSA300_2011 SAUSA300_0036...”
- Inactivation of thyA in Staphylococcus aureus attenuates virulence and has a strong impact on metabolism and virulence gene expression
Kriegeskorte, mBio 2014 - “...decarboxylase 8.06 7.74 SACOL1217 pyrE Orotate phosphoribosyltransferase 9.70 7.65 SACOL2119 pyrG CTP synthase 12.31 6.20 SACOL2606 pyrD Dihydroorotate dehydrogenase 8.73 11.92 SACOL0524 tmk Thymidylate kinase 3.30 Nucleotide and nucleoside interconversions SACOL0603 Deoxynucleoside kinase family protein 7.46 SACOL0604 Deoxynucleoside kinase family protein 6.68 SACOL1277 pyrH Uridylate kinase...”
- An antibiotic that inhibits a late step in wall teichoic acid biosynthesis induces the cell wall stress stimulon in Staphylococcus aureus
Campbell, Antimicrobial agents and chemotherapy 2012 - “...dehydrogenase SAV2561 SAV0390 SAR0406 SACOL2606 Pyrimidine ribonucleotide biosynthesis Pyrimidine ribonucleotide biosynthesis Pyrimidine ribonucleotide...”
- Mode-of-action studies of the novel bisquaternary bisnaphthalimide MT02 against Staphylococcus aureus
Menzel, Antimicrobial agents and chemotherapy 2011 - “...ORF and functional group SACOL0792 SACOL0793 SACOL2606 Annotation Fold change nrdE nrdF pyrD Ribonucleotide-diphosphate reductase subunit alpha...”
- Complete and SOS-mediated response of Staphylococcus aureus to the antibiotic ciprofloxacin
Cirz, Journal of bacteriology 2007 - “...SACOL1214 SACOL1215 SACOL1216 SACOL1371 SACOL1969 SACOL2130 SACOL2606 SACOL2635 Up-regulated ORFs SACOL0790.1 SACOL0791 SACOL0792 SACOL0793 Gene 536 CIRZ ET...”
SAPIG2639 quinone-dependent dihydroorotate dehydrogenase from Staphylococcus aureus subsp. aureus ST398
37% identity, 95% coverage
- Genome-wide high-throughput screening to investigate essential genes involved in methicillin-resistant Staphylococcus aureus Sequence Type 398 survival
Christiansen, PloS one 2014 - “...SAPIG2156 529.71 5.51 6.5882 0.0296 SAPIG0647 1739.26 31.92 5.7678 0.0497 SAPIG2568 751.50 15.43 5.6056 0.0259 SAPIG2639 1449.27 77.16 4.2314 0.0360 SAPIG0185 120.11 2868.20 4.5777 0.0328 The table lists the mutants that significantly changed in clone number from input to output (pre- and post-selection in whole porcine...”
- “...blue pigment. Oxidative stress ph shock. SAPIG2568 (fbp) Fructose-1,6-bisphosphatase Gluconeogenesis Response to depletion of glucose. SAPIG2639 (pyrD) Dihydroorotate oxidase Pyrimidine biosynthesis Nucleic acids biosynthesis. SAPIG0185 pANL51 Unknown function ? Discussion The purpose of the work was to generate a high complexity transposon mutant library and assess...”
SA2375 dihydroorotate dehydrogenase from Staphylococcus aureus subsp. aureus N315
37% identity, 95% coverage
- Global transcriptome analysis of Staphylococcus aureus biofilms in response to innate immune cells
Scherr, Infection and immunity 2013 - “...SA1546 SA1568 SA2180 SA0876 SA1610 SA1549 SA1588 SA2627 SA2375 SA1804 SA0666 SA0877 SA1280 SA0024 SA1429 SA1818 SA0155 SA2475 SA0712 SA0687 SA2278 SA1235 SA0024...”
- An RpoB mutation confers dual heteroresistance to daptomycin and vancomycin in Staphylococcus aureus
Cui, Antimicrobial agents and chemotherapy 2010 - “...SA1043 SA1044 SA1045 SA1046 SA1047 SA1048 SA1049 SA1439 SA2375 Arginine metabolism and urea cycle SA0175 SA0176 SA0177 SA0178 SA0179 SA0821 SA0822 SA2082 SA2083...”
- Regulation of hemolysin expression and virulence of Staphylococcus aureus by a serine/threonine kinase and phosphatase
Burnside, PloS one 2010 - “...alpha subunits - 1 LH SA2271 Molybdenum ABC transporter, permease protein - cations 1 LH SA2375 Transporter - unknown substrate 1 LH SA2534 NAD(P)H-flavin oxidoreductase 1 LH SA2572 Cation-transporting atpase, E1-E2 family 1 LH SA2624 Acetyl-CoA synthetase, putative 3 LH SA2735 Chromosome partioning protein, ParB family...”
- 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 - “...family protein sa_c5160s4458_a_at * 12.5 2.5 2.5 SA2319 Na+/H+ antiporter family sa_c5500s4763_a_at 5.8 2.5 2.5 SA2375 CorA family sa_c5522s4780_a_at * 5.1 2.5 2.5 SA2382 proton/sodium-glutamate symporter sa_c5534s4791_a_at * 7.6 2.5 ND SA2386 nitrite extrusion protein sa_c10691s11141cv_s_at 5.3 2.5 2.5 SA2718 anion transporter family protein sa_c422s9317_a_at 4.0...”
- Transcriptome and functional analysis of the eukaryotic-type serine/threonine kinase PknB in Staphylococcus aureus
Donat, Journal of bacteriology 2009 - “...minor subunit SA1921 tdk Thymidine kinase SA2375 Hypothetical protein, similar to dihydroorotate dehydrogenase SA2410 Anaerobic ribonucleoside triphosphate...”
- Global regulatory impact of ClpP protease of Staphylococcus aureus on regulons involved in virulence, oxidative stress response, autolysis, and DNA repair
Michel, Journal of bacteriology 2006 - “...protein homolog 0.4 0.5 0.5 Up SA2091d SA2375 SA2473 LexA consensus sequenced fnb Fibronectin-binding protein homolog Similar to dihydroorotate dehydrogenase...”
- Characterization of the Staphylococcus aureus heat shock, cold shock, stringent, and SOS responses and their effects on log-phase mRNA turnover
Anderson, Journal of bacteriology 2006 - “...clpB gltC ctsR kdpE lacE lacF hla eprH SA2375 SA2450 ABC transporter N315-SA0895 N315-SA1833 SA0900 SA0901 SA1173 SA1265 SA2668 Pathogenicity island protein...”
PYRD / P32746 dihydroorotate dehydrogenase (EC 1.3.5.2) from Arabidopsis thaliana (see 2 papers)
PYRD_ARATH / P32746 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Arabidopsis thaliana (Mouse-ear cress) (see paper)
P32746 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Arabidopsis thaliana (see paper)
AT5G23300 PYRD (pyrimidine d); dihydroorotate dehydrogenase from Arabidopsis thaliana
39% identity, 72% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN Note=Binds 1 FMN per subunit - Comparison of the Effects of UV-C Light in the Form of Flash or Continuous Exposure: A Transcriptomic Analysis on <i>Arabidopsis thaliana</i> L
Jazayeri, International journal of molecular sciences 2024 - “...protein 1.40 1.53 10 10 AT5G15700 AT5G15700 DNA/RNA polymerases superfamily protein 1.29 3.99 10 21 AT5G23300 PYRD Pyrimidine d 1.04 1.50 10 7 AT5G23930 AT5G23930 Mitochondrial transcription termination factor family protein 1.07 3.80 10 3 AT5G26860 LON1 Lon protease 1 1.76 1.10 10 37 AT5G27395 AT5G27395...”
- A Novel mechanism of herbicide action through disruption of pyrimidine biosynthesis
Kang, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...were confirmed by Sanger sequencing. Among this list, one gene encoded an antiproliferative enzyme, DHODH (At5g23300, DHODH) with a G198E (nucleotide G593A) mutation located in exon 4 of the DHODH gene ( Fig. 2 C ). The second independent resistant line, designated 60R1 , was found...”
- “...by next-generation sequencing of RNA transcripts (RNA-Seq), and metabolomics ultimately pointed to class II DHODH (At5g23300) as a candidate worth detailed investigation. Transgenic experiments with resistant DHODH further confirmed DHODH as the target of pyrrolidinone chemistry. Production of the functional enzyme by recombinant means following isolation...”
- New Insights into rice pyrimidine catabolic enzymes
Lopez, Frontiers in plant science 2023 - “...411 residues; DHODHs: OsDHODH, class 2, O.sativum, DQ269457.1, 469 residues; AtDHODH, class 2, A. thaliana, At5g23300, 460 residues; HsDHODH, class 2, Homo sapiens, BC065245.1, 395 residues, TcDHODH, class 1A, Trypanosoma cruzi, EAN87213.1, 314 residues, LlDHODH, class 1B, PyrDb, Lactobacillus lactis, CAL97700.1;, 311 residues; LlDHODH, class 1B,...”
- Nucleotide Imbalance, Provoked by Downregulation of Aspartate Transcarbamoylase Impairs Cold Acclimation in Arabidopsis
Bellin, Molecules (Basel, Switzerland) 2023 - “...AT3G01820 AMK7 2.97 3.16 0.80 de novo AT4G34740 ATase2 2.34 2.34 0.63 0.58 de novo AT5G23300 DHODH 1.62 1.09 de novo AT1G30820 CTPS1 1.84 2.29 2.82 2.31 de novo AT3G12670 CTPS2 1.95 2.03 0.99 0.82 de novo AT2G16370 DHFR-TS 1.45 1.22 de novo AT3G06200 GMK 1.52...”
- Genome- and transcriptome-wide association studies reveal the genetic basis and the breeding history of seed glucosinolate content in Brassica napus
Tan, Plant biotechnology journal 2022 - “...to GTR2 , HAG1/MYB28 , APO3 ( AT5G61930 ), TAF5 ( AT5G25150 ), PYRD ( AT5G23300 ), and ORE14 ( AT5G62000 ), were present in 15 stable QTLs (Figure 2c ; Dataset S15 ). The POCKET algorithm, which integrates multiomics data and is based on machine...”
- Genome-Wide Identification and Analysis of the Cytochrome B5 Protein Family in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)
Zheng, International journal of genomics 2019 - “...BrCB5o Bra031692 AT1G09960, SUT4 (Sucrose Transporter 4) Bra019972 Bra035720 AT4G32360, NADP adrenodoxin-like ferredoxin reductase Bra026504 AT5G23300, PYRD (pyrimidine d); dihydroorotate dehydrogenase Bra009669 Bra022246 AT3G17810, dihydroorotate dehydrogenase family protein Bra021275 Bra001684 Bra035130 AT1G79610, NHX6|sodium proton exchanger Bra007824 AT5G50375, CPI1 (cyclopropyl isomerase) Bra000625 Bra015335 AT1G04620, coenzyme F420 hydrogenase...”
- Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds
Mao, International journal of molecular sciences 2018 - “...AT3G15660 Monothiol glutaredoxin-S1, mitochondrial Oryza sativa subsp. japonic a ns 0.78 ns Nucleotide metabolism K3ZE81 AT5G23300 Dihydroorotate dehydrogenase (quinone), mitochondrial Setaria italica ns ns 0.75 C1-metabolism formate dehydrogenase A0A0D3GGT7 AT5G14780 Formate dehydrogenase, mitochondrial Oryza barthii ns 0.72 0.67 Major CHO metabolism, Degradation, sucrose, Invertases, nautral Q10MC0...”
- A Microsomal Proteomics View of H₂O₂- and ABA-Dependent Responses
Alqurashi, Proteomes 2017 - “...Cysteine synthase C1 0.00074 ns 5 AT4G14880 O-acetylserine (thiol) lyase isoform A1 0.015 0.1 7.9 AT5G23300 Pyrimidine d 0.013 0.2 ns AT3G09820 Adenosine kinase 1 0.0042 0.1 14.0 AT5G17770 NADH:cytochrome B5 reductase 1 0.017 0.4 2.5 AT1G74790 Catalytics 0.045 5.7 4.6 AT4G23850 AMP-dep. synthetase and ligase...”
- More
- A Novel mechanism of herbicide action through disruption of pyrimidine biosynthesis
Kang, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...was included. Coding sequences for H. sapiens (Uniprot accession Q02127), Z. mays (B6U892), A. thaliana (P32746), S. italica (A0A368QCC1), and O. sativa (Q7XKC8) DHODH were initiated at sequence positions M29, D82, A72, E82, and G88, respectively. For the O. sativa sequence, the hexapeptide MADEAN precedes the...”
- A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi
Garrett, Frontiers in microbiology 2023 - “...from Solanum tuberosum DHODH (UniProtID: M1BCR0), Phytophthora infestans DHODH (UniProtID: I7EMP0), Arabidopsis thaliana DHODH (UniProtID: P32746), Plasmodium falciparum DHODH (UniProtID: Q08210), and Homo sapiens DHODH (UniProtID: Q02127) ( Supplementary Figure S1 ), yielding residue 21 from EhDHODH as an appropriate start site. Classification of the excluded...”
SAR2669 putative dihydroorotate dehydrogenase from Staphylococcus aureus subsp. aureus MRSA252
37% identity, 95% coverage
- The Staphylococcus aureus response to unsaturated long chain free fatty acids: survival mechanisms and virulence implications
Kenny, PloS one 2009 - “...8.78E-04 SAR2472 gltT putative proton/sodium-glutamate symport protein 2.04 2.97E-02 SAR2621 cidA holin-like protein 2.27 1.18E-02 SAR2669 putative dihydroorotate dehydrogenase 2.86 3.75E-03 Fatty Acid Metabolism SAR0225 fadD putative acyl-CoA dehydrogenase 2.17 3.27E-02 SAR0227 fadX putative acetyl-CoA transferase 2.13 4.95E-02 SAR0803 conserved hypothetical protein 3.23 1.02E-02 Carotenoid Biosynthesis...”
