Family Search for PF04167 (DUF402)
PF04167 hits 28 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.
BSU08680 hypothetical protein from Bacillus subtilis subsp. subtilis str. 168
Aligns to 59:124 / 176 (37.5%), covers 98.5% of PF04167, 71.2 bits
7d8gA / Q7A4T2 The crystal structure of nucleotide phosphatase sa1684 from staphylococcus aureus (see paper)
Aligns to 58:123 / 174 (37.9%), covers 98.5% of PF04167, 69.8 bits
- Ligand: magnesium ion (7d8gA)
NTDP_STAA8 / Q2G2M8 Nucleoside triphosphate/diphosphate phosphatase; Nucleoside diphosphatase; NDPase; EC 3.6.1.15; EC 3.6.1.6 from Staphylococcus aureus (strain NCTC 8325 / PS 47) (see paper)
NTDP_STAAN / Q7A4T2 Nucleoside triphosphate/diphosphate phosphatase; Nucleoside tri- and diphosphatase; Ntdp; EC 3.6.1.15; EC 3.6.1.6 from Staphylococcus aureus (strain N315) (see paper)
Q7A4T2 nucleoside diphosphate phosphatase (EC 3.6.1.6) from Staphylococcus aureus (see paper)
SA1684 hypothetical protein from Staphylococcus aureus subsp. aureus N315
NWMN_RS10060 DUF402 domain-containing protein from Staphylococcus aureus subsp. aureus str. Newman
Aligns to 62:127 / 180 (36.7%), covers 98.5% of PF04167, 69.7 bits
- function: Has nucleoside phosphatase activity towards nucleoside triphosphates and nucleoside diphosphates (By similarity). Can hydrolyze nucleoside diphosphates (NDPs) and deoxynucleoside diphosphates (dNDPs), including ADP, GDP, UDP, CDP, IDP, TDP, dADP, dGDP and dCDP (PubMed:27422825).
function: Plays an important role in S.aureus virulence (PubMed:27422825). Required for hemolysin production, nuclease production and colony spreading, and contributes to the expression of extracellular proteins and cell wall proteins (PubMed:27422825).
catalytic activity: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'- diphosphate + H(+) + phosphate (RHEA:23680)
catalytic activity: a ribonucleoside 5'-diphosphate + H2O = a ribonucleoside 5'- phosphate + H(+) + phosphate (RHEA:36799)
catalytic activity: a 2'-deoxyribonucleoside 5'-diphosphate + H2O = a 2'- deoxyribonucleoside 5'-phosphate + H(+) + phosphate (RHEA:64920)
catalytic activity: ADP + H2O = AMP + H(+) + phosphate (RHEA:61436)
catalytic activity: GDP + H2O = GMP + H(+) + phosphate (RHEA:22156)
catalytic activity: H2O + UDP = H(+) + phosphate + UMP (RHEA:64876)
catalytic activity: CDP + H2O = CMP + H(+) + phosphate (RHEA:64880)
catalytic activity: H2O + IDP = H(+) + IMP + phosphate (RHEA:35207)
catalytic activity: dADP + H2O = dAMP + H(+) + phosphate (RHEA:64928)
catalytic activity: dGDP + H2O = dGMP + H(+) + phosphate (RHEA:64940)
catalytic activity: dCDP + H2O = dCMP + H(+) + phosphate (RHEA:64952)
cofactor: Mg(2+) Mn(2+) Co(2+) (Activity is highest with Mn(2+), followed by Co(2+) (PubMed:27422825). Has low activity with Mg(2+) at high magnesium concentrations (PubMed:27422825). The enzyme probably uses Mg(2+) under physiological conditions (By similarity). Cannot use Cu(2+), Ni(2+), Zn(2+) or Ca(2+) ions (PubMed:27422825).)
disruption phenotype: Deletion mutant exhibits drastically decreased virulence in a silkworm infection model (PubMed:27422825). It has decreased hemolysin production, nuclease production and colony- spreading ability compared with the parent strain (PubMed:27422825). Deletion of the gene alters the expression of various genes, including the virulence regulatory genes agr, hla, sarZ and sarX, as well as metabolic genes involved in nucleotide metabolism, glycolysis and fermentation pathways (PubMed:27422825). - function: Has nucleoside phosphatase activity towards nucleoside triphosphates and nucleoside diphosphates (PubMed:33955674). Can hydrolyze GTP, ATP, GDP and ADP (PubMed:33955674). GTP is the most preferred substrate, with the highest substrate affinity and catalytic efficiency (PubMed:33955674).
