Family Search for PF04167 (DUF402)

Running HMMer for PF04167

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

• Distinct co-evolution patterns of genes associated to DNA polymerase III DnaE and PolC
  Engelen, BMC genomics 2012
  • “..." _ conserved hypothetical protein group 3 BSU15840 yloV dhaL putative dihydroxyacetone/glyceraldehyde kinase group 3 BSU08680 ygaC " _ putative factor, domain associated with ribonuclease E and G, possibly involved in Fe-S group formation 2 degradosome network group 3 BSU15970 ylxM "- conserved hypothetical protein 2...”

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...”

Spy49_1243 hypothetical protein from Streptococcus pyogenes NZ131
Aligns to 59:124 / 177 (37.3%), covers 98.5% of PF04167, 67.1 bits

• Identification of novel growth phase- and media-dependent small non-coding RNAs in Streptococcus pyogenes M49 using intergenic tiling arrays
  Patenge, BMC genomics 2012
  • “...49 - Spy49_1217c Spy49_1218c SR1251900 [ 20 ] b 34 sRNASpy491243 1246370 1246419 49 + Spy49_1243 Spy49_1244 a 35 sRNASpy491275c 1282084 1282413 329 - Spy49_1275c Spy49_1276c RNaseP_bact b RNA1320100 [ 20 ] c 36 sRNASpy491311c 1321638 1321853 d 84 - e glyQ Spy49_1312c b 37 sRNASpy491336c...”

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...”

LSA1475 Hypothetical protein from Lactobacillus sakei subsp. sakei 23K
Aligns to 59:124 / 178 (37.1%), covers 98.5% of PF04167, 66.9 bits

• Alternative sigma factor σH activates competence gene expression in Lactobacillus sakei
  Schmid, BMC microbiology 2012
  • “...LSA0991 Hypothetical protein with putative NAD-binding domain, NmrA structural superfamily 1.02E-04 > threshold 1.6 0.2 LSA1475 Hypothetical protein, conserved in bacteria 1.62-12 > threshold 2.1 0.5 CDS Gene Name Product qPCR LSA0487 recA DNA recombinase A 2.7 0.7 LSA0992 dprA DNA protecting protein, involved in DNA...”

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...”

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

• Listeria monocytogenes MDR transporters are involved in LTA synthesis and triggering of innate immunity during infection
  Tadmor, Frontiers in cellular and infection microbiology 2014
  • “...protein Mobility and chemotaxis LMRG_00402.2 lmo0713 Flagellar basal-body M-ring protein fliF Mobility and chemotaxis LMRG_02761.6 lmo1687 N/A Unknown LMRG_02767.6 lmo1693 N/A Unknown LMRG_01002.6 lmo1855 D-alanyl-D-alanine carboxipeptidase Cell wall LMRG_01003.6 lmo1856 Purine nucleoside phosphorylase Nucleotide metabolism (B) L. monocytogenes MUTANTS THAT INDUCE HIGH LEVELS OF IFN- LMRG_00151.6...”
• Membrane chaperone SecDF plays a role in the secretion of Listeria monocytogenes major virulence factors
  Burg-Golani, Journal of bacteriology 2013
  • “...lmo0713 lmo0724 lmo0847 20bp upstream lmo1072 lmo1527 lmo1687 lmo1693 lmo1855 lmo1856 lmo2110 lmo2531 lmo2715 lmo2461 and lmo1606 PrfA main virulence regulator...”