- “...increase the pool of L-lysine in the cell. Up-regulation of SAR2420 (hutG), and down-regulation of SAR2669 encoding a putative dihydroorotate dehydrogenase, SAR0228 encoding a putative glutamine amidotransferase and SAR1752 ( hemA ), in concert, would maintain glutamate levels within the cell. SAR2269 , a putative alanine...”
U6KL66 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Eimeria tenella (see paper)
XP_013227840 dihydroorotate dehydrogenase, putative from Eimeria tenella
39% identity, 78% coverage
Q7XKC8 Dihydroorotate dehydrogenase (quinone), mitochondrial from Oryza sativa subsp. japonica
37% identity, 69% coverage
- A Novel mechanism of herbicide action through disruption of pyrimidine biosynthesis
Kang, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...(Uniprot accession Q02127), Z. mays (B6U892), A. thaliana (P32746), S. italica (A0A368QCC1), and O. sativa (Q7XKC8) DHODH were initiated at sequence positions M29, D82, A72, E82, and G88, respectively. For the O. sativa sequence, the hexapeptide MADEAN precedes the indicated starting residue. Site-specific mutants were generated...”
- ITRAQ-based quantitative proteomic analysis of japonica rice seedling during cold stress
Qing, Breeding science 2022 - “...1 11 68.88 0.48 Q7XCS3 Cys/Met metabolism PLP-dependent enzyme family protein, expressed 5 11.42 3.16 Q7XKC8 Dihydroorotate dehydrogenase (quinone), mitochondrial 5 13.22 0.25 Q306J3 Dirigent protein 16 58.50 1.82 Q69JX7 Drought-induced S-like ribonuclease 3 13.10 0.49 Q2QN11 Eukaryotic aspartyl protease family protein, expressed 10 25.34 0.43...”
B6U892 Dihydroorotate dehydrogenase (quinone), mitochondrial from Zea mays
NP_001152058 dihydroorotate dehydrogenase from Zea mays
37% identity, 69% coverage
- A Novel mechanism of herbicide action through disruption of pyrimidine biosynthesis
Kang, Proceedings of the National Academy of Sciences of the United States of America 2023 - “...decahistidine affinity tag was included. Coding sequences for H. sapiens (Uniprot accession Q02127), Z. mays (B6U892), A. thaliana (P32746), S. italica (A0A368QCC1), and O. sativa (Q7XKC8) DHODH were initiated at sequence positions M29, D82, A72, E82, and G88, respectively. For the O. sativa sequence, the hexapeptide...”
- Phytophthora infestans Dihydroorotate Dehydrogenase Is a Potential Target for Chemical Control - A Comparison With the Enzyme From Solanum tuberosum
Garavito, Frontiers in microbiology 2019 - “...XP_966023; Pinf, P. infestans , PITG_01913; Stub, S. tuberosum , PGSC0003DMG401016396; Zmay, Zea mays , NP_001152058; Atha, A. thaliana , AAN64025. Expression Constructs Solanum tuberosum cDNA was prepared from commercially available potato plants (Sabanera variety). Total RNA was extracted from frozen mycelia or from 300 mg...”
8ofwA / P9WHL1 Crystal structure of the full-length dihydroorotate dehydrogenase from mycobacterium tuberculosis (see paper)
42% identity, 95% coverage
- Ligand: flavin mononucleotide (8ofwA)
K3ZE81 Dihydroorotate dehydrogenase (quinone), mitochondrial from Setaria italica
37% identity, 71% coverage
- Nitric Oxide Regulates Seedling Growth and Mitochondrial Responses in Aged Oat Seeds
Mao, International journal of molecular sciences 2018 - “...Q0JQ97 AT3G15660 Monothiol glutaredoxin-S1, mitochondrial Oryza sativa subsp. japonic a ns 0.78 ns Nucleotide metabolism K3ZE81 AT5G23300 Dihydroorotate dehydrogenase (quinone), mitochondrial Setaria italica ns ns 0.75 C1-metabolism formate dehydrogenase A0A0D3GGT7 AT5G14780 Formate dehydrogenase, mitochondrial Oryza barthii ns 0.72 0.67 Major CHO metabolism, Degradation, sucrose, Invertases, nautral...”
Q8MXD1 dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) from Toxoplasma gondii (see paper)
TGME49_210790, XP_002371234 dihydroorotate dehydrogenase reveal, putative from Toxoplasma gondii ME49
38% identity, 55% coverage
- Transcriptional changes in Toxoplasma gondii in response to treatment with monensin
Zhai, Parasites & vectors 2020 - “...pathway. Additional file 7 : Figure S5 shows T. gondii PPIs at 24 h where TGME49_210790 (XM_002371193.2), TGME49_266460 (XM_002368694.2), TGME49_297140 (XM_018782303.1), TGME49_275750 (XM_002371561.2) and TGME49_305010 (XM_002370254.1) are some of the proteins that warrant further studies. Fig.8 Transcriptional regulatory network analysis of Toxoplasma gondii . Proteinprotein interaction...”
- “...T. gondii . The PPI analysis revealed several proteins that were downregulated by monensin, including TGME49_210790, TGME49_305010, TGME49_266460 and TGME49_002580. TGME49_002580 is ATPase, AAA family protein, which plays critical roles in various cellular processes [ 44 ]. TGME49_210790 (XM_002371193.2) encodes a putative dihydroorotate dehydrogenase (DHODH), which...”
- Biochemical and molecular characterization of the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase from Toxoplasma gondii.
Hortua, Molecular and biochemical parasitology 2012 - GeneRIF: the pyrimidine biosynthetic enzyme dihydroorotate dehydrogenase from Toxoplasma gondii localized to mitochondria
PYRD_SCHPO / P32747 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOD; DHODase; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Schizosaccharomyces pombe (strain 972 / ATCC 24843) (Fission yeast) (see 3 papers)
ura3 / RF|NP_593317.1 dihydroorotate dehydrogenase Ura3; EC 1.3.3.1 from Schizosaccharomyces pombe (see paper)
NP_593317, SPAC57A10.12c dihydroorotate dehydrogenase Ura3 from Schizosaccharomyces pombe
38% identity, 73% coverage
- function: In the de novo pyrimidine biosynthesis pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate with reduction of flavin and the transfer of electrons to ubiquinone, which is part of the respiratory chain. Does not use fumarate and NAD as electron acceptors.
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN Note=Binds 1 FMN per subunit - CharProtDB Source (per GeneDB): GeneDB_Spombe
- Duplication and Transformation of the Schizosaccharomyces pombe Collection of Deletion Strains
Rai, Methods in molecular biology (Clifton, N.J.) 2018 - “...kinase Ppk38 V2-11-F03 SPBC18H10.06c swd2 Set1C complex subunit Swd2.1 V2-12-G02 SPAC24H6.03 cul3 cullin 3 V2-13-A10 SPAC57A10.12c ura3 dihydroorotate dehydrogenase Ura3 (This was due to the ura selection) V2-15-G03 SPBC2G2.01c liz1 pantothenate transporter Liz1 V2-15-G11 SPCC553.01c dbl2 meiotic chromosome segregation protein Dbl2 V2-16-F06 SPAC25H1.05 meu29 calcium transport...”
- Gene responses to oxygen availability in Kluyveromyces lactis: an insight on the evolution of the oxygen-responding system in yeast
Fang, PloS one 2009 - “...bayanus . Sequences as queries (NCBI accession numbers): UAP (CAA50681), UOX (P78609), DHODases (NP_012706 and NP_593317). Oxygen-dependent regulation of KlHEM13 , KlHYP2 ( ANB1 ) and KlCOX5A ( 5B ) is not mediated by KlROX1 in K. lactis The analysis of possible ROX1 orthologs found in...”
- Proteasome regulation of petite-negativity in fission yeast.
Amberg, bioRxiv : the preprint server for biology 2024 - “...shock protein, Hsp70 family, ribosome associated Sks2 O94514 nop56 0.24 0.029 U3 snoRNP-associated protein Nop56 P32747 ura3 0.23 0.025 mitochondrial dihydroorotate dehydrogenase Ura3 P40373 his1 0.23 0.023 ATP phosphoribosyltransferase Q09755 SPAC24H6.10c 0.22 0.029 phospho-2-dehydro-3-deoxyheptonate aldolase P36620 ilv1 0.20 0.049 acetolactate synthase catalytic subunit Q10499 aif1 0.27...”
- Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis
Bouwknegt, Fungal biology and biotechnology 2021 - “...orthologs were retrieved from the Uniprot database for Sch. pombe (SpUra3; Uniprot KB accession number P32747); L. kluyveri (LkUra9; Q6V3W9), O. parapolymorpha (OpUra9; W1QJ07), K. marxianus (KmUra9; Q6SZS6), E. coli (EcUra9; P0A7E1), D. bruxellensis (DbUra9; I2JUI3), Sch. japonicus (SjUra9; B6JXQ5), A. robustus (ArUra9; A0A1Y1XN91), N. californiae...”
G8BA68 Dihydroorotate dehydrogenase (quinone), mitochondrial from Candida parapsilosis (strain CDC 317 / ATCC MYA-4646)
CPAR2_804900 uncharacterized protein from Candida parapsilosis
39% identity, 68% coverage
G4VFD7 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Schistosoma mansoni (see 2 papers)
XP_018651255 dihydroorotate dehydrogenase from Schistosoma mansoni
40% identity, 85% coverage
6uy4A / G4VFD7 Crystal structure of dihydroorotate dehydrogenase from schistosoma mansoni (see paper)
39% identity, 92% coverage
- Ligands: 2-[(4-fluorophenyl)amino]-3-hydroxynaphthalene-1,4-dione; flavin mononucleotide (6uy4A)
HVO_2943 dihydroorotate oxidase from Haloferax volcanii DS2
39% identity, 94% coverage
PBANKA_010210 dihydroorotate dehydrogenase, putative from Plasmodium berghei ANKA
37% identity, 61% coverage
- Identification and Mechanistic Understanding of Dihydroorotate Dehydrogenase Point Mutations in Plasmodium falciparum that Confer in Vitro Resistance to the Clinical Candidate DSM265
White, ACS infectious diseases 2019 - “...NCBI protein data-base: P. falciparum (PF3D7_0603300), P. vivax (PVX_113330), P. cynomolgi ( PCYB_115310), P. berghei (PBANKA_010210), Human (NP_001352.2), dog (XP_853399.2), rat (NP_001008553.1) and mouse (NP_064430.1), The sequence alignment was generated using the web server http://www.ebi.ac.uk and CLUSTAL O(1.2.1) multiple sequence alignment program. Pf DHODH Residues 282519...”
- Host reticulocytes provide metabolic reservoirs that can be exploited by malaria parasites
Srivastava, PLoS pathogens 2015 - “...II (PBANKA_140670), act : Aspartate carbamoyltransferase (PBANKA_135770), dhoase : Dihydroorotase (PBANKA_133610), dhodh : Dihydroorotate dehydrogenase (PBANKA_010210), oprt : Orotate phosphoribosyltransferase (PBANKA_111240), ompdc : Orotidine 5-monophosphate decarboxylase (PBANKA_050740). (Also see Fig B in S1 Text for gene deletion strategy and confirmation) Metabolites involved in TCA cycle and...”
- “...carbamoyltransferase ( act ) (PBANKA_135770), dihydroorotase ( dhoase ) (PBANKA_133610), dihydroorotate dehydrogenase ( dhodh ) (PBANKA_010210), orotate phosphoribosyltransferase ( oprt ) (PBANKA_111240) and orotidine 5-monophosphate decarboxylase ( ompdc ) (PBANKA_050740). While the first four enzymes in this pathway were refractory to deletion, the last two enzymes...”
PYRD_LACK1 / Q6V3W9 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOD; DHODase; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Lachancea kluyveri (strain ATCC 58438 / CBS 3082 / BCRC 21498 / NBRC 1685 / JCM 7257 / NCYC 543 / NRRL Y-12651) (Yeast) (Saccharomyces kluyveri) (see paper)
40% identity, 66% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor.
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN (Binds 1 FMN per subunit.) - Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis
Bouwknegt, Fungal biology and biotechnology 2021 - “...(DHOD Class I-A, UniProt KB accession number Q7Z892) and LkUra9 (DHOD Class II, accession number Q6V3W9) amino acid sequences as queries Sequence comparison with LkUra1 provided no evidence for presence of a Class-I DHOD in the Neocallimastigomycetes Piromyces finnis, Neocallimastix californiae and A. robustus . Instead,...”
- “...orthologs. An orthology search using L. kluyveri Class-II dihydroorotate dehydrogenase (LkUra9; UniProt KB accession number: Q6V3W9) as query yielded 331 fungal and 73 bacterial Ura9 orthologs (Additional file 1 ). These Ura9 orthologs were used to calculate a maximum-likelihood phylogenetic tree which was rooted using the...”
7l01B / Q08210 Crystal structure of plasmodium falciparum dihydroorotate dehydrogenase bound with inhibitor dsm782 (n-(1-(5-cyano-1h-pyrazol- 3-yl)ethyl)-3-methyl-4-(1-(6-(trifluoromethyl)pyridin-3-yl) cyclopropyl)-1h-pyrrole-2-carboxamide) (see paper)
40% identity, 71% coverage
- Ligands: n-[(1r)-1-(5-cyano-1h-pyrazol-3-yl)ethyl]-3-methyl-4-{1-[6-(trifluoromethyl)pyridin-3-yl]cyclopropyl}-1h-pyrrole-2-carboxamide; flavin mononucleotide (7l01B)
PCHAS_0102800 dihydroorotate dehydrogenase, putative from Plasmodium chabaudi chabaudi
39% identity, 60% coverage
- The malaria parasite has an intrinsic clock
Rijo-Ferreira, Science (New York, N.Y.) 2020 - “...binding protein (PCHAS_0101100), elongation factor G (PCHAS_0101900), transcription factor AP2 (PCHAS_0103600) and DHODH, dihydroorotate dehydrogenase (PCHAS_0102800). K . Host liver gene expression of clock genes and two metabolic genes. Each time point is composed of 34 mice per condition, with line connecting them being only for...”