catalytic activity: a ribonucleoside 5'-triphosphate + H2O = a ribonucleoside 5'- diphosphate + H(+) + phosphate (RHEA:23680)
catalytic activity: a ribonucleoside 5'-diphosphate + H2O = a ribonucleoside 5'- phosphate + H(+) + phosphate (RHEA:36799)
catalytic activity: GTP + H2O = GDP + H(+) + phosphate (RHEA:19669)
catalytic activity: ATP + H2O = ADP + H(+) + phosphate (RHEA:13065)
catalytic activity: GDP + H2O = GMP + H(+) + phosphate (RHEA:22156)
catalytic activity: ADP + H2O = AMP + H(+) + phosphate (RHEA:61436)
cofactor: Mg(2+) Mn(2+) Co(2+) (Activity is highest with Mn(2+), followed by Co(2+) and Mg(2+), but the enzyme probably uses Mg(2+) under physiological conditions (PubMed:33955674). Has low activity with Ca(2+) (PubMed:33955674). Cannot use Cu(2+) or Zn(2+) ions (PubMed:33955674).)
subunit: Monomer in solution. - The structural mechanism for the nucleoside tri- and diphosphate hydrolysis activity of Ntdp from Staphylococcus aureus
Wang, The FEBS journal 2021 (PubMed) (secret) - Exploiting biofilm phenotypes for functional characterization of hypothetical genes in Enterococcus faecalis
Willett, NPJ biofilms and microbiomes 2019 - “...in the literature. From this database, we found that Bph has high sequence homology to SA1684, a Staphylococcus aureus nucleoside diphosphatase required for expression of secreted proteins and genes regulating virulence and metabolism. 58 The Tn insertions identified in the primary biofilm screen (Fig. 2b )...”
- “...FomD, Ca 2+ for SC4828). b Alignment (Clustal2 Omega) of active site residues in SC4828, SA1684, and Bph. Asterisks and dots (bottom) indicated amino acid relatedness. Filled squares (top) signify ligand-binding residues and open squares (top) signify residues that coordinate Ca 2+ in SC4828. Numbers (right)...”
- Novel Nucleoside Diphosphatase Contributes to Staphylococcus aureus Virulence
Imae, The Journal of biological chemistry 2016 - “...California, Berkeley on February 12, 2017 We identified SA1684 as a Staphylococcus aureus virulence gene using a silkworm infection model. The SA1684 gene...”
- “...exotoxin production and colony-spreading ability. Purified SA1684 protein had Mn2- or Co2-dependent hydrolyzing activity against nucleoside diphosphates....”
- Transcription profiling-based identification of Staphylococcus aureus genes regulated by the agr and/or sarA loci
Dunman, Journal of bacteriology 2001 - “...SA0184 SA0185 SA0271 SA1037 SA1275 SA1319 SA1379 SA1436 SA1684 SA2128 SA2161 SA2321 SA2343 SA2491 SAS013 SAS016 SA0309 SA1007 SAS065 SA2209 SA2208 SA2463 SA2284...”
- “...SA0453 SA0754 SA1037 SA1240 SA1275 SA1319 SA1388 SA1611 SA1684 SA1889 SA1928 SA1944 SA2161 SA2321 SA2343 SA2491 SAS016 SA2291 SA2291 SA1007 SAS065 SA2209 SA2208...”
- Isocyanides inhibit bacterial pathogens by covalent targeting of essential metabolic enzymes
Geißler, Chemical science 2024 - “...melting points ( X ) for the most stabilized protein nucleoside triphosphate/diphosphate phosphatase (Uniprot ID: Q2G2M8) of I16-treated (violet) and DMSO-treated (orange) cells. Two biological replicates are shown. (D) Thermal-response curves and calculated melting points ( X ) of I16-treated (violet) and DMSO-treated (orange) cells for...”
- “...in the TPP experiment passing all significance criteria is a nucleoside triphosphate/diphosphate phosphatase (Uniprot ID: Q2G2M8) ( Fig. 3C ). It is noteworthy that this non-essential phosphatase has been reported to play a crucial role in virulence and is required for hemolysin production, 43 providing a...”