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

• Environmental influences on Streptococcus sanguinis membrane vesicle biogenesis
  Helliwell, The ISME journal 2023
  • “...SSA_1797 SSA_1909 A3CLJ9 SSA_0613 SSA_0159 A3CMV6 SSA_1099 A3CPV9 A3CPU4 SSA_1817 A3CPY0 A3CQM2 SSA_2109 SSA_1832 A3CPK9 SSA_1732 SSA_1854 A3CNC9 SSA_1283...”
• Environmental influences on Streptococcus sanguinis membrane vesicle biogenesis
  Helliwell, The ISME journal 2023
  • “...4 2 4 Number detected SSA_1291 SSA_0647 SSA_1909 SSA_0159 SSA_1832 SSA_1854 zmpB SSA_1505 ukp SSA_1249 cpsY pabC gtfP SSA_1099 SSA_1817 fusA upp nrd fba ftsH...”
  • “...SSA_1099 A3CPV9 A3CPU4 SSA_1817 A3CPY0 A3CQM2 SSA_2109 SSA_1832 A3CPK9 SSA_1732 SSA_1854 A3CNC9 SSA_1283 A3CQB9 A3CQA8 SSA_1992 SSA_2004 A3CJX9 A3CM70 SSA_0848...”

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

• The bacterial tyrosine kinase system CpsBCD governs the length of capsule polymers
  Nakamoto, Proceedings of the National Academy of Sciences of the United States of America 2021 (secret)
• 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)
• Exploration of Streptococcus core genome to reveal druggable targets and novel therapeutics against S. pneumoniae
  Chowdhury, PloS one 2022
  • “...1 MULTISPECIES: DNA-dependent RNA polymerase auxiliary subunit epsilon family protein [ Streptococcus ] 27 . PCS8235_RS10555 J1NSH0_STREE UPF0374 protein AMCSP13_002284 OS = S . pneumoniae 2070335 OX = 914141 GN = AMCSP13_002284 PE = 3 SV = 1 UPF0374 protein SSU05 [ S . pneumoniae ]...”
  • “...DEG10070224 7.65E-55 164 PCS8235_RS08090 DEG10070008 9.91E-61 179 PCS8235_RS08125 DEG10210140 0.29 31.6 PCS8235_RS08375 DEG10070005 4.49E-50 151 PCS8235_RS10555 DEG10620252 1.79E-77 228 PCS8235_RS10805 DEG10390037 7.16E-50 174 Virulence factors and pathogenicity Virulence factors are the basis of bacterial infections. The virulent and pathogenic proteins help microbes invade the host and...”
• Prophage Excision in Streptococcus pneumoniae Serotype 19A ST320 Promote Colonization: Insight Into Its Evolution From the Ancestral Clone Taiwan 19F-14 (ST236)
  Chen, Frontiers in microbiology 2019
  • “...a single copy of the integrase gene was inserted into the non-coding region between the HMPREF0837_12134 and HMPREF0837_12135 as follows. The integrase gene was PCR amplified from 19A ST320 by using the primer pair Pint-F/int-R, and then cloned into the pGEM -T easy plasmid to generate...”

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

• The transcriptional and gene regulatory network of Lactococcus lactis MG1363 during growth in milk
  de, PloS one 2013
  • “...purine biosynthesis; it was found upstream of only three other genes, yajC , llmg_1234 and llmg_1550 previously unlinked to purine biosynthesis. Strikingly, a tiled motif is present upstream of genes coding for other proteins involved in purine biosynthesis, namely purL, pbuO, purM, purC . This motif...”

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

• The intriguing biology and chemistry of fosfomycin: the only marketed phosphonate antibiotic
  Cao, RSC advances 2019
  • “...enzyme catalyzing this reaction is FomD, which shows a 34% identity to a putative phosphatase SCO5041 in Streptomyces coelicolor A3(2) and is a DUF402 domain-containing protein. Currently, the crystal structure of FomD has been elucidated. 64,65 8.1.5 The conversion of ( S )-HPP to fosfomycin The...”