HP1011 dihydroorotate dehydrogenase (pyrD) from Helicobacter pylori 26695
35% identity, 97% coverage
CNAG_02794 dihydroorotate dehydrogenase (fumarate) from Cryptococcus neoformans var. grubii H99
37% identity, 60% coverage
- Membrane Integrity Contributes to Resistance of Cryptococcus neoformans to the Cell Wall Inhibitor Caspofungin
Moreira-Walsh, mSphere 2022 - “...encoded by CDC50 ( CNAG_06465 ), and a dihydroorotate dehydrogenase (DHOH), encoded by URA1 ( CNAG_02794 ), that both play a role in resistance to caspofungin ( 8 , 10 ). More recently, the Cdc50 protein was proposed to interact with a calcium channel protein to...”
- Characterization of additional components of the environmental pH-sensing complex in the pathogenic fungus Cryptococcus neoformans
Pianalto, The Journal of biological chemistry 2018 - “...CNAG_04111 CNAG_00092 CNAG_03606 CNAG_03270 CNAG_02372 CNAG_00522 CNAG_02794 CNAG_01083 CNAG_01961 CNAG_06813 Gene product C. neoformans Nap1 and pH sensing...”
- De Novo Pyrimidine Biosynthesis Connects Cell Integrity to Amphotericin B Susceptibility in Cryptococcus neoformans
Banerjee, mSphere 2016 - “...15 , 18 , 22 ). The predicted annotation of the C.neoformans var. grubii DHODH (CNAG_02794) appears to lack the N-terminal extension present in all other eukaryotic family 2 DHODH enzymes analyzed ( Fig.1A ), with an N terminus similar in length to that of prokaryotic...”
W1QJ07 Dihydroorotate dehydrogenase (quinone), mitochondrial from Ogataea parapolymorpha (strain ATCC 26012 / BCRC 20466 / JCM 22074 / NRRL Y-7560 / DL-1)
38% identity, 74% coverage
Q6SZS6 Dihydroorotate dehydrogenase (quinone), mitochondrial from Kluyveromyces marxianus
38% identity, 74% coverage
- Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis
Bouwknegt, Fungal biology and biotechnology 2021 - “...KB accession number P32747); L. kluyveri (LkUra9; Q6V3W9), O. parapolymorpha (OpUra9; W1QJ07), K. marxianus (KmUra9; Q6SZS6), E. coli (EcUra9; P0A7E1), D. bruxellensis (DbUra9; I2JUI3), Sch. japonicus (SjUra9; B6JXQ5), A. robustus (ArUra9; A0A1Y1XN91), N. californiae (NcUra9; A0A1Y2ELQ6) and P. finnis (PfUra9; A0A1Y1VDI5) and C. reversa (CmUra9; A0A2G5BHD4),...”
- Genome-wide metabolic (re-) annotation of Kluyveromyces lactis
Dias, BMC genomics 2012 - “...coli (strain K12) Bacteria beta-galactosidase KLLA0C00715g P0A9H8 2.1.1.79 Escherichia coli O6 Bacteria cyclopropane-fatty-acyl-phospholipid synthase KLLA0C09240g Q6SZS6 1.3.5.2 Kluyveromyces marxianus Eukaryota dihydroorotate dehydrogenase KLLA0C11803g O74492 3.5.2.17 Schizosaccharomyces pombe Eukaryota hydroxyisourate hydrolase KLLA0C19107g Q9P903 3.5.2.2 Saccharomyces kluyveri Eukaryota dihydropyrimidinase KLLA0D00330g P07337 3.2.1.21 Kluyveromyces marxianus Eukaryota beta-glucosidase KLLA0D00506g O59832...”
PYRD_CANAL / Q874I4 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOD; DHODase; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Candida albicans (strain SC5314 / ATCC MYA-2876) (Yeast) (see paper)
Q874I4 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Candida albicans (see paper)
URA1 / GB|AAO74621.1 dihydroorotate dehydrogenase, mitochondrial (DHOdehase) (DHODase) (DHOD); EC 1.3.5.2 from Candida albicans (see paper)
37% identity, 74% coverage
- function: In the de novo pyrimidine biosynthesis pathway, catalyzes the stereospecific oxidation of (S)-dihydroorotate to orotate with reduction of flavin and the transfer of electrons to ubiquinone, which is part of the respiratory chain. Does not use fumarate and NAD as electron acceptors.
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN (Binds 1 FMN per subunit.) - CharProtDB CGD description: Dihydroorotate dehydrogenase (DHODH); enzyme of de novo pyrimidine biosynthesis; putative bipartite mitochondrial targeting motif, membrane spanning region; transcription is regulated upon yeast-hyphal switch, or by Nrg1p, Mig1p, Tup1p
- Identifying Potential Molecular Targets in Fungi Based on (Dis)Similarities in Binding Site Architecture with Proteins of the Human Pharmacolome
Bedoya-Cardona, Molecules (Basel, Switzerland) 2023 - “...93 A0A2H0ZU47 83 G8BDX2 80 Q5KMR8 90 A0A0D2XCF2 87 DHOdehase Q02127 F0UDX1 87 Q4X169 87 Q874I4 100 G8BA68 100 Q5KK62 100 Histone deacetylase 7 Q8WUI4 F0UVW7 85 Q4WE71 75 Q5A960 80 G8BBK1 80 Q5KL48 80 A0A0D2YC83 72.7 Thymidylate synthase P04818 F0URV8 84 Q4W9N9 88 A0A2H0ZCG7 88...”
- “...77 P43063 73 G8BG79 73 A0A0D2Y7P8 71 Thioredoxin reductase 1 Q16881 Q4WRK8 73.9 DHOdehase Q02127 Q874I4 84 G8BA68 84 Q5KK62 74 Tyrosine kinase CSK P41240 A0A1D8PR87 80 G8BKZ2 80 ROCK-I Q13464 Q6FP74 71 Q5KEJ1 70 BCNG-2 Q9UL51 Q59V20 70,6 Proto-oncogene c-Src P12931 Q9Y7W4 70 NTK38 P51813...”
PVX_113330 dihydroorotate dehydrogenase, mitochondrial precursor, putative from Plasmodium vivax
35% identity, 57% coverage
Q5KK62 Dihydroorotate dehydrogenase (quinone), mitochondrial from Cryptococcus neoformans var. neoformans serotype D (strain JEC21 / ATCC MYA-565)
37% identity, 61% coverage
PYRD_PLAF7 / Q08210 Dihydroorotate dehydrogenase (quinone), mitochondrial; DHOdehase; Dihydroorotate oxidase; EC 1.3.5.2 from Plasmodium falciparum (isolate 3D7) (see 3 papers)
Q08210 dihydroorotate dehydrogenase (quinone) (EC 1.3.5.2) from Plasmodium falciparum (see 10 papers)
PF3D7_0603300, XP_966023 dihydroorotate dehydrogenase from Plasmodium falciparum 3D7
36% identity, 48% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with quinone as electron acceptor
catalytic activity: (S)-dihydroorotate + a quinone = orotate + a quinol (RHEA:30187)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Monomer. - Exploration and characterization of the antimalarial activity of cyclopropyl carboxamides that target the mitochondrial protein, cytochrome b
Awalt, European journal of medicinal chemistry 2024 - “...Notably, this region of chromosome 6 encodes a putative mitochondrial chaperone BCS1 (PF3D7_0603200) and DHODH (PF3D7_0603300). This amplification event in DHODH has been seen in other inhibitors of cyt b and is likely a compensatory mechanism to overcome disruption to the mitochondria electron transport chain [...”
- Diverse evolutionary pathways challenge the use of collateral sensitivity as a strategy to suppress resistance
Mandt, eLife 2023 - “...Designation Source or reference Identifiers Additional information Gene ( Plasmodium falciparum ) dhodh; Pfdhodh PlasmoDB PF3D7_0603300 Strain, strain background ( Plasmodium falciparum ) 3D7 A10 Goldberg lab at Washington University, St. Louis, MO, USA 3D7 A10; 3D7_A10 Cowell et al., 2018 Cell line ( Plasmodium falciparum...”
- Susceptibility of Ugandan Plasmodium falciparum Isolates to the Antimalarial Drug Pipeline
Kreutzfeld, Microbiology spectrum 2023 - “...encoded by PF3D7_0319700), acetyl-CoA synthetase (PfAcAS; PF3D7_0627800), cytochrome b (PfCYTB; Pf3D7_MIT02300, mal_mito_3), dihydroorotate dehydrogenase (PfDHODH; PF3D7_0603300), elongation factor 2 (PfeEF2; PF3D7_1451100), lysyl-tRNA synthetase (PfKRS; PF3D7_1350100), phenylalanyl-tRNA ligase alpha subunit (PfFRS; PF3D7_0109800), plasmepsin X (PfPMX; PF3D7_0808200), prodrug activation and resistance esterase (PfPARE; PF3D7_0709700), and the V-type H+...”
- Antimalarial drug discovery: progress and approaches
Siqueira-Neto, Nature reviews. Drug discovery 2023 - “...ribosome Approved Essential for protein synthesis Macrolide antibiotics (such as azithromycin) 187 Dihydroorotate dehydrogenase; DHODH (PF3D7_0603300) Phase II trials Generates pyrimidine precursors for DNA synthesis DSM265 81 , 188 191 PfATPase4; ATP4 (PF3D7_1211900) Phase II trials Maintains sodium homeostasis in parasite blood stages SJ733; cipargamin 62...”
- New targets for antimalarial drug discovery
Guerra, Current opinion in microbiology 2022 - “...DHFR-TS (PF3D7_0417200) Bifunctional dihydrofolate reductase-thymidylate synthase MMV027634(TS), pyrimethamine (DHFR), P218 3QGT [ 56 ] DHODH (PF3D7_0603300) Dihydroorotate dehydrogenase DSM265, BRD7539, BRD9185, DSM1 4CQ8 [ 10 , 57 , 58 ] DPCK (PF3D7_1443700) Dephospho-CoA kinase, putative Amb3377585, STK740987 [ 59 61 ] eEF2 (PF3D7_1451100) Elongation factor 2...”
- Characterization of the dynamics of Plasmodium falciparum deoxynucleotide-triphosphate pool in a stage-specific manner
Babai, Scientific reports 2022 - “...Adenosine-5-monophosphate deaminase (AMPD) PF3D7_1308200 Carbamoyl-phosphate synthetase II (CPSII) PF3D7_1344800 Aspartate transcarbamoylase (ATCase) PF3D7_1472900 Dihydroorotase (DHOase) PF3D7_0603300 Dihydroorotate dehydrogenase (DHODH) PF3D7_0512700 Orotate phosphoribosyl transferase (OPRT) PF3D7_1023200 Orotidine-5-monophosphate decarboxylase (ODC) PF3D7_1366500 Nucleoside diphosphate kinase (NDPK) PF3D7_1410200 Cytidine-5-triphosphate synthase (CTPS) PF3D7_1437200 Ribonucleotide reductase large subunit (RNR R1) PF3D7_1405600 Ribonucleotide...”
- Atypical Molecular Basis for Drug Resistance to Mitochondrial Function Inhibitors in Plasmodium falciparum
Painter, Antimicrobial agents and chemotherapy 2021 (secret) - Genomic and Genetic Approaches to Studying Antimalarial Drug Resistance and Plasmodium Biology
Okombo, Trends in parasitology 2021 - “...in vitro resistance-conferring mutations to P. falciparum prodrug activation and resistance esterase (PF3D7_0709700), dihydroorotate dehydrogenase (PF3D7_0603300), the 20S proteasome 5 subunit (PF3D7_1011400), or coronin (PF3D7_1251200), respectively ( Table 2 ). Selections with the imidazolopiperazines KAF156 and GNF179 also associated resistance with SNPs in the cyclic amine...”
- “..., NCT02573857 , NCT02123290 a ) Dihydroorotate dehydrogenase (PfDHODH) Mitochondrion Pyrimidine biosynthesis Dd2, K1 pfdhodh (PF3D7_0603300) [ 58 ] GNF-Pf-5640 Hexahydroquinoline Pre-clinical Unknown Unknown Unknown Dd2-B2 pfmdr1 (PF3D7_0523000) [ 65 ] KAF156 and GNF179 Imidazolopiperazines KAF156: Phase II ( NCT01753323 , NCT04546633 , NCT03167242 a );...”
- More
- A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi
Garrett, Frontiers in microbiology 2023 - “...M1BCR0), Phytophthora infestans DHODH (UniProtID: I7EMP0), Arabidopsis thaliana DHODH (UniProtID: P32746), Plasmodium falciparum DHODH (UniProtID: Q08210), and Homo sapiens DHODH (UniProtID: Q02127) ( Supplementary Figure S1 ), yielding residue 21 from EhDHODH as an appropriate start site. Classification of the excluded 20-residue sequence as a mitochondrial...”
- Multistage antiplasmodial activity of hydroxyethylamine compounds, in vitro and in vivo evaluations
Sharma, RSC advances 2020 - “...CDK calcium-dependent protein kinase 1 P62344; GR glutathione reductase Q94655; DOD dihydroorotate dehydrogenase (quinone), mitochondrial Q08210; FR ferredoxin-NADP reductase, apicoplast C6KT68; DRTS bifunctional dihydrofolate reductase-thymidylate synthase P13922. The analyses of the active site of the crystal structure of PLM (PDB ID 1LEE ) showed that the...”
- Open Source Drug Discovery: Highly Potent Antimalarial Compounds Derived from the Tres Cantos Arylpyrroles
Williamson, ACS central science 2016 - “...significance, carboxy-terminal domain RNA polymerase II polypeptide A small phosphatase 1 (Q8I3U9), dihydroorotate dehydrogenase (DHODH, Q08210), SUMO-activating enzyme subunit 2 (Q8I553) and 1 (Q8IHS2), and cyclin-dependent kinase 1 (P61075). To kick-start the process of exploring these predictions, this compound and 24 others representative of both the...”