- Coordinated adaptation of Staphylococcus aureus to calprotectin-dependent metal sequestration
Reyes, mBio 2024 - “...putative DNA binding protein ( NWMN_ RS06710 ), and hypothetical proteins such as NWMN_RS05475 and NWMN_RS10060 (Table S10). In response to WTCP, 24 genes with decreased expression showed an increased bacterial fitness when mutated ( Fig. 4E ; Table S10). These included de novo purine biosynthesis...”
BA0527 conserved hypothetical protein from Bacillus anthracis str. Ames
Aligns to 59:124 / 176 (37.5%), covers 98.5% of PF04167, 69.4 bits
- Involvement of NF-κB in the reversal of CYP3A down-regulation induced by sea buckthorn in BCG-induced rats
Liu, PloS one 2020 - “...sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), rat IL-1 ELISA (No. BA2913), TNF- ELISA (No. BA0527), and rabbit polyclonal antibodies against CYP3A (No. A00339), iNOS (No. EK0394), LMNA(Lamin A/C) (Cat. No. BA1227), and GAPDH (No. BA2913) were obtained from Wuhan Boster Biological Engineering Co. Ltd., Wuhan,...”
- NF-κB-mediated regulation of rat CYP2E1 by two independent signaling pathways
Lin, PloS one 2019 - “...enzyme-linked immunosorbent assay (ELISA) kit (catalog number: BA2913), and rat TNF- ELISA kit (catalog number: BA0527) were obtained from Wuhan Boster Biological Engineering Limited Company. The RT-PCR Kit (catalog number: BMB05M1) was purchased from Biosystems Research Corp. (Nanjing, China). The RT-PCR primers were synthesized by Sangon...”
OG1RF_10435 biofilm phosphatase Bph from Enterococcus faecalis OG1RF
EF0697 conserved hypothetical protein from Enterococcus faecalis V583
Aligns to 59:124 / 177 (37.3%), covers 98.5% of PF04167, 69.0 bits
- A previously uncharacterized gene, PA2146, contributes to biofilm formation and drug tolerance across the ɣ-Proteobacteria
Kaleta, NPJ biofilms and microbiomes 2022 - “...and identified eight uncharacterized predicted protein-coding genes required for both early and late biofilms, with OG1RF_10435 harboring phosphatase activity being required for surface attachment, and OG1RF_10435 leading to widespread differences in protein expression and altered arginine catabolism. Likewise, Moorthy and Watnick 18 inferred the expression of...”
- Comparative Biofilm Assays Using Enterococcus faecalis OG1RF Identify New Determinants of Biofilm Formation
Willett, mBio 2021 - “...name Description Intergenic_442 427629 IGR between OG1RF_10412 and OG1RF_10413 Intergenic_464 449894 IGR between OG1RF_10434 and OG1RF_10435 OG1RF_10435 450277, 450467 bph Biofilm phosphatase Intergenic_482 469369 IGR between OG1RF_10452 and OG1RF_10453 OG1RF_10506 530068, 530167, 530274 Hypothetical protein Intergenic_563 558335 IGR between OG1RF_10532 and OG1RF_10533 OG1RF_10533 559075 atlA or...”
- Exploiting biofilm phenotypes for functional characterization of hypothetical genes in Enterococcus faecalis
Willett, NPJ biofilms and microbiomes 2019 - “...regions and identified eight uncharacterized predicted protein-coding genes required for biofilm formation. We demonstrate that OG1RF_10435 encodes a phosphatase that modulates global protein expression and arginine catabolism and propose renaming this gene bph (biofilm phosphatase). We present a workflow for combining phenotype-driven experimental and computational evaluation...”
- “...biofilm formation, three of which are important for in vitro surface attachment. Further experiments identified OG1RF_10435 ( bph ) as a phosphatase We found Tn mutations in eight hypothetical genes (OG1RF_10435, OG1RF_10506, OG1RF_10733, OG1RF_10877, OG1RF_11263, OG1RF_11769, OG1RF_12322, and OG1RF_12502) that lead to a defect in early...”