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

• Something old, something new, something borrowed; how the thermoacidophilic archaeon Sulfolobus solfataricus responds to oxidative stress
  Maaty, PloS one 2009
  • “...1.735 COG0719 N ABC transporter, permease protein SSO2671 1.61E-02 1.704 COG1173 Y Conserved hypothetical protein SSO1093 3.07E-02 1.68 COG1530 Y Phosphoribosylamineglycine ligase (GAR synthetase) (GARS) (purD) SSO0635 4.28E-02 1.666 COG0151 Y hypothetical protein SSO1373 2.46E-03 1.659 hypothetical protein SSO3128 1.34E-03 1.629 COG1848 Y Oxidoreductase SSO3014 3.52E-02...”

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

• Ligand: rna (8wo8A)

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

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

• The catabolite control protein E (CcpE) affects virulence determinant production and pathogenesis of Staphylococcus aureus
  Hartmann, The Journal of biological chemistry 2014
  • “...ccpE::lox72 TH01 harboring plasmid pTH2c cis-integrated at the NWMN_0640 locus, leading to a duplication of the NWMN_0640 gene, ccpE, Tcr Escherichia coli-S....”
• Catabolite control protein E (CcpE) is a LysR-type transcriptional regulator of tricarboxylic acid cycle activity in Staphylococcus aureus
  Hartmann, The Journal of biological chemistry 2013
  • “...Regulation of TCA Cycle Activity by CcpE (1) Newman NWMN_0640 NWMN_0640` (2) pTH2 (3) THa (4) TH01 ccpE aphAIII lox66 NWMN_0640 aphAIII (6) TH01c NWMN_0642...”
  • “...lox71 lox66 NWMN_0640 NWMN_0642 lox72 ccpE pBT NWMN_0640 ccpE NWMN_0640 lox72 pBT FIGURE 1. Schematic representation of the ccpE region of S. aureus and the...”

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

• Comparative genomics and transcriptional profiles of Saccharopolyspora erythraea NRRL 2338 and a classically improved erythromycin over-producing strain
  Peano, Microbial cell factories 2012
  • “...Type III restriction enzyme, res subunit. SACE_5105: Transposase SACE_5311 835 Missense (G411R) Frameshift Unknown function SACE_5423 184 (-G 372, -G 473, -C 481,-G 493,-T 409,-C 540) Unknown function SACE_5446 1184 Frameshift (-C 2898) Unknown function SACE_5460 330 Missense (P162F) Unknown function SACE_5482 632 Missense (L509P) Unknown...”

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

• In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
  Araújo, PeerJ 2020
  • “...D9Q9R4 Cell wall-anchor domain LPxTG Cp1002B_1865 D9Q9Q9 Ferric reductase FhuF Cp1002B_1885 D9Q9N9 DivIVA-containing protein Cp1002B_1903 D9Q9M1 Fosfomycin biosynthetic protein FomD Cp1002B_1935 D9Q9I9 LGFP peptidoglycan-binding protein Cp1002B_1942 D9Q9I1 Flavodoxin-like protein Cp1002B_1944 D9Q9H9 PgaD-like protein Cp1002B_1949 D9Q9H4 Bax1-inhibitor protein Cp1002B_1975 D9Q9E9 Sulfolipid-1-addressing protein SfLAP Cp1002B_1992 D9Q9D3 Substrate-binding periplasmic...”
• In silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis
  Araújo, PeerJ 2020
  • “...Cp1002B_1860 D9Q9R4 Cell wall-anchor domain LPxTG Cp1002B_1865 D9Q9Q9 Ferric reductase FhuF Cp1002B_1885 D9Q9N9 DivIVA-containing protein Cp1002B_1903 D9Q9M1 Fosfomycin biosynthetic protein FomD Cp1002B_1935 D9Q9I9 LGFP peptidoglycan-binding protein Cp1002B_1942 D9Q9I1 Flavodoxin-like protein Cp1002B_1944 D9Q9H9 PgaD-like protein Cp1002B_1949 D9Q9H4 Bax1-inhibitor protein Cp1002B_1975 D9Q9E9 Sulfolipid-1-addressing protein SfLAP Cp1002B_1992 D9Q9D3 Substrate-binding...”

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 B₁₂-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 (...”

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