PCYB_115310 dihydroorotate dehydrogenase mitochondrial precursor from Plasmodium cynomolgi strain B
35% identity, 82% coverage
B6JXQ5 Dihydroorotate dehydrogenase (quinone), mitochondrial from Schizosaccharomyces japonicus (strain yFS275 / FY16936)
36% identity, 73% coverage
6b8sB / B5Z6I2 Crystal structure of dihydroorotate dehydrogenase from helicobacter pylori with bound fmn
34% identity, 100% coverage
- Ligand: flavin mononucleotide (6b8sB)
F0UDX1 Orotate reductase from Ajellomyces capsulatus (strain H88)
32% identity, 57% coverage
Pc22g21410 uncharacterized protein from Penicillium rubens
30% identity, 58% coverage
AFUA_2G11010, Afu2g11010 dihydroorotate reductase PyrE, putative from Aspergillus fumigatus Af293
Q4X169 Dihydroorotate dehydrogenase (quinone), mitochondrial from Aspergillus fumigatus (strain ATCC MYA-4609 / CBS 101355 / FGSC A1100 / Af293)
31% identity, 53% coverage
BLGT_RS02540 quinone-dependent dihydroorotate dehydrogenase from Bifidobacterium longum subsp. longum GT15
30% identity, 88% coverage
- Oxidative Stress Response of Probiotic Strain Bifidobacterium longum subsp. longum GT15
Averina, Foods (Basel, Switzerland) 2023 - “...9 Class_I_pyridine_nucleotide-disulfideoxidoreductase BLGT_RS08540 9.02 2.79 1.34 10 NADH_oxidase BLGT_RS09280 0.74 0.72 3.74 11 Dihydroorotate dehydrogenase BLGT_RS02540 6.59 9.02 8.68 *: Fold ratio to the abundance across different samples before and after oxidative stress. foods-12-03356-t002_Table 2 Table 2 Comparative data from proteomic and transcriptomic analyses of cells...”
pyrE dihydroorotate dehydrogenase; EC 1.3.1.14 from Emericella nidulans (see 2 papers)
Q12610 Dihydroorotate dehydrogenase (quinone), mitochondrial from Emericella nidulans
33% identity, 51% coverage
BBMN68_979 quinone-dependent dihydroorotate dehydrogenase from Bifidobacterium longum subsp. longum BBMN68
30% identity, 88% coverage
IHV18_09925 quinone-dependent dihydroorotate dehydrogenase from Bifidobacterium breve
29% identity, 88% coverage
- Bifidobacterium breve PRL2020: Antibiotic-Resistant Profile and Genomic Detection of Antibiotic Resistance Determinants
Di, Microorganisms 2023 - “...regulator IHV18_09915 15,276 17,553 1 transglycosylase domain-containing protein IHV18_09920 17,697 19,002 1 NADH:flavin oxidoreductase/NADH oxidase IHV18_09925 19,146 20,298 1 quinone-dependent dihydroorotate dehydrogenase IHV18_09930 20,602 21,406 1 DeoR/GlpR transcriptional regulator IHV18_09935 galT 21,411 22,662 1 galactose-1-phosphate uridylyltransferase IHV18_09940 galK 22,679 23,930 1 galactokinase IHV18_09945 24,698 24,971 1...”
MGG_08814 dihydroorotate dehydrogenase from Pyricularia oryzae 70-15
29% identity, 62% coverage
- The target site of the novel fungicide quinofumelin, Pyricularia oryzae class II dihydroorotate dehydrogenase
Higashimura, Journal of pesticide science 2022 - “...010ppm. 2.Effect of quinofumelin on the inhibitory activity of recombinant PoDHODH II The gene PoPYR4 (MGG_08814) was found from the P. oryzae gene database at NCBI (https://www.ncbi.nlm.nih.gov/gene/2678980). It potentially encoded a 514-amino acid polypeptide possessing a DHOD II-like region (https://www.ncbi.nlm.nih.gov/Structure/cdd/cddsrv.cgi?uid=240089), and the amino acid sequence of...”
- “...PyrE with 61% identity. To determine the enzymatic function of PoPYR4 , the gene PoPYR4 (MGG_08814) was subcloned, introduced into the expression vector, and then expressed in E. coli . The enzymatic activity of class II dihydroorotate dehydrogenase (quinone type) of the purified PoPYR4 protein was...”
R1EHA9 Dihydroorotate dehydrogenase from Emiliania huxleyi
29% identity, 68% coverage
- A bacterial quorum sensing signal is a potent inhibitor of de novo pyrimidine biosynthesis in the globally abundant Emiliania huxleyi
Garrett, Frontiers in microbiology 2023 - “...Approximation Type. Heterologous EhDHODH expression and purification The sequence coding for the enzyme DHODH (UniProtID: R1EHA9) from E. huxleyi CCMP1516 genome was used for heterologous expression. Class 2 DHODHs previously expressed and purified often have the N-terminal transmembrane domain and mitochondrial localization region truncated, enhancing solubility...”
- “...et al., 2021 ) was queried with the non-truncated amino acid sequence of EhDHODH (UniProtID: R1EHA9), and the resulting structure was used as the basis for molecular docking. The substrate DHO, cofactors FMN and decylubiquinone, and putative inhibitors HHQ and brequinar were docked to the predicted...”
DET1372 dihydroorotate dehydrogenase from Dehalococcoides ethenogenes 195
31% identity, 85% coverage
PYRDB_DESRM / A4J560 Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit; DHOD B; DHODase B; DHOdehase B; Dihydroorotate oxidase B; Orotate reductase (NADH); EC 1.3.1.14 from Desulforamulus reducens (strain ATCC BAA-1160 / DSM 100696 / MI-1) (Desulfotomaculum reducens) (see paper)
Dred_1686 dihydroorotate dehydrogenase family protein from Desulfotomaculum reducens MI-1
30% identity, 80% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor.
function: Together with PyrK, also forms a metal reductase complex able to reduce Fe(III)-chelates to Fe(II)-chelates, as well as soluble Cr(VI) and U(VI), using NADH as electron donor. To a lesser extent, can also use NADPH as an electron donor. Is unable to reduce riboflavin and FMN with NADH as electron donor. May have an in vivo role in metal reduction in D.reducens, which is an organism capable of reducing contaminant heavy metals and radionuclides.
catalytic activity: (S)-dihydroorotate + NAD(+) = orotate + NADH + H(+) (RHEA:13513)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Heterotetramer of 2 PyrK and 2 PyrD type B subunits (By similarity). However, the metal reductase complex seems to be composed of a heterooctamer of 4 PyrK and 4 PyrD subunits (PubMed:25389064). - Identification of proteins capable of metal reduction from the proteome of the Gram-positive bacterium Desulfotomaculum reducens MI-1 using an NADH-based activity assay
Otwell, Environmental microbiology 2015 - “...(Dred_2421) and a protein complex composed of oxidoreductase FAD/NAD(P)-binding subunit (Dred_1685) and dihydroorotate dehydrogenase 1B (Dred_1686). Dred_2421 was identified in the soluble proteome and is predicted to be a cytoplasmic protein. Dred_1685 and Dred_1686 were identified in both the soluble as well as the insoluble protein...”
- “...band by at least two unique peptides including oxidoreductase FAD/NAD(P)-binding subunit (Dred_1685), dihydroorotate dehydrogenase 1B (Dred_1686), 4Fe-4S ferredoxin (Dred_0137), and pyruvate flavodoxin/ferredoxin oxidoreductase domain-containing protein (Dred_0047) ( Supplementary Table 1b ). Specific iron reduction activity of active fractions identified following separation of the soluble proteome is...”
- Molecular dissection of a putative iron reductase from Desulfotomaculum reducens MI-1
Li, Biochemical and biophysical research communications 2015 - “...metal reductases, including a soluble protein, Dred_2421, and a potentially membrane-associated protein complex, Dred_1685 and Dred_1686 [ 14 ]. Dred_2421 is annotated as a member of the NADH:flavin oxidoreductase (NFO) family (pfam00724) [ 16 ]. However, this annotation is not based on the full length protein...”
TDE0982 dihydroorotate dehydrogenase/oxidoreductase, FAD-binding from Treponema denticola ATCC 35405
26% identity, 41% coverage
LM6179_2603 dihydroorotate dehydrogenase from Listeria monocytogenes 6179
27% identity, 87% coverage
Q7Z892 Dihydroorotate dehydrogenase (fumarate) from Lachancea kluyveri (strain ATCC 58438 / CBS 3082 / BCRC 21498 / NBRC 1685 / JCM 7257 / NCYC 543 / NRRL Y-12651)
26% identity, 88% coverage
- Identification of fungal dihydrouracil-oxidase genes by expression in Saccharomyces cerevisiae
Bouwknegt, Antonie van Leeuwenhoek 2022 - “...for orthologs of Class I-A dihydroorotate dehydrogenases using Lachancea kluyveri LkUra1 (UniProt KB accession number: Q7Z892) as query resulted in 203 proteins (Dataset S01). Sequence identifiers corresponding to the phyla Basidiomycota, Ascomycota and Mucoromycota are indicated in color. Sequences that were functionally analysed in this study,...”
- “...1,754,192) and Piromyces sp. E2 (taxid 73,868). The Ura1 sequence of Lachancea kluyveri CBS3082 (LkUra1, Q7Z892; Gojkovi et al. 2004 ) was used as query for a HMMER search of these sequences (Mistry et al. 2013 ). Cutoff values of 1e-5 were used, and hits were...”
- Class-II dihydroorotate dehydrogenases from three phylogenetically distant fungi support anaerobic pyrimidine biosynthesis
Bouwknegt, Fungal biology and biotechnology 2021 - “...(559292) were subjected to blastp searches using LkUra1 (DHOD Class I-A, UniProt KB accession number Q7Z892) and LkUra9 (DHOD Class II, accession number Q6V3W9) amino acid sequences as queries Sequence comparison with LkUra1 provided no evidence for presence of a Class-I DHOD in the Neocallimastigomycetes Piromyces...”
- “...to protein blast search in NCBI [ 92 ], using LkUra1 (UniProt KB accession number Q7Z892) and LkUra9 (Q6V3W9) as queries and applying default settings. Similarly, the proteomes of A. robustus , P. finnis , N. californiae , Sch. japonicus and that of D. bruxellensis were...”
pyrD / P25996 dihydroorotate dehydrogenase (catalytic subunit) (EC 1.3.1.14) from Bacillus subtilis (strain 168) (see 2 papers)
PYRDB_BACSU / P25996 Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit; DHOD B; DHODase B; DHOdehase B; Dihydroorotate oxidase B; Orotate reductase (NADH); EC 1.3.1.14 from Bacillus subtilis (strain 168) (see paper)
pyrD / GB|CAB13428.1 dihydroorotate oxidase, catalytic subunit; EC 1.3.3.1 from Bacillus subtilis (see paper)
BSU15540 dihydroorotate dehydrogenase 1B from Bacillus subtilis subsp. subtilis str. 168
26% identity, 84% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor
catalytic activity: (S)-dihydroorotate + NAD(+) = orotate + NADH + H(+) (RHEA:13513)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Heterotetramer of 2 PyrK and 2 PyrD type B subunits. - rocF affects the production of tetramethylpyrazine in fermented soybeans with Bacillus subtilis BJ3-2
Liu, BMC biotechnology 2022 - “...Down BSU15560 2006.169 21.44 6.54 4.81E-12 1.46E-09 Down BSU11990 94,545.251 1019.604 6.53 2.08E-12 9.01E-10 Down BSU15540 1912.399 23.571 6.34 1.31E-11 3.69E-09 Down BSU15490 268.461 3.331 6.29 2.98E-10 7.78E-08 Down BSU37350 2,666,228.43 69,847.529 5.25 8.15E-09 1.65E-06 Down BSU01620 379.143 10.008 5.23 2.88E-08 5.01E-06 Down BSU37770 3233.527 117.411...”
- The Blueprint of a Minimal Cell: MiniBacillus
Reuß, Microbiology and molecular biology reviews : MMBR 2016 - “...6.3.5.5 1JDB E. coli pyrB pyrC pyrD BSU15490 BSU15500 BSU15540 No No No 2.1.3.2 3.5.2.3 1.3.3.1 3R7D 3MPG 1EP1 B. subtilis B. anthracis Lactococcus lactis...”
- Regulon of the N-acetylglucosamine utilization regulator NagR in Bacillus subtilis
Bertram, Journal of bacteriology 2011 - “...pyrD pyrE pyrF pyrK BSU33950 BSU15510 BSU15520 BSU15500 BSU15540 BSU15560 BSU15550 BSU15530 Genes downregulated in the yvoA mutant compared to parental strain...”
lmo1833 highly similar to dihydroorotase dehydrogenase from Listeria monocytogenes EGD-e
27% identity, 87% coverage
LBA1384 dihydroorotate dehydrogenase B, catalytic unit from Lactobacillus acidophilus NCFM
27% identity, 79% coverage
LOTGIDRAFT_233044 hypothetical protein from Lottia gigantea
27% identity, 29% coverage
- Proteomics Studies on the three Larval Stages of Development and Metamorphosis of Babylonia areolata
Shen, Scientific reports 2018 - “...protein 4-like 1445.64 789 c264438_g1 spectrin alpha chain-like isoform X7 1513.82 778 c267460_g1 ghypothetical protein LOTGIDRAFT_233044 1642.48 777 c258721_g2 vigilin-like 1579.69 773 Table 3 The number of differential proteins. V/III VI/III VI/V Qualitative difference Quantitative difference Qualitative difference Quantitative difference Qualitative difference Quantitative difference Up-regulation 214...”
- “...4-like protein binding c264438_g1 spectrin alpha chain-like isoform X7 calcium ion binding c267460_g1 hypothetical protein LOTGIDRAFT_233044 calcium ion binding c258721_g2 vigilin-like RNA binding c265676_g3 collagen alpha-3(VI) chain-like isoform X9 protein binding c264079_g1 cilia- and flagella-associated protein 58-like protein binding GO Enrichment Analysis of DEPs The GO...”