- Transcriptome analysis of Enterococcus faecalis during mammalian infection shows cells undergo adaptation and exist in a stringent response state
Frank, PloS one 2014 - “...EF0246 ABC superfamily ATP binding cassette transporter, ABC protein EF0475 ferrous iron transport protein A EF0697 hypothetical protein EF0849 alanine racemase EF1084 universal stress protein EF2355 chaperone protein ClpB EF2987 integrating conjugative element protein 8 h microarray UP+RIVET sense EF0383 hypothetical protein 2 h microarray DOWN...”
SpyM3_1356 conserved hypothetical protein from Streptococcus pyogenes MGAS315
Aligns to 59:124 / 177 (37.3%), covers 98.5% of PF04167, 67.1 bits
- Novel regulatory small RNAs in Streptococcus pyogenes
Tesorero, PloS one 2013 - “...SSRC30 * SPyM3_1280 3-dehydroquinate synthase >>> SPyM3_1281 putative acetate kinase <<< Q, Z, P SSRC31 SPyM3_1356 hypothetical protein >>> SPyM3_1357 hypothetical protein >>> Q, Z SSRC32 * SPyM3_1386 putative N6-adenine-specific DNA methylase <<< SPyM3_1387 hypothetical protein <<< Q, Z, P [20] , [42] SSRC33 * SPyM3_1391...”
Spy49_1243 hypothetical protein from Streptococcus pyogenes NZ131
Aligns to 59:124 / 177 (37.3%), covers 98.5% of PF04167, 67.1 bits
LSA1475 Hypothetical protein from Lactobacillus sakei subsp. sakei 23K
Aligns to 59:124 / 178 (37.1%), covers 98.5% of PF04167, 66.9 bits
lmo1687 similar to hypothetical proteins from Listeria monocytogenes EGD-e
Aligns to 59:124 / 175 (37.7%), covers 98.5% of PF04167, 66.4 bits
FAU1_THEKO / Q5JHN3 Probable ribonuclease FAU-1; RNA-binding protein FAU-1; EC 3.1.26.- from Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1) (Pyrococcus kodakaraensis (strain KOD1)) (see paper)
TK2227 RNA-binding protein FAU-1 from Thermococcus kodakaraensis KOD1
Aligns to 376:443 / 471 (14.4%), covers 100.0% of PF04167, 66.4 bits
- function: Probable RNase involved in rRNA stability through maturation and/or degradation of precursor rRNAs. Preferentially cleaves UA sequences in the 5' precursor region of 5S rRNA (PubMed:28978920). Binds to RNA in loop regions with AU-rich sequences (By similarity).
disruption phenotype: Deletion mutant shows a delay of exponential phase, reduction of maximum cell number and significant changes in the nucleotide sequence lengths of its 5S, 16S, and 23S rRNAs in early exponential phase. - An archaeal RNA binding protein, FAU-1, is a novel ribonuclease related to rRNA stability in Pyrococcus and Thermococcus
Ikeda, Scientific reports 2017 - “...as follows. To construct pET-tko-FAU-1His, a DNA fragment encoding the tko fau-1 gene (KEGG ID: TK2227) was amplified from the T. kodakarensis chromosomal DNA with PCR and the primer set T0005/T0006 containing Nde I and Xho I sites. The amplified fragment was digested with Nde I...”
- “...phosphatase (Takara bio) for 30 min at 37C. Construction of a gene disruption plasmid for TK2227 A gene disruption plasmid encoding the tko fau-1 gene (TK2227) (designated pUD3_2227D) was constructed as follows. The TK2227 gene, together with its 5- and 3-flanking regions (~1 kbp), was amplified...”
- Affinity purification of an archaeal DNA replication protein network
Li, mBio 2010 - “...589 16,212 35 82 Unknown TK1633 352 29,757 15 46 Exosome complex RNA-binding protein Rrp42 TK2227 235 54,037 11 12 RNA-binding protein FAU-1 TK1634 202 27,668 10 23 Exosome complex exonuclease Rrp41 Fen1, TK1281 TK1281 2,608 38,786 581 82 Fen1 TK0535 1,967 28,222 361 89 PCNA1...”
A3CPV9 Nucleoside triphosphate/diphosphate phosphatase from Streptococcus sanguinis (strain SK36)
SSA_1832 hypothetical protein from Streptococcus sanguinis SK36
Aligns to 59:124 / 177 (37.3%), covers 98.5% of PF04167, 65.8 bits
SPD_1706 hypothetical protein from Streptococcus pneumoniae D39
HMPREF0837_12134, PCS8235_RS10555 DUF402 domain-containing protein from Streptococcus pneumoniae PCS8235
Aligns to 59:124 / 177 (37.3%), covers 98.5% of PF04167, 64.6 bits
llmg_1550 hypothetical protein from Lactococcus lactis subsp. cremoris MG1363
Aligns to 59:124 / 176 (37.5%), covers 98.5% of PF04167, 64.4 bits
3cbtA / Q9FBN7 Crystal structure of sc4828, a unique phosphatase from streptomyces coelicolor
Aligns to 81:148 / 210 (32.4%), covers 95.6% of PF04167, 62.8 bits
- Ligand: magnesium ion (3cbtA)
SCO5041 hypothetical protein from Streptomyces coelicolor A3(2)
Aligns to 103:170 / 236 (28.8%), covers 95.6% of PF04167, 62.5 bits
SAOUHSC_00678 hypothetical protein from Staphylococcus aureus subsp. aureus NCTC 8325
SAUSA300_0657 hypothetical protein from Staphylococcus aureus subsp. aureus USA300_FPR3757
AYM28_03635 DUF402 domain-containing protein from Staphylococcus aureus
Aligns to 61:128 / 214 (31.8%), covers 100.0% of PF04167, 61.7 bits
- Genome-wide CRISPRi screens for high-throughput fitness quantification and identification of determinants for dalbavancin susceptibility in Staphylococcus aureus
Liu, mSystems 2024 - “...SAOUHSC_00892 _00892 Unknown 2.2 6.2E12 0.045 b SAOUHSC_00646 pbp4 Penicillin-binding protein 4 1.9 7.1E12 0.03 SAOUHSC_00678 _00678 Unknown 2.1 4.3E09 0.045 SAOUHSC_01055 imp Inositol monophosphatase family protein 1.8 1.2E08 n.t. SAOUHSC_02383 facZ EVE-domain protein 3.0 3.3E06 0.045 SAOUHSC_00743 nrdF Ribonucleotide-diphosphate reductase 2.4 5.9E-06 0.045 b SAOUHSC_00472...”
- “...Targeted genes were dltA ( D ), vraFG ( E ), ezrA ( F ), SAOUHSC_00678 ( G ), SAOUHSC_ 00892 ( H ), rpsF-ssb-rpsR ( I ), and nrdF ( J ). Averages of triplicates with standard errors are shown. Fig 5 Contribution of pbp4...”
- Blunted blades: new CRISPR-derived technologies to dissect microbial multi-drug resistance and biofilm formation
Gager, mSphere 2024 - “...operon ( rpsF-ssb-rpsR ), and biosynthesis of deoxyribonucleotides ( nrdF ). Additionally, the uncharacterized genes SAOUHSC_00678 and SAOUHSC_00892 (a putative RNA-binding protein) were found to be involved in antimicrobial susceptibility. Interestingly, silencing the lipoprotein KapB, a non-essential gene ( kapB ), only confers resistance to dalbavancin...”
- Genome-wide CRISPRi screens reveal the essentialome and determinants for susceptibility to dalbavancin inStaphylococcus aureus
Liu, 2023 - Identification of Methicillin-Resistant Staphylococcus aureus (MRSA) Genetic Factors Involved in Human Endothelial Cells Damage, an Important Phenotype Correlated with Persistent Endovascular Infection
Xiao, Antibiotics (Basel, Switzerland) 2022 - “...hypothetical glycine dehydrogenase subunit 1 14.08 4.09 SAUSA300_1682 ccpA catabolite control protein A 14.04 8.43 SAUSA300_0657 hypothetical hypothetical protein 14.02 7.45 SAUSA300_1955 hypothetical putative endodeoxyribonuclease RusA 13.92 10.12 SAUSA300_0924 ktrD sodium transport family protein 13.85 14.78 SAUSA300_0077 hypothetical ABC transporter ATP-binding protein 13.80 6.67 SAUSA300_0504 pdxS...”