B5X54_RS07485 dihydroorotate dehydrogenase from Caldicellulosiruptor bescii
27% identity, 85% coverage
- Gene targets for engineering osmotolerance in Caldicellulosiruptor bescii
Sander, Biotechnology for biofuels 2020 - “...B5X54_RS04290 Site-specific recombinase XerD No Deletion/missing B5X54_RS07480 Dihydroorotate dehydrogenase electron transfer subunit No Partial deletion B5X54_RS07485 Dihydroorotate dehydrogenase (NAD+) catalytic subunit, pyrD No Deletion/missing B5X54_RS07490 Probable phosphoglycerate mutase No Deletion/missing B5X54_RS07495 Orotate phosphoribosyltransferase, pyrE No Deletion/missing B5X54_RS07500 Double zinc ribbon No Deletion/missing B5X54_RS07505 Amino acid/amide ABC...”
- “...based genetic modifications possible. PCR amplification of a region spanning the genomic region between genes B5X54_RS07485 and B5X54_RS07515 resulted in a single product of expected size when using genomic DNA from strain JWCB018 (an auxotrophic derivative of strain JWCB005) as template, though no PCR product could...”
CS401_RS10030 dihydroorotate dehydrogenase from Fusobacterium vincentii
26% identity, 80% coverage
PYRDB_ENTFA / P0DH74 Dihydroorotate dehydrogenase B (NAD(+)), catalytic subunit; DHOD B; DHODase B; DHOdehase B; Dihydroorotate oxidase B; Orotate reductase (NADH); EC 1.3.1.14 from Enterococcus faecalis (strain ATCC 700802 / V583) (see paper)
EF1714 dihydroorotate dehydrogenase from Enterococcus faecalis V583
25% identity, 87% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with NAD(+) as electron acceptor
catalytic activity: (S)-dihydroorotate + NAD(+) = orotate + NADH + H(+) (RHEA:13513)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Heterotetramer of 2 PyrK and 2 PyrD type B subunits. - Functional studies of E. faecalis RNase J2 and its role in virulence and fitness
Gao, PloS one 2017 - “...3.13 0.017 ef1712 pyrE orotate phosphoribosyltransferase 5.88 0.019 ef1713 pyrF orotidine 5`-phosphate decarboxylase 6.25 0.004 ef1714 pyrD-2 dihydroorotate dehydrogenase 8.33 0.030 ef1715 pyrDII electron transfer protein, putative 5.88 0.037 ef1716 pyrAb carbamoyl-phosphate synthase 10.00 0.043 ef1717 pyrAa carbamoyl-phosphate synthase 9.09 0.043 ef1718 pyrC dihydroorotase 6.25 0.047...”
- Nutritional control of antibiotic resistance via an interface between the phosphotransferase system and a two-component signaling system
Snyder, Antimicrobial agents and chemotherapy 2014 - “...To construct a plasmid expressing C-terminally Strep-tagged EF1714, Gateway technology (Invitrogen) was used. E. faecalis open reading frames (ORFs) of interest...”
- “...reaction between the destination vector pHH6 and the EF1714 entry clone. All Gateway recombination reactions were transformed into One Shot Mach 1 T1...”
- Transcriptome, proteome, and metabolite analyses of a lactate dehydrogenase-negative mutant of Enterococcus faecalis V583
Mehmeti, Applied and environmental microbiology 2011 - “...EF1713 pyrF Orotidine 5-phosphate decarboxylase EF1714 pyrD2 Dihydroorotate dehydrogenase EF1718 pyrC Dihydroorotase EF1719 pyrB Aspartate carbamoyltransferase...”
- “...mutant (Table 3), but the transcriptional data for the EF1714, EF1715, and EF1716 genes were more doubtful due to poor P values. Also, the EF0677 gene, encoding...”
- Transcriptional response of Enterococcus faecalis V583 to erythromycin
Aakra, Antimicrobial agents and chemotherapy 2005 - “...EF0224 EF0225 EF0226 EF0970 EF1694 EF2395 EF2397 EF2473 EF2474 EF2679 EF2731 EF3070 EF0285 EF1714 EF1718 EF2362 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...”
URA1 / P28272 dihydroorotate dehydrogenase subunit (EC 1.3.98.1) from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (see 3 papers)
PYRD_YEAST / P28272 Dihydroorotate dehydrogenase (fumarate); DHOD; DHODase; DHOdehase; Dihydroorotate oxidase; EC 1.3.98.1 from Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) (see 7 papers)
NP_012706 dihydroorotate dehydrogenase from Saccharomyces cerevisiae S288C
NP_012706, YKL216W Dihydroorotate dehydrogenase, catalyzes the fourth enzymatic step in the de novo biosynthesis of pyrimidines, converting dihydroorotic acid into orotic acid from Saccharomyces cerevisiae
26% identity, 80% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro. Does not use oxaloacetate or NAD or NADP as electron acceptors.
catalytic activity: (S)-dihydroorotate + fumarate = orotate + succinate (RHEA:30059)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer. - Function and structural organization of Mot1 bound to a natural target promoter.
Sprouse, The Journal of biological chemistry 2008 - GeneRIF: Mot1-mediated activation of URA1 transcription involves at least two steps, one of which is the removal of TBP bound to the promoter in the opposite orientation required for URA1 transcription.
- De Novo Pyrimidine Biosynthesis Connects Cell Integrity to Amphotericin B Susceptibility in Cryptococcus neoformans.
Banerjee, mSphere 2016 - “...), and Plasmodium falciparum ( AB070244 ), and the family 1 enzyme from S.cerevisiae ( P28272 ) (bottom line), with only the respective N-terminal regions shown. The first 25amino acids are important for mitochondrial import and membrane anchorage. The boxes highlight the hydrophobic residues that make...”
- Contribution of horizontal gene transfer to the evolution of Saccharomyces cerevisiae
Hall, Eukaryotic cell 2005 - “...(17) has previously shown that URA1 (GenPept accession no. P28272) is of bacterial origin. We show additional evidence supporting this claim and also that the...”
- Divergent evolution of a beta/alpha-barrel subclass: detection of numerous phosphate-binding sites by motif search
Bork, Protein science : a publication of the Protein Society 1995 - “...pyrd_yeast 245 EIKVIGTGGIKSGKDAFEHL.LCGASMLQIGTELQKE ....GVKIFER P28272 pyrd-bacsu 235 NIPIIGMGGVQTAEDALEFL.LAGASAVAVGTANFVN.... PFACPEI P25996 trpa-metvo 211...”
- HGTphyloDetect: facilitating the identification and phylogenetic analysis of horizontal gene transfer
Yuan, Briefings in bioinformatics 2023 - “...gene candidates were previously reported ( Figure 2A ), that is, YNR058W (BIO3), YDR540C, YJL217W, YKL216W (URA1), YFR055W, YOL164W (BDS1), YMR090W and YNR057C (BIO4), respectively. The remaining 15 genes that HGTphyloDetect identified were not previously reported to be linked to HGT, although the Alien Index, out_pct...”
- Decoupling gene functions from knockout effects by evolutionary analyses
Liu, National science review 2020 - “...the various conditions examined. Genes of the uracil biosynthesis pathway (YBL039C, YEL021W, YJL130C, YJR103W, YKL024C, YKL216W, YLR420W, YML106W and YMR271C) were excluded from further analysis. The expression level measured by RPKM of HAP2, HAP3, HAP4 and HAP5 in wild-type BY4741 is 84.4, 64, 194 and 90.5,...”
- The flavoproteome of the yeast Saccharomyces cerevisiae
Gudipati, Biochimica et biophysica acta 2014 - “...YNR015W Nucleus/cytoplasm dus3 YLR401C dus4 YLR405W 6 1.3.3.1 Dihydroorotate dehydrogenase FMN TIM_barrel (DHO_dh) Cytoplasm ura1 YKL216W 7 1.3.3.4 Protoporphyrinogen IX oxidase FAD NADP_Rossmann (Amino_oxidase) I. mito. membr. hem14 YER014W 8 1.3.3.6 Acyl-CoA oxidase FAD Acyl-CoA_dh (ACOX, acyl-CoA_dh_1) Peroxisome pox1 YGL205W 9 1.3.5.1 Succinate dehydrogenase 8-(N3-His) NAPH_Rossmann...”
- Regulation of amino acid, nucleotide, and phosphate metabolism in Saccharomyces cerevisiae
Ljungdahl, Genetics 2012 - “...URA1 URA5 URA10 URA3 URA6 YNK1 YLR420W YKL216W YML106W YMR271C YEL021W YKL024C YKL067W Activity in UTP synthesis References Bifunctional: carbamoylphosphate...”
- Deletion of a subgroup of ribosome-related genes minimizes hypoxia-induced changes and confers hypoxia tolerance
Shah, Physiological genomics 2011 - “...gi 836788 gi 6322633 gi 731693 YER042W YBL064C YFR033C YKL216W YHR104W MXR1 PRX1 QCR6 URA1 GRE3 up Others gi 6320240 gi 73921293 gi 6324298 gi 9864778 gi...”
- Gene responses to oxygen availability in Kluyveromyces lactis: an insight on the evolution of the oxygen-responding system in yeast
Fang, PloS one 2009 - “..., S. bayanus . Sequences as queries (NCBI accession numbers): UAP (CAA50681), UOX (P78609), DHODases (NP_012706 and NP_593317). Oxygen-dependent regulation of KlHEM13 , KlHYP2 ( ANB1 ) and KlCOX5A ( 5B ) is not mediated by KlROX1 in K. lactis The analysis of possible ROX1 orthologs...”
- Predicting functional upstream open reading frames in Saccharomyces cerevisiae
Selpi,, BMC bioinformatics 2009 - “...YDL069C - 1 - INO2 YDR123C - - 1 PPR1 YLR014C - - 1 URA1 YKL216W - - 1 LEU4 YNL104C - - 1 RCK1 YGL158W - - 2 DCD1 YHR144C - - 1 SCH9 YHR205W - - 1 18 Genes 21 2 8 Features that...”
- Cell-to-cell stochastic variation in gene expression is a complex genetic trait
Ansel, PLoS genetics 2008 - “...mutations, strain GY329 was obtained by amplifying the ura1::Kan R mutation from the EUROSCARF strain YKL216W with primers 5-CGGACGATAAACTTCGAAACAATTC-3 and 5-GGCACTTAACAATGTTTCGGAACTC-3 , and transforming strain GY51 with this amplicon; strain GY325 was obtained by amplifying the ura2::Kan R mutation from the EUROSCARF strain YJL130C with primers...”
- More
CAC2650 Dihydroorotate dehydrogenase from Clostridium acetobutylicum ATCC 824
26% identity, 79% coverage
B7X933 dihydroorotate dehydrogenase (NAD+) (EC 1.3.1.14) from Bifidobacterium bifidum (see paper)
28% identity, 83% coverage
2b4gB / Q57U83 Dihydroorotate dehydrogenase (see paper)
26% identity, 84% coverage
- Ligand: flavin mononucleotide (2b4gB)
pyrDB / Q9CFW8 dihydroorotate dehydrogenase, catalytic subunit (EC 1.3.1.14) from Lactococcus lactis subsp. lactis (strain IL1403) (see 6 papers)
29% identity, 80% coverage
PYRD_TRYB2 / Q57U83 Dihydroorotate dehydrogenase (fumarate); DHOD; DHODase; DHOdehase; Dihydroorotate oxidase; EC 1.3.98.1 from Trypanosoma brucei brucei (strain 927/4 GUTat10.1) (see paper)
XP_845053 dihydroorotate dehydrogenase, putative from Trypanosoma brucei brucei TREU927
28% identity, 84% coverage
BC3884 Dihydroorotate dehydrogenase, catalytic subunit from Bacillus cereus ATCC 14579
26% identity, 84% coverage
- Biofilm formation displays intrinsic offensive and defensive features of Bacillus cereus
Caro-Astorga, NPJ biofilms and microbiomes 2020 - “...biosynthesis pathway. Orotate phosphoribosyltransferase * BC3883 3.73 0.65 0.84 Pyrimidine biosynthesis pathway. Orotidine 5'-phosphate decarboxylase BC3884 4.14 1.06 1.54 Pyrimidine biosynthesis pathway. Dihydroorotate dehydrogenase 1B BC3885 4.18 0.98 1.12 Pyrimidine biosynthesis pathway. Dihydroorotate dehydrogenase electron transfer subunit BC3886 4.29 0.22 0.95 Pyrimidine biosynthesis pathway. Carbamoyl phosphate...”
LSA0446 Putative dihydroorotate oxidase, catalytic subunit from Lactobacillus sakei subsp. sakei 23K
24% identity, 84% coverage
- Global transcriptome response in Lactobacillus sakei during growth on ribose
McLeod, BMC microbiology 2011 - “...monophosphate synthase (glutamine amidotransferase) -0.5 -0.8 LSA0252 iunH1 Inosine-uridine preferring nucleoside hydrolase 2.6 2.6 1.8 LSA0446 pyrDB Putative dihydroorotate oxidase, catalytic subunit 0.9 LSA0489 lsa0489 Putative metal-dependent phosphohydrolase precursor 0.5 LSA0533* iunH2 Inosine-uridine preferring nucleoside hydrolase 1.2 LSA0785 lsa0785 Putative NCAIR mutase, PurE-related protein -2.3 -1.3...”
NP_727320 suppressor of rudimentary from Drosophila melanogaster
26% identity, 29% coverage
D2V5Y1 dihydropyrimidine dehydrogenase (NADP(+)) from Naegleria gruberi
26% identity, 28% coverage
Q8CHR6 Dihydropyrimidine dehydrogenase [NADP(+)] from Mus musculus
27% identity, 29% coverage
- Development of a Global Metabo-Lipid-Prote-omics Workflow to Compare Healthy Proximal and Distal Colonic Epithelium in Mice
Hemmati, Journal of proteome research 2024 - “...observed for the DC tissue and a strong protein expression for Dpyd, a dihydropyrimidine dehydrogenase (Q8CHR6, 1.3.1.2), and Cda, a cytidine deaminase (P56389, 3.5.4.5), in the PC tissue. In addition, the GO-term GO:0015020_F:glucuronosyltransferase activity was increased in PC tissue which represents 5 UDP-glucuronosyltransferases [Ugt2b17 (P17717), Ugt1a1...”