- Protein CoAlation and antioxidant function of coenzyme A in prokaryotic cells
Tsuchiya, The Biochemical journal 2018 - “...VALDGGFDC*PNR 116.87 yjlD NADH dehydrogenase 39.399 IYNC*DEPK 160.72 SAZ172_2586 Mutator mutT protein 11.465 C*DLIVGDK 63.073 AYM28_03635 Protein of uncharacterized function 14.312 IMYC*FNK 132.08 SAKOR_01397 ATP-dependent helicase, DinG family protein 104.19 C*LVLFTSYK 112.13 SAOUHSC_02393 Uncharacterized protein 25.34 C*LANNDVQIMNSIK 78.674 panD Aspartate 1-decarboxylase 14.05 IC*LNGAASR 112.64 purA Adenylosuccinate...”
SSO1093 Conserved hypothetical protein from Sulfolobus solfataricus P2
Aligns to 325:392 / 424 (16.0%), covers 98.5% of PF04167, 60.9 bits
FAU-1 / BAB91152.1 RNA-binding protein FAU-1 from Pyrococcus furiosus (see paper)
Aligns to 377:444 / 472 (14.4%), covers 100.0% of PF04167, 59.5 bits
8wo8A / Q8U4Q7 Crystal structure of an RNA-binding protein, fau-1, from pyrococcus furiosus (see paper)
Aligns to 368:435 / 463 (14.7%), covers 100.0% of PF04167, 59.5 bits
FAU1_PYRFU / Q8U4Q7 Probable ribonuclease FAU-1; FAU-1 protein; P.furiosus AU-binding; RNA-binding protein AU-1; RNA-binding protein FAU-1; EC 3.1.26.- from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (see 2 papers)
Aligns to 374:441 / 469 (14.5%), covers 100.0% of PF04167, 59.5 bits
- function: Probable RNase involved in rRNA stability through maturation and/or degradation of precursor rRNAs. Preferentially cleaves UA sequences in the 5' precursor region of 5S rRNA (PubMed:28978920). Binds to RNA in loop regions with AU-rich sequences. Binds to the consensus sequence GGC(U/A)(U/A)U(U/C) in vitro (PubMed:12614195).
subunit: Mainly homotrimer, but may form homohexamer, and homononamer. - Domain atrophy creates rare cases of functional partial protein domains
Prakash, Genome biology 2015 - “...RNase_E_G domain (Pfam: PF10150) The RNase E domain of Pyrococcus furiosus RNA-binding protein AU-1 (UniProt: Q8U4Q7) shows atrophy at the C-terminus with a score of 0.19. The P. furiosus RNA-binding protein is a large oligomeric complex that binds specifically to AU-rich RNA sequences and may be...”
NWMN_0640 hypothetical protein from Staphylococcus aureus subsp. aureus str. Newman
Aligns to 61:128 / 214 (31.8%), covers 100.0% of PF04167, 58.5 bits
Rv1632c hypothetical protein from Mycobacterium tuberculosis H37Rv
Aligns to 28:95 / 147 (46.3%), covers 100.0% of PF04167, 55.5 bits
- Structure-Aware Mycobacterium tuberculosis Functional Annotation Uncloaks Resistance, Metabolic, and Virulence Genes
Modlin, mSystems 2021 - “...Conserved protein Rv0738 2nsg 17% 5.2.1.- None Reduced specificity Putative thiol-dependent DinB-like metalloenzyme Conserved protein Rv1632c 2p12 59% 3.6.1.- 3.6.1.- Verified Putative cytidylyl-2-hydroxypropylphosphonate hydrolase Hypothetical protein Rv1727 2nsg 12% 5.2.1.- None Reduced specificity Putative thiol-dependent DinB-like metalloenzyme Conserved hypothetical protein Rv1734c 3l60 26% 1.2.4.- 2.3.-.- Changed...”
- The gene expression data of Mycobacterium tuberculosis based on Affymetrix gene chips provide insight into regulatory and hypothetical genes
Fu, BMC microbiology 2007 - “...ACCD6 KASB Rv2052C Rv1728C ARGH) Intermediate and lipid metabolism 2 (DRRB Rv1251C EFPA Rv2054 MURC Rv1632C Rv2395 Rv1378C QCRA CTAE RHO PARB Rv3321C ATPH Rv3921C ATPD Rv3805C Rv2901C PARA Rv2949C CTAC Rv1576C ATPB Rv0546C Rv2781C Rv0526 Rv3104C POLA PYRH Rv1870C Rv1711 Rv3672C Rv0514 DAPF Rv2554C Rv1869C...”