- Proteomic analysis of Nrf2 deficient transgenic mice reveals cellular defence and lipid metabolism as primary Nrf2-dependent pathways in the liver.
Kitteringham, Journal of proteomics 2010 - “...0.92 0.96 0.90 0.94 0.90 0.99 1.22 1.18 1.00 1.06 1.11 1.01 1.22 1.18 0.178 Q8CHR6 Dihydropyrimidine dehydrogenase [NADP+] 2 2.0 2.6 1.00 0.96 1.00 1.01 0.99 0.97 1.01 1.33 1.13 1.16 1.14 1.18 1.10 1.28 1.20 0.072 P00405 Cytochrome c oxidase subunit 2 2 2.5...”
Dpyd / O89000 dihydropyrimidine dehydrogenase monomer (EC 1.3.1.2) from Rattus norvegicus (see 3 papers)
O89000 Dihydropyrimidine dehydrogenase [NADP(+)] from Rattus norvegicus
26% identity, 29% coverage
- Peptidomic Analysis of Rat Plasma: Proteolysis in Hemorrhagic Shock.
Aletti, Shock (Augusta, Ga.) 2016 - “...Apoa2 chymotrypsin-like AEVTGLSPGVTYLFKVF P04937 Fn1 chymotrypsin-like AGQAFRKFLPLF P26772 Hspe1 chymotrypsin-like AGQAFRKFLPLFDRVL P26772 Hspe1 chymotrypsin-like AGVLSRDAPDIESIL O89000 Dpyd chymotrypsin-like AHKSEIAHRFKDLGEQHFKGLVL P02770 Alb chymotrypsin-like AKLLGLTL P55159 Pon1 chymotrypsin-like ALKNVPFRSEVLAWNPDNLADY Q920L0 Lcp2 chymotrypsin-like ALKPLAPLLRGYHVVL D4AA35 Asmtl chymotrypsin-like ALSMPLNGLKEEDKEPLIEL G3V8C4 Clic4 chymotrypsin-like APPSFFAQVPQAPPVLVFKL P13221 Got1 chymotrypsin-like ARGSVSDEEMMELREAF Q5XI38 Lcp1 chymotrypsin-like...”
- “...x Deleted in malignant brain tumors 1 protein Q8CIZ5 Dmbt1 x x Dihydropyrimidine dehydrogenase [NADP(+)] O89000 Dpyd x x Ac2-067 Q7TPK5 Eef1b2l x x Elongation factor 1-gamma Q68FR6 Eef1g x x Elongation factor 2 P05197 Eef2 x x Beta-enolase P15429 Eno3 x x Ectonucleoside triphosphate diphosphohydrolase...”
- Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil
Hidese, Journal of bacteriology 2011 - “...Burkholderia xenovorans, Q13WL3 and Q13WL4; Rattus norvegicus, O89000; Homo sapiens, Q12882; Sus scrofa, Q28943. by a Grant-in-Aid for Encouragement of Young...”
BAD_RS04070 dihydroorotate dehydrogenase from Bifidobacterium adolescentis ATCC 15703
28% identity, 84% coverage
Q80XT4 Dihydropyrimidine dehydrogenase [NADP(+)] (Fragment) from Mus musculus
27% identity, 34% coverage
XP_003722973 dihydroorotate dehydrogenase from Leishmania braziliensis MHOM/BR/75/M2904
27% identity, 86% coverage
Q8DTV0 Dihydroorotate dehydrogenase from Streptococcus mutans serotype c (strain ATCC 700610 / UA159)
27% identity, 78% coverage
LCA_RS04790 dihydroorotate dehydrogenase from Latilactobacillus sakei subsp. sakei 23K
26% identity, 86% coverage
- Transcriptome Analysis Reveals the Role of Sucrose in the Production of Latilactobacillus sakei L3 Exopolysaccharide
Wang, International journal of molecular sciences 2024 - “...large chain LCA_RS04775 1.53 Carbamoyl-phosphate synthase small subunit LCA_RS04765 1.58 Aspartate carbamoyltransferase LCA_RS04770 2.03 Dihydroorotase LCA_RS04790 2.27 Dihydroorotate dehydrogenase LCA_RS04785 1.73 Dihydroorotate dehydrogenase electron transfer subunit LCA_RS04800 1.96 Orotate phosphoribosyltransferase LCA_RS04795 2.85 Orotidine-5-phosphate decarboxylase LCA_RS04115 1.12 Hypothetical protein LCA_RS04105 1.79 3-oxoacyl-ACP synthase III LCA_RS04125 1.57 Beta-ketoacyl-[acyl-carrier-protein]...”
I3U217 dihydroorotate oxidase (fumarate) from Enterococcus faecium (strain ATCC BAA-472 / TX0016 / DO)
25% identity, 74% coverage
- Proteomic characterization of persisters in Enterococcus faecium
Pont, BMC microbiology 2024 - “...oxidoreductase/NADH oxidase -2.09 -2.02 10,028 Q3XYZ5 Haloacid dehalogenase (HAD) superfamily hydrolase -1.92 -2.50 p yrD2 I3U217 Dihydroorotate oxidase (fumarate) -1.90 12,850 Q3Y0Z2 Uncharacterized protein -1.82 clpX Q3XZ71 ATP-dependent Clp protease ATP-binding subunit ClpX -1.82 12,761 I3U5U7 Uncharacterized protein -1.78 11,804 Q3Y303 MarR family transcriptional regulator -1.72...”
XP_025008718 dihydropyrimidine dehydrogenase [NADP(+)] isoform X3 from Gallus gallus
27% identity, 30% coverage
SGRA_p0002 dihydroorotate oxidase from Saprospira grandis str. Lewin
24% identity, 79% coverage
DPYD / Q12882 Dihydropyrimidine dehydrogenase [NADP+] (EC 1.3.1.2) from Homo sapiens (see 3 papers)
DPYD_HUMAN / Q12882 Dihydropyrimidine dehydrogenase [NADP(+)]; DHPDHase; DPD; Dihydrothymine dehydrogenase; Dihydrouracil dehydrogenase; EC 1.3.1.2 from Homo sapiens (Human) (see 5 papers)
24% identity, 29% coverage
- function: Involved in pyrimidine base degradation (PubMed:1512248). Catalyzes the reduction of uracil and thymine (PubMed:1512248). Also involved the degradation of the chemotherapeutic drug 5-fluorouracil (PubMed:1512248).
catalytic activity: 5,6-dihydrouracil + NADP(+) = uracil + NADPH + H(+) (RHEA:18093)
catalytic activity: 5,6-dihydrothymine + NADP(+) = thymine + NADPH + H(+) (RHEA:58284)
cofactor: FAD (Binds 2 FAD.)
cofactor: FMN (Binds 2 FMN.)
cofactor: [4Fe-4S] cluster (Binds 4 [4Fe-4S] clusters. Contains approximately 16 iron atoms per subunit.)
subunit: Homodimer - Novel predictive biomarkers for atonic postpartum hemorrhage as explored by proteomics and metabolomics.
Qu, BMC pregnancy and childbirth 2025 - “...0.240 Down Q96C86 m7GpppX diphosphatase DCPS 0.048 0.243 Down P17050 Alpha-N-acetylgalactosaminidase NAGA 0.035 0.268 Down Q12882 Dihydropyrimidine dehydrogenase [NADP (+)] DPYD 0.017 0.273 Down O95498 Vascular non-inflammatory molecule2 VNN2 0.030 0.297 Down Q9Y3D6 Mitochondrial fission 1 protein FIS1 0.011 0.298 Down P28065 Proteasome subunit beta type...”
- Explorative study of stimulated saliva proteome in head and neck cancer patients pre- and post-treatment
Almhöjd, Heliyon 2024 - “...1 Q subcomponent-binding protein, Mitochondrial 1.480.28 0.900.27 0.017 P00751 Complement factor B 0.990.13 0.720.12 0.013 Q12882 Dihydropyrimidine dehydrogenase [NADP(+)] 1.250.18 0.930.20 0.032 P24534 Elongation factor 1-beta 1.050.15 0.650.18 0.015 P11021 Endoplasmic reticulum chaperone BiP 1.110.06 0.780.16 0.013 P00367 Glutamate dehydrogenase 1, mitochondrial 1.150.11 0.780.22 0.025 P09488...”
- Human xenobiotic metabolism proteins have full-length and split homologs in the gut microbiome.
Rendina, bioRxiv : the preprint server for biology 2024 - “...38 O95340 PAPS2_HUMAN Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 2 0 28 Q9NQX3 GEPH_HUMAN Gephyrin 0 27 Q12882 DPYD_HUMAN Dihydropyrimidine dehydrogenase 24 26 O43252 PAPS1_HUMAN Bifunctional 3-phosphoadenosine 5-phosphosulfate synthase 1 0 24 P11172 UMPS_HUMAN Uridine 5-monophosphate synthase 0 22 Q86Z14 KLOTB_HUMAN Beta-klotho 0 12 Q709F0 ACD11_HUMAN Acyl-CoA dehydrogenase...”
- Force Field Parameters for Fe2+4S2-4 Clusters of Dihydropyrimidine Dehydrogenase, the 5-Fluorouracil Cancer Drug Deactivation Protein: A Step towards In Silico Pharmacogenomics Studies.
Tendwa, Molecules (Basel, Switzerland) 2021 - “...file ( Table S9 ). At first, the target sequence (human DPD enzyme: UniProt accession: Q12882) was obtained from the Universal Protein Resources [ 87 ]. Both HHPred [ 88 ] and PRIMO [ 89 ] were used to identify a suitable template for modeling the...”
- “...1 , 2 ]. A pir alignment file was prepared between the Uniprot (UniProt accession: Q12882) target sequence and that of template using multiple sequence comparison by log-expectation (MUSCLE). Therefore, the template PDB ID: 1H7X was utilized. In MODELLER v9.15 [ 90 ], a total of...”
- Identification of lysine acetylome in cervical cancer by label-free quantitative proteomics
Zhang, Cancer cell international 2020 - “...Histone cluster 2, H2bf B4DR52 SAPAPK(ac)KGSKKAVTK Histone H2B type 1-L Q99880 SAPAPK(ac)KGSKKAVTK Dihydropyrimidine dehydrogenase [NADP(+)] Q12882 EEK(ac)CEFLPFLSPR 3-hydroxymethyl-3-methylglutaryl-Coenzyme A lyase (Hydroxymethylglutaricaciduria), isoform CRA_b B1AK13 DGLQNEK(ac)NIVSTPVK cDNA FLJ58863, highly similar to Protein NipSnap3A B4DW81 SYYLKPSK(ac)MNEFLENFEK Annexin Q5TZZ9 AAYLQETGKPLDETLK(ac)K cDNA FLJ54081, highly similar to Keratin, type II cytoskeletal...”
- Oral Glucose Mobilizes Triglyceride Stores From the Human Intestine
Xiao, Cellular and molecular gastroenterology and hepatology 2019 - “...P48637 Glutathione synthetase GSS 0.4944 .0440 Other (glutathione synthesis) O76003 Glutaredoxin-3 GLRX3 0.4953 .0403 Mitochondria/redox Q12882 Dihydropyrimidine dehydrogenase [NADP(+)] DPYD 0.5076 .0165 Mitochondria/redox Q9NWU5 39S ribosomal protein L22; mitochondrial MRPL22 0.526 .0101 Transcription/RNA processing/translation Q9NVS9 Pyridoxine-5'-phosphate oxidase PNPO 0.5395 .0337 Mitochondria/redox Q9UHY7 Enolase-phosphatase E1 ENOPH1 0.5544...”
- Synergistic Effect of Network-Based Multicomponent Drugs: An Investigation on the Treatment of Non-Small-Cell Lung Cancer with Compound Liuju Formula.
Su, Evidence-based complementary and alternative medicine : eCAM 2019 - “...4 Q00534 Cyclin-dependent kinase 6 CDK6 12 Q12791 Calcium-activated potassium channel subunit alpha-1 KCNMA1 4 Q12882 Dihydropyrimidine dehydrogenase [NADP(+)] DPYD 4 Q16539 Mitogen-activated protein kinase 14 MAPK14 15 Q16678 Cytochrome P450 1B1 CYP1B1 14 Q9BVA1 Tubulin beta-2B chain TUBB2B 15 Q9UNQ0 ATP-binding cassette subfamily G member...”
- Systems Pharmacology Uncovers the Multiple Mechanisms of Xijiao Dihuang Decoction for the Treatment of Viral Hemorrhagic Fever
Liu, Evidence-based complementary and alternative medicine : eCAM 2016 - “...D(3) 24-hydroxylase, mitochondrial CYP24A1 Homo sapiens Q12791 Calcium-activated potassium channel subunit alpha-1 KCNMA1 Homo sapiens Q12882 Dihydropyrimidine dehydrogenase [NADP(+)] DPYD Homo sapiens Q13822 Ectonucleotide pyrophosphatase/phosphodiesterase family member 2 ENPP2 Homo sapiens Q13887 Krppel-like factor 5 KLF5 Homo sapiens Q14524 Sodium channel protein type 5 subunit alpha...”
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SUB1264 dihydroorotate dehydrogenase from Streptococcus uberis 0140J
25% identity, 74% coverage
- Vru (Sub0144) controls expression of proven and putative virulence determinants and alters the ability of Streptococcus uberis to cause disease in dairy cattle
Egan, Microbiology (Reading, England) 2012 - “...exponential phase of growth; those downregulated in the Vru mutant included sub0155 , sub1095 , sub1264 and sub1025 . Other CDSs ( sub0176 , sub0177 , sub0543 , sub0544 , sub1173 , sub0118 and sub0137 ) were found to be downregulated in the Vru mutant only...”
- “...ABC type transporters (Sub0137, 1174 and 1173), while others were linked to metabolism of pyrimidines (Sub1264 and 1025). However, these did not affect growth of the Vru mutant in either THB or milk. In conclusion, it would appear justified to speculate that the observed reduced virulence...”
DPYD_PIG / Q28943 Dihydropyrimidine dehydrogenase [NADP(+)]; DHPDHase; DPD; Dihydrothymine dehydrogenase; Dihydrouracil dehydrogenase; EC 1.3.1.2 from Sus scrofa (Pig) (see 5 papers)
Q28943 dihydropyrimidine dehydrogenase (NADP+) (EC 1.3.1.2) from Sus scrofa (see 4 papers)
NP_999209 dihydropyrimidine dehydrogenase [NADP(+)] precursor from Sus scrofa
26% identity, 29% coverage
- function: Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine.
catalytic activity: 5,6-dihydrouracil + NADP(+) = uracil + NADPH + H(+) (RHEA:18093)
catalytic activity: 5,6-dihydrothymine + NADP(+) = thymine + NADPH + H(+) (RHEA:58284)
cofactor: FAD (Binds 2 FAD.)
cofactor: FMN (Binds 2 FMN.)
cofactor: [4Fe-4S] cluster (Binds 4 [4Fe-4S] clusters. Contains approximately 16 iron atoms per subunit.)
subunit: Homodimer. - Transient-State Analysis of Porcine Dihydropyrimidine Dehydrogenase Reveals Reductive Activation by NADPH.
Beaupre, Biochemistry 2020 (PubMed)- GeneRIF: Transient-State Analysis of Porcine Dihydropyrimidine Dehydrogenase Reveals Reductive Activation by NADPH.
- Insights into the mechanism of dihydropyrimidine dehydrogenase from site-directed mutagenesis targeting the active site loop and redox cofactor coordination.
Lohkamp, Biochimica et biophysica acta 2010 (PubMed)- GeneRIF: Data show that dihydropyrimidine dehydrogenase residue H673 is required for active site closure, while S670 is important for substrate recognition.
- Label-Free Quantitative Analysis of Pig Liver Proteome after Hepatitis E Virus Infection
Martino, Viruses 2024 - “...A0A4X1UZ96 UPB1 beta-ureidopropionase 16 94.43 0.0086 1.98 P23687 PREP prolyl endopeptidase 16 71.89 0.0139 2.11 Q28943 DPYD dihydropyrimidine dehydrogenase [NADP(+)] precursor 15 67.95 0.0017 1.98 Q06AA3 RGN regucalcin 14 94.49 0.0034 1.71 A0A5G2QAG3 LAP3 cytosol aminopeptidase isoform X1 14 79.04 0.0016 1.78 P46410 GLUL glutamine synthetase...”
- Composition and physiological functions of the porcine colostrum.
Inoue, Animal science journal = Nihon chikusan Gakkaiho 2021 - “...member 4 40 Q28944 Cathepsin L1 0.1 41 P02540 Desmin 26 Q8MJ30 Dihydropteridine reductase 20 Q28943 Dihydropyrimidine dehydrogenase [NADP(+)] 0.03 20 Q6UAQ8 Electron transfer flavoprotein subunit beta 0.14 43 O97939 Enamelin 26 Q29042 Ficolin1 26 A4GVD1 Gap junction gamma1 protein 23 P20305 Gelsolin (fragment) 19 A5A779...”
- Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.
Le, BMC bioinformatics 2016 - “...Q96HE7 P00390 P37747 P66004 Q5UVJ4 Q96329 Q9YHT1 P07342 P38038 Q0QLF4 Q709F0 Q9AL95 P55931 O53355 P39662 Q28943 Q7SID9 C6ELC9 A3KEZ1 O54050 P41367 P97275 Q7WZ62 D0VWY5 O60341 P45954 Q2GBV9 Q7X2H8 O52582 P0A6U3 P47989 Q389T8 Q7ZA32 Q9RSY7 P15651 P49748 Q47PU3 Q8DMN3 Q9UBK8 P19920 P55789 Q52437 Q8X1D8 Q9UKU7 P07872 P09622...”
- Escherichia coli dihydropyrimidine dehydrogenase is a novel NAD-dependent heterotetramer essential for the production of 5,6-dihydrouracil
Hidese, Journal of bacteriology 2011 - “...Rattus norvegicus, O89000; Homo sapiens, Q12882; Sus scrofa, Q28943. by a Grant-in-Aid for Encouragement of Young Scientists 21780094 (to H.M.). REFERENCES 1....”
Q4DGV2 dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) from Trypanosoma cruzi (see paper)
DHOD3 / GI|81295309 dihydroorotate dehydrogenase; EC 1.3.5.2 from Trypanosoma cruzi (see 2 papers)
25% identity, 88% coverage
SP70585_1004 dihydroorotate dehydrogenase B, catalytic subunit (dihydroorotate oxidase b) (dhodehase b) (dhodase b) (dhod b) from Streptococcus pneumoniae 70585
28% identity, 80% coverage
1gthA / Q28943 Dihydropyrimidine dehydrogenase (dpd) from pig, ternary complex with NADPH and 5-iodouracil (see paper)
26% identity, 29% coverage
- Ligands: iron/sulfur cluster; flavin mononucleotide; flavin-adenine dinucleotide; nadph dihydro-nicotinamide-adenine-dinucleotide phosphate; (5s)-5-iododihydro-2,4(1h,3h)-pyrimidinedione (1gthA)
3c61A / D0VWT2 Crystal structure of dihydroorotate dehydrogenase from leishmania donovani
26% identity, 86% coverage
- Ligands: azide ion; flavin mononucleotide (3c61A)
SP_0964 dihydroorotate dehydrogenase 1B from Streptococcus pneumoniae TIGR4
SPCG_RS04890 dihydroorotate dehydrogenase from Streptococcus pneumoniae CGSP14
28% identity, 80% coverage
- Multi-omic profiling to assess the effect of iron starvation in Streptococcus pneumoniae TIGR4
Jiménez-Munguía, PeerJ 2018 - “...SP_0785, SP_0786, SP_0787 3/3 Downregulated 38655 SP_0918, SP_0919, SP_0920, SP_0921, SP_0922 5/5 Downregulated 38665 SP_0963, SP_0964 2/2 Downregulated 38674 SP_1013, SP_1014 2/2 Downregulated 38682 SP_1069, SP_1070, SP_1071 3/6 Downregulated 38684 SP_1079, SP_1080 2/2 Downregulated 38726 SP_1276, SP_1277, SP_1278 3/3 Downregulated 38731 SP_1294, SP_1295 2/3 Downregulated 38751...”
- The transcriptomic response of Streptococcus pneumoniae following exposure to cigarette smoke extract
Manna, Scientific reports 2018 - “...0.004 SPCG_RS06420 Carbamoyl-phosphate synthase small chain CarA 1.82 0.004 SPCG_RS06425 Aspartate carbamoyltransferase PyrB 1.80 0.004 SPCG_RS04890 Dihydroorotate dehydrogenase PyrD 1.73 0.004 SPCG_RS06415 Carbamoyl-phosphate synthase large chain CarB 1.52 0.005 SPCG_RS06470 Uracil permease PyrP 1.44 0.010 SPCG_RS04885 Dihydroorotate dehydrogenase PyrDII 1.34 0.012 Virulence SPCG_RS09950 Pneumolysin Ply 3.39...”
spr0866 dihydroorotate dehydrogenase 1B from Streptococcus pneumoniae R6
SPD_0852 dihydroorotate dehydrogenase, catalytic subunit from Streptococcus pneumoniae D39
28% identity, 80% coverage
- Whole genome sequencing of penicillin-resistant Streptococcus pneumoniae reveals mutations in penicillin-binding proteins and in a putative iron permease
Fani, Genome biology 2011 - “...(FtsE) C410T P137L spr0764 30S Ribosomal protein S1 G1173A M391I spr0776 D-Alanyl-D-alanine carboxypeptidase C287T A96V spr0866 Dihydroorotate dehydrogenase C575T P192L spr0878 Exoribonuclease R G280T G94W spr0895 Conserved hypothetical protein G134C R45T spr0917 Citrulline cluster-linked gene C59T A20V spr0934 ABC transporter substrate-binding protein - iron transport G486A...”
- Eukaryotic-type serine/threonine protein kinase StkP is a global regulator of gene expression in Streptococcus pneumoniae
Sasková, Journal of bacteriology 2007 - “...2.08 2.01 2.58 Pyrimidine metabolism spr0613 spr0614 spr0865 spr0866 spr1053 spr1153 spr1154 spr1155 spr1156 1.54 1.55 2.07 2.38 1.50 1.43 1.27 1.30 1.49...”
- Regulation of iron transport in Streptococcus pneumoniae by RitR, an orphan response regulator
Ulijasz, Journal of bacteriology 2004 - “...spr0451 spr0502 spr0113 spr0139 spr0322 spr0893 spr1706 spr0866 spr0597 spr1319 spr1824 spr1897 spr0992 spr0465 spr1378 spr0522 spr0698 spr1504 spr1856 spr0042...”
- Pivotal Roles for Ribonucleases in Streptococcus pneumoniae Pathogenesis
Sinha, mBio 2021 - “...1.33E03 SPD_0803 f Putative phage shock protein C 2.60 1.24E04 SPD_0806 Hypothetical protein 2.18 5.09E04 SPD_0852 pyrDb Dihydroorotate dehydrogenase, catalytic subunit 1.84 1.85E03 SPD_0853 d lytB Endo-beta- N -acetylglucosaminidase LytB 1.87 3.88E02 SPD_0872 b Membrane protein, putative 1.84 1.23E03 SPD_0882 IS630-Spn1, transposase Orf2, truncation 2.76 6.41E08...”
- Deletion of the Zinc Transporter Lipoprotein AdcAII Causes Hyperencapsulation of Streptococcus pneumoniae Associated with Distinct Alleles of the Type I Restriction-Modification System
Durmort, mBio 2020 - “...acid ABC transporter permease 1.71 2.51 1.20 SPD_0851 pyrK Dihydroorotate dehydrogenase II 1.90 1.90 1.16 SPD_0852 pyrD Dihydroorotate dehydrogenase IB 2.32 2.28 1.11 SPD_0853 lytB Endo-beta- N -acetylglucosaminidase 1.71 1.65 1.09 SPD_0888 adcAII Zn 2+ ABC transporter lipoprotein 3.87 3.03 5.95 SPD_0889 phtD Hypothetical protein 1.78...”
- S1 Domain RNA-Binding Protein CvfD Is a New Posttranscriptional Regulator That Mediates Cold Sensitivity, Phosphate Transport, and Virulence in Streptococcus pneumoniae D39
Sinha, Journal of bacteriology 2020 (secret) - N-acetylgalatosamine-Mediated Regulation of the aga Operon by AgaR in Streptococcus pneumoniae
Afzal, Frontiers in cellular and infection microbiology 2016 - “...FlaR, putative 31.3 spd_0850 Lactoylglutathione lyase 19.0 spd_0851 Dihydroorotate dehydrogenase electron transfer subunit, PyrK 66.2 spd_0852 Dihydroorotate dehydrogenase, catalytic subunit, PyrDb 32.5 spd_1050 Tagatose 1,6-diphosphate aldolase, LacD 29.6 spd_1051 Tagatose-6-phosphate kinase, LacC 15.3 spd_1052 Galactose-6-phosphate isomerase, LacB subunit 20.2 spd_1053 Galactose-6-phosphate isomerase, LacA subunit 19.4 spd_1133...”
- The Small Molecule DAM Inhibitor, Pyrimidinedione, Disrupts Streptococcus pneumoniae Biofilm Growth In Vitro
Yadav, PloS one 2015 - “...isochorismatase family protein catalytic activity -1.4 (0.04) SPD_1555 isochorismatase family protein catalytic activity -1.4 (0.01) SPD_0852 (pyrDb) dihydroorotate dehydrogenase, catalytic subunit -1.4 (0.02) Homeostasis process SPD_1714 thioredoxin family protein protein disulfide oxidoreductase activity cell redox homeostasis/glycerol ether metabolic process -1.4 (0.05) SPD_1464 (psaD) thiol peroxidase thioredoxin...”
- Regulation of arginine acquisition and virulence gene expression in the human pathogen Streptococcus pneumoniae by transcription regulators ArgR1 and AhrC
Kloosterman, The Journal of biological chemistry 2011 - “...were down-regulated (Table 1) among which was pyrD (spd_0852) that is involved in pyrimidine synthesis, which is closely connected to arginine metabolism....”
- “...spd_0610 spd_0611 spd_0719 spd_0720 spd_0721 spd_0781 spd_0852 spd_0887 spd_0888 spd_0889 spd_1063 spd_1225 spd_1226 spd_1356 spd_1357 spd_1515 spd_1516...”
pyrD / CAA91006.2 dihydroorotate dehydrogenase from Lactobacillus plantarum (see 2 papers)
P77887 Dihydroorotate dehydrogenase A (fumarate) from Lactiplantibacillus plantarum (strain ATCC BAA-793 / NCIMB 8826 / WCFS1)
lp_2699 dihydroorotate oxidase from Lactobacillus plantarum WCFS1
28% identity, 87% coverage
- Role of the luxS gene in bacteriocin biosynthesis by Lactobacillus plantarum KLDS1.0391: A proteomic analysis.
Jia, Scientific reports 2017 - “...Sequence name Map Name Sequence description Quantitative change and significance C/D b P value 1 P77887 pyrDI Dihydroorotate dehydrogenase catalytic subunit 2.760886385 0.031 2 A0A0G9FAP4 Transcriptional regulator family 2.945902345 0.003 3 A0A0G9FCW2 GNAT family acetyltransferase 2.070695848 0.030 4 A0A0L7XZQ3 Gamma-D-glutamyl-meso-diaminopimelate peptidase 2.747063118 0.036 5 A0A0R1UXL5 E4.1.1.15...”
- Comparative study of sugar fermentation and protein expression patterns of two Lactobacillus plantarum strains grown in three different media.