- “...Rv3672c Rv2554c Rv3856c Rv3212 Rv1043c Rv0525 Rv1339 Rv2956 Rv2759c Rv2879c Rv1780 Rv2475c Rv2752c Rv0177 Rv2367c) (Rv1632c Rv2808 Rv3122 Rv1907c) Zone-3 (Information Pathways) (Rv2147c Rv3267 Rv1697 Rv3909 Rv2574 Rv3376 Rv2125 Rv1546 Rv1099c Rv2908c Rv1073 Rv0636 Rv0637 Rv0277c) (Rv2826c Rv2360c Rv2827c Rv3647c Rv0299 Rv2822c Rv0057) Zone-4 (Cell Wall,...”
NCgl1051 DUF402 domain-containing protein from Corynebacterium glutamicum ATCC 13032
cg1246 hypothetical protein from Corynebacterium glutamicum ATCC 13032
Aligns to 52:119 / 179 (38.0%), covers 100.0% of PF04167, 53.6 bits
- High-throughput screening of a Corynebacterium glutamicum mutant library on genomic and metabolic level
Reimer, PloS one 2014 - “...+ P8F10 2380663 NCgl2167 Pyruvate dehydrogenase subunit E1 1.2.4.1 0.96 48 + + P8F12 1142652 NCgl1051 Hypothetical protein + 0.95 55 + + P8G3 1690962 NCgl1533 GTP cyclohydrolase II + 3.5.4.25 0.94 40 + + P21D2 3119587 intergenic 0.98 81 + P21E9 1525622 NCgl1392 Hypothetical protein...”
- “...mutant which showed an increased proline level is P8F12. The function of the disrupted gene NCgl1051 is still unknown. As shown in figure 5B , this mutant had a highly increased proline level (10 fold), but only a slightly increased level of glutamine (1.4 fold). The...”
- Cg1246, a new player in mycolic acid biosynthesis in Corynebacterium glutamicum
de, Microbiology (Reading, England) 2022 (PubMed)- “...other mycolate-containing compounds. Using a random transposition mutagenesis, we recently identified a new uncharacterized protein (Cg1246) involved in mycolic acid metabolism. Cg1246 belongs to the DUF402 protein family that contains some previously characterized nucleoside phosphatases. In this study, we performed a functional and structural characterization of...”
- “...glutamicum, resulting in a decrease in all other mycolate-containing compounds. We found that, in vitro, Cg1246 has phosphatase activity on organic pyrophosphate substrates but is most likely not a nucleoside phosphatase. Using a computational approach, we identified important residues for phosphatase activity and constructed the corresponding...”
- Genome-wide identification of novel genes involved in Corynebacteriales cell envelope biogenesis using Corynebacterium glutamicum as a model
de, PloS one 2020 - “...R , derivative of RES167 (originally the gene was named accD4 ) [ 22 ] cg1246 cg1246 derivative of RES167 This work cg1247 cg1247 derivative of RES167 This work Plasmids pCR2.1-TOPO E . coli cloning vector with f1 and pUC origins, lac Z, Km R ,...”
- “...[ 23 ] pK18MobSac Km r sacB RP4 oriT ColE1 ori [ 24 ] pK18MobSac- cg1246 pK18MobSac containing the upstream and downstream regions of the cg1246 ORF, construct for cg1246 deletion This work pCGL482 Shuttle vector E coli / C . glutamicum , Cm R [...”