Plumed-Ferrer, Applied and environmental microbiology 2008 - Characterization of transcriptional response of Lactobacillus plantarum under acidic conditions provides insight into bacterial adaptation in fermentative environments
Jung, Scientific reports 2020 - “...1.48E116 3.01E114 Oligopeptide ABC transporter lp_0783 F9UM05 COG4166 K15580 pyrD 1.11 1.66E29 4.61E28 Dihydroorotate dehydrogenase lp_2699 F9URI1 COG0167 K17828 pyrAB 1.19 2.37E26 5.73E25 Carbamoyl-phosphate synthase lp_2700 F9URI2 COG0458 K01955 pyrAA 1.49 1.70E30 5.17E29 Carbamoyl-phosphate synthase lp_2701 F9URI3 COG0505 K01956 pyrC 1.54 8.42E30 2.39E28 Dihydroorotase lp_2702 F9URI4...”
- Identification of prebiotic fructooligosaccharide metabolism in Lactobacillus plantarum WCFS1 through microarrays
Saulnier, Applied and environmental microbiology 2007 - “...which were significantly differentially expressed (lp_2697, lp_2698, lp_2699, lp_2700, lp_2702, and lp_2371). These genes are predicted to participate in the...”
- “...lp_0242 lp_2374 lp_2591 lp_2697 lp_2698 lp_2699 lp_2700 lp_2702 Nucleoside-diphosphate kinase Uracil phosphoribosyltransferase Purine nucleosidase Orotate...”
- An agr-like two-component regulatory system in Lactobacillus plantarum is involved in production of a novel cyclic peptide and regulation of adherence
Sturme, Journal of bacteriology 2005 - “...of California, Berkeley lp_0256 lp_2371 lp_2684 lp_2685 lp_2698 lp_2699 lp_2700 Description 5232 STURME ET AL. J. BACTERIOL. FIG. 8. Structure of peptide...”
DPYD_CAEEL / Q18164 Dihydropyrimidine dehydrogenase [NADP(+)]; DHPDHase; DPD; Dihydrothymine dehydrogenase; Dihydrouracil dehydrogenase; EC 1.3.1.2 from Caenorhabditis elegans (see paper)
26% identity, 27% coverage
XP_005270619 dihydropyrimidine dehydrogenase [NADP(+)] isoform X2 from Homo sapiens
28% identity, 18% coverage
DPYD_BOVIN / Q28007 Dihydropyrimidine dehydrogenase [NADP(+)]; DHPDHase; DPD; Dihydrothymine dehydrogenase; Dihydrouracil dehydrogenase; EC 1.3.1.2 from Bos taurus (Bovine) (see paper)
30% identity, 17% coverage
- function: Involved in pyrimidine base degradation. Catalyzes the reduction of uracil and thymine. Also involved the degradation of the chemotherapeutic drug 5-fluorouracil.
catalytic activity: 5,6-dihydrouracil + NADP(+) = uracil + NADPH + H(+) (RHEA:18093)
catalytic activity: 5,6-dihydrothymine + NADP(+) = thymine + NADPH + H(+) (RHEA:58284)
cofactor: FAD (Binds 2 FAD.)
cofactor: FMN (Binds 2 FMN.)
cofactor: [4Fe-4S] cluster (Binds 4 [4Fe-4S] clusters. Contains approximately 16 iron atoms per subunit.)
subunit: Homodimer.
LOC410207 dihydropyrimidine dehydrogenase [NADP(+)] from Apis mellifera
23% identity, 29% coverage
- Differential gene expression between hygienic and non-hygienic honeybee (Apis mellifera L.) hives
Boutin, BMC genomics 2015 - “...LOC408734 Chr3 6.43168 2.8719 0.00755 succinate dehydrogenase LOC410149 Chr12 217.491 122.044 0.0138823 plasma glutamate carboxypeptidase-like LOC410207 Chr10 2.67182 1.459 0.00755 dihydropyrimidine dehydrogenase LOC410689 Chr1 18.0555 11.8371 0.0457819 hypothetical protein LOC410479 LOC412162 Chr7 1.65605 0.661079 0.0367372 armadillo repeat-containing protein 4-like LOC551908 Chr15 2.32533 0.728909 0.00755 hypothetical protein...”
EF0285 dihydroorotate dehydrogenase from Enterococcus faecalis V583
27% identity, 72% coverage
- Type II Fatty Acid Synthesis Pathway and Cyclopropane Ring Formation Are Dispensable during Enterococcus faecalis Systemic Infection
Hays, Journal of bacteriology 2021 (secret) - The transcriptome of the nosocomial pathogen Enterococcus faecalis V583 reveals adaptive responses to growth in blood
Vebø, PloS one 2009 - “...rejection level. The corresponding orf-numbers for the genes tested are: lrgB ; EF3193, fabI ; EF0285, fabK ; EF2883, fabT ; EF2886, bopA ; EF0957, efaA ; EF2076, dltA ; EF2749, cpsC; EF2493 ace; EF1099, gelE ; EF1818, fsrB ; EF1821. 10.1371/journal.pone.0007660.t002 Table 2 List of...”
- Transcriptional response of Enterococcus faecalis V583 to erythromycin
Aakra, Antimicrobial agents and chemotherapy 2005 - “...EF0223 EF0224 EF0225 EF0226 EF0970 EF1694 EF2395 EF2397 EF2473 EF2474 EF2679 EF2731 EF3070 EF0285 EF1714 EF1718 EF2362 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0...”
PYRDA_LACLM / A2RJT9 Dihydroorotate dehydrogenase A (fumarate); DHOD A; DHODase A; DHOdehase A; EC 1.3.98.1 from Lactococcus lactis subsp. cremoris (strain MG1363) (see 4 papers)
A2RJT9 dihydroorotate dehydrogenase (NAD+) (EC 1.3.1.14) from Lactococcus lactis (see paper)
2bslA / A2RJT9 Crystal structure of l. Lactis dihydroorotate dehydrogense a in complex with 3,4-dihydroxybenzoate (see paper)
25% identity, 74% coverage
- function: Catalyzes the conversion of dihydroorotate to orotate with fumarate as the electron acceptor. Molecular oxygen can replace fumarate in vitro, but cannot use NAD(+) as an electron acceptor.
catalytic activity: (S)-dihydroorotate + fumarate = orotate + succinate (RHEA:30059)
cofactor: FMN (Binds 1 FMN per subunit.)
subunit: Homodimer. - Ligands: flavin mononucleotide; magnesium ion (2bslA)
Q6F4D1 dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) from Neobodo saliens (see paper)
26% identity, 46% coverage
L192589 dihydroorotate dehydrogenase A (EC 1.3.3.1) from Lactococcus lactis subsp. lactis Il1403
24% identity, 74% coverage
- Strain-Dependent Transcriptome Signatures for Robustness in Lactococcus lactis
Dijkstra, PloS one 2016 - “...2.7 L0151 rgrB GntR family transcription regulator negative 4.1 L188392 ybiH hypothetical protein positive 0.2 L192589 pydA dihydroorotate dehydrogenase 1A negative 4.8 L19745 bar acyltransferase negative 2.4 L117821 yxdC cation-transporting ATPase negative 0.5 L67463 yuiB hypothetical protein negative 7.9 L199277 ps305 prophage ps3 protein 05 negative...”
SPy_1432 dihydroorotate oxidase from Streptococcus pyogenes M1 GAS
SPy1432 putative dihydroorotate dehydrogenase from Streptococcus pyogenes M1 GAS
25% identity, 73% coverage
- RNA sequencing uncovers antisense RNAs and novel small RNAs in Streptococcus pyogenes
Le, RNA biology 2016 - “...SPy_0938 hypothetical protein 405 Spy_sRNA1110925 SPy_1340 major facilitator superfamily permease SPy_1343 hypothetical protein 82 Spy_sRNA1186876 SPy_1432 pyrD: dihydroorotate dehydrogenase 1A SPy_1434 heavy metal-transporting ATPase 23 Spy_sRNA1212757 370.2 + SPy_1469 hypothetical protein SPy_1470 hypothetical protein 37 Spy_sRNA1222613 370.2 SPy_1488 int2: integrase SPy_1489 hlpA: histone-like DNA binding protein...”
- “...Manfredo and NZ131 S. pyogenes strains and Streptococcus parauberis KCTC 11537. Spy_sRNA1186876 is encoded between SPy_1432 ( pyrD dihydroorotate dehydrogenase 1A) and SPy_1434 (heavy metal-transporting ATPase). We detected 2 forms of this sRNA of 500nt and >200nt in size by Northern blot analysis. We could not...”
- Adaptation of group A Streptococcus to human amniotic fluid
Sitkiewicz, PloS one 2010 - “...M28_Spy1109 SPy1368 udk 2.04 Uridine kinase M28_Spy1118 SPy1378 nrdF.2 2.32 Ribonucleoside-diphosphate reductase beta chain M28_Spy1159 SPy1432 pyrD 2.15 Dihydroorotate dehydrogenase M28_Spy1466 SPy1736 - 5.01 3.02 5.14 Guanine-hypoxanthine permease M28_Spy1580 SPy1869 udp 2.83 Uridine phosphorylase M28_Spy1599 SPy1894 pyrG 2.64 CTP synthase M28_Spy1758 SPy2085 fhs.2 3.32 2.32 Formatetetrahydrofolate...”
M28_Spy1159 dihydroorotate dehydrogenase from Streptococcus pyogenes MGAS6180
25% identity, 73% coverage
- Adaptation of group A Streptococcus to human amniotic fluid
Sitkiewicz, PloS one 2010 - “...protein M28_Spy1109 SPy1368 udk 2.04 Uridine kinase M28_Spy1118 SPy1378 nrdF.2 2.32 Ribonucleoside-diphosphate reductase beta chain M28_Spy1159 SPy1432 pyrD 2.15 Dihydroorotate dehydrogenase M28_Spy1466 SPy1736 - 5.01 3.02 5.14 Guanine-hypoxanthine permease M28_Spy1580 SPy1869 udp 2.83 Uridine phosphorylase M28_Spy1599 SPy1894 pyrG 2.64 CTP synthase M28_Spy1758 SPy2085 fhs.2 3.32 2.32...”
CD630_01860, CDIF630erm_00307 dihydroorotate dehydrogenase from Clostridioides difficile
25% identity, 87% coverage
- Iron Regulation in Clostridioides difficile
Berges, Frontiers in microbiology 2018 - “...0.47 1.01 0.60 CD630_01850 CDIF630erm_00306 pyrK Dihydroorotate dehydrogenase electron transfer subunit 2.94 0.82 2.82 0.74 CD630_01860 CDIF630erm_00307 pyrD Dihydroorotate dehydrogenase 1B 1.96 0.21 2.72 0.16 CD630_01870 CDIF630erm_00308 pyrE Orotatephosphoribosyltransferase 3.92 0.19 3.38 0.54 CD630_25940 CDIF630erm_02848 uraA Uracil-specific ABC transporter permease 0.96 0.17 3.83 -0.46 CD630_25950 CDIF630erm_02849...”
- “...1.01 0.60 CD630_01850 CDIF630erm_00306 pyrK Dihydroorotate dehydrogenase electron transfer subunit 2.94 0.82 2.82 0.74 CD630_01860 CDIF630erm_00307 pyrD Dihydroorotate dehydrogenase 1B 1.96 0.21 2.72 0.16 CD630_01870 CDIF630erm_00308 pyrE Orotatephosphoribosyltransferase 3.92 0.19 3.38 0.54 CD630_25940 CDIF630erm_02848 uraA Uracil-specific ABC transporter permease 0.96 0.17 3.83 -0.46 CD630_25950 CDIF630erm_02849 pyrR...”
gbs0553 unknown from Streptococcus agalactiae NEM316
26% identity, 84% coverage
PF1539 dihydroorotate dehydrogenase (dihydroorotate oxidase) (dhodehase) from Pyrococcus furiosus DSM 3638
24% identity, 86% coverage
- Genome-wide binding analysis of the transcriptional regulator TrmBL1 in Pyrococcus furiosus
Reichelt, BMC genomics 2016 - “...phosphorylase same promoter region downstream PF1536 hypothetical protein PF1537 hypothetical protein PF1538 N-ethylammeline chlorohydrolase singleton PF1539 dihydroorotate dehydrogenase 1B singleton PF2016 preprotein translocase subunit SecG - downstream singleton PF2047 l-asparaginase - upstream Genes containing a TrmBL1 binding site in their promoter region are depicted in bold...”
- “...from PF1538 to PF1535. On the other hand it enhances forward transcription of the gene PF1539. A comparable transcriptional regulation mechanism was already shown for the archaeal sulphur response regulator SurR, which controls hydrogen and elemental sulfur metabolism in P. furiosus [ 9 ]. ChIP-seq experiments...”
Q8DVA1 dihydroorotate dehydrogenase (fumarate) (EC 1.3.98.1) from Streptococcus mutans (see paper)
25% identity, 74% coverage
3oixA / Q8DVA1 Crystal structure of the putative dihydroorotate dehydrogenase from streptococcus mutans (see paper)
25% identity, 74% coverage
- Ligand: flavin mononucleotide (3oixA)
Q5L029 dihydrouracil dehydrogenase (NAD(+)) from Geobacillus kaustophilus (strain HTA426)
28% identity, 33% coverage
pydA / Q846U6 (NADP)-dependent dihydropyrimidine dehydrogenase (EC 1.3.1.2) from Brevibacillus agri (see paper)
Q846U6 dihydrouracil dehydrogenase (NAD(+)) from Brevibacillus agri
25% identity, 39% coverage
Ac3H11_2954 Dihydropyrimidine dehydrogenase (NADP(+)) (EC 1.3.1.2) from Acidovorax sp. GW101-3H11
27% identity, 39% coverage
- mutant phenotype: Specifically important for utilizing Uridine. Automated validation from mutant phenotype: the predicted function (1.3.1.2) was linked to the condition via a SEED subsystem. This annotation was also checked manually.
For advice on how to use these tools together, see
Interactive tools for functional annotation of bacterial genomes.
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