SACE_5423 hypothetical protein from Saccharopolyspora erythraea NRRL 2338
Aligns to 64:131 / 184 (37.0%), covers 98.5% of PF04167, 53.1 bits
D9Q9M1 DUF402 domain-containing protein from Corynebacterium pseudotuberculosis (strain C231)
Cp1002B_1903 DUF402 domain-containing protein from Corynebacterium pseudotuberculosis
Aligns to 52:119 / 177 (38.4%), covers 100.0% of PF04167, 53.1 bits
5zdmA / D2SNF7 The ligand-free structure of fomd (see paper)
Aligns to 69:138 / 198 (35.4%), covers 95.6% of PF04167, 43.1 bits
- Ligand: calcium ion (5zdmA)
FOMD_STRFR / D2SNF7 Cytidylyl-2-hydroxypropylphosphonate hydrolase; EC 3.6.1.- from Streptomyces fradiae (Streptomyces roseoflavus) (see paper)
Aligns to 78:147 / 207 (33.8%), covers 95.6% of PF04167, 42.4 bits
- function: Involved in fosfomycin biosynthesis (PubMed:30010320). Catalyzes the hydrolysis of cytidylyl (S)-2-hydroxypropylphosphonate ((S)-HPP-CMP) to give (S)-2-hydroxypropylphosphonate ((S)-HPP) and CMP (PubMed:30010320). Can also hydrolyze (R)-HPP-CMP and cytidylyl 2- hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation, but the catalytic efficiency is much higher with (S)-HPP-CMP (PubMed:30010320).
catalytic activity: cytidine 5'-({hydroxy[(S)-2- hydroxypropyl]phosphonoyl}phosphate) + H2O = (S)-2- hydroxypropylphosphonate + CMP + H(+) (RHEA:77231)
cofactor: Mn(2+) Co(2+)
fomD / O83033 cytidylyl-2-hydroxypropylphosphonate hydrolase from Streptomyces wedmorensis (see paper)
FOMD_STRWE / O83033 Cytidylyl-2-hydroxypropylphosphonate hydrolase; EC 3.6.1.- from Streptomyces wedmorensis (see paper)
Aligns to 80:149 / 209 (33.5%), covers 95.6% of PF04167, 42.4 bits
- function: Involved in fosfomycin biosynthesis (PubMed:30010320). Catalyzes the hydrolysis of cytidylyl (S)-2-hydroxypropylphosphonate ((S)-HPP-CMP) to give (S)-2-hydroxypropylphosphonate ((S)-HPP) and CMP (PubMed:30010320). Can also hydrolyze (R)-HPP-CMP and cytidylyl 2- hydroxyethylphosphonate (HEP-CMP), which is a biosynthetic intermediate before C-methylation, but the catalytic efficiency is much higher with (S)-HPP-CMP (PubMed:30010320).
catalytic activity: cytidine 5'-({hydroxy[(S)-2- hydroxypropyl]phosphonoyl}phosphate) + H2O = (S)-2- hydroxypropylphosphonate + CMP + H(+) (RHEA:77231)
cofactor: Mn(2+) Co(2+)
subunit: Monomer in solution. - Overall Retention of Methyl Stereochemistry during B12-Dependent Radical SAM Methyl Transfer in Fosfomycin Biosynthesis
McLaughlin, Biochemistry 2021 - “...with modifications described in the Supporting Information Materials and Methods . His 6 -FomD (UniProtKB O83033) was expressed and purified as described previously. 17 Codon-optimized synthetic genes encoding the B. subtilis SAM synthetase (MetK, UniProtKB P54419) I317V variant and Saccharomyces cerevisiae malate synthase (ScMLS1, UniProtKB P30952)...”
- “...Table S1 ( PDF ) Supplementary Material bi1c00113_si_001.pdf Accession Codes Fom3, UniProtKB Q56184; FomD, UniProtKB O83033; MetK, UniProtKB P54419; ScMLS1, UniProtKB P30952; acetate kinase, UniProtKB P0A6A3; phosphotransacetylase, UniProtKB P39646; fumarase, UniProtKB P10173. Author Contributions M.I.M. and K.P. contributed equally to this work. This study was supported...”
- Stereospecific Radical-Mediated B<sub>12</sub>-Dependent Methyl Transfer by the Fosfomycin Biosynthesis Enzyme Fom3
McLaughlin, Biochemistry 2018 - “...convert 2-HPP-CMP to 2-HPP, we expressed N-terminally His 6 -tagged FomD from S. wedmorensis (UniProtKB O83033), the previously suggested candidate for catalysis of the hydrolysis step. 10 , 11 FomD indeed hydrolyzed both the putative native substrate (2 S )-2-HPP-CMP and the 2 R diastereomer (...”
Or search for genetic data about PF04167 in the Fitness Browser
by Morgan Price,
Arkin group
Lawrence Berkeley National Laboratory