Family Search for PF06973 (DUF1297)

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PF06973 hits 17 sequences in PaperBLAST's database above the trusted cutoff. Showing all hits. Or show only hits to curated sequences or try another family.

2r7kA / Q57600 Crystal structure of faicar synthetase (purp) from m. Jannaschii complexed with amppcp and aicar (see paper)
Aligns to 171:358 / 358 (52.5%), covers 99.5% of PF06973, 292.9 bits

• Ligands: phosphomethylphosphonic acid adenylate ester; aminoimidazole 4-carboxamide ribonucleotide (2r7kA)

purP / Q57600 FAICAR synthetase monomer (EC 6.3.4.23) from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (see 2 papers)
PURP_METJA / Q57600 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate--formate ligase; EC 6.3.4.23 from Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii) (see 2 papers)
Q57600 formate-phosphoribosylaminoimidazolecarboxamide ligase (EC 6.3.4.23) from Methanocaldococcus jannaschii (see 2 papers)
MJ0136 conserved hypothetical protein from Methanocaldococcus jannaschii DSM 2661
Aligns to 174:361 / 361 (52.1%), covers 99.5% of PF06973, 292.9 bits

• function: Catalyzes the ATP- and formate-dependent formylation of 5- aminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (FAICAR) in the absence of folates.
  catalytic activity: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + ATP + formate = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide + ADP + phosphate (RHEA:24836)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homohexamer. Dimer of trimers.
• Purine biosynthesis in archaea: variations on a theme
  Brown, Biology direct 2011
  • “...His 27 ( M. jannaschii numbering), which make contacts to the formyl group in the MJ0136 crystal structure [ 66 ]. Residues contacting the 5' monophosphate of AICAR were largely conserved, although we found conservative substitution with Thr at Ser 94. Ser 94 was not conserved...”
  • “...only a few gene products in the PurP-like family have been experimentally characterized. M. jannaschii MJ0136, in cluster Ia, is the formate-dependent AICAR formyltransferase originally designated PurP [ 8 ]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have...”
• Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
  Zhang, Biochemistry 2008
  • “...NIH-PA Author Manuscript Methanocaldococcus jannaschii purP gene Mj0136 was cloned into the expression vector pET19b and overexpressed in Escherichia coli...”
• A Methanocaldococcus jannaschii archaeal signature gene encodes for a 5-formaminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate synthetase. A new enzyme in purine biosynthesis
  Ownby, The Journal of biological chemistry 2005 (PubMed)
  • “...the product of the Methanocaldococcus jannaschii purP gene (MJ0136), which is a signature gene for Archaea. As is characteristic of reactions catalyzed by this...”
  • “...formate as substrates. Only the protein derived from the MJ0136 gene, which we designate as purP, catalyzed the desired reaction. Here we present the data on...”

MTH1201 conserved protein from Methanothermobacter thermautotrophicus str. Delta H
Aligns to 190:377 / 377 (49.9%), covers 100.0% of PF06973, 288.8 bits

• More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus
  Kaster, Archaea (Vancouver, B.C.) 2011
  • “...formyl phosphate as intermediate, as catalyzed by 5-formaminoimidazole-4-carboxamide-1 - d -ribofuranosyl 5-monophosphate synthetase (PurP) (MTBMA_c15790; MTH1201) [ 128 ]. CO 2 reduction to formate is their only means of generating formate. Accordingly, formate-dehydrogenase-negative mutants of M. marburgensis require formate for growth on H 2 and CO...”

MTBMA_c15790 formate--phosphoribosylaminoimidazolecarboxamide ligase from Methanothermobacter marburgensis str. Marburg
Aligns to 176:363 / 363 (51.8%), covers 100.0% of PF06973, 287.0 bits

• More than 200 genes required for methane formation from H₂ and CO₂ and energy conservation are present in Methanothermobacter marburgensis and Methanothermobacter thermautotrophicus
  Kaster, Archaea (Vancouver, B.C.) 2011
  • “...with formyl phosphate as intermediate, as catalyzed by 5-formaminoimidazole-4-carboxamide-1 - d -ribofuranosyl 5-monophosphate synthetase (PurP) (MTBMA_c15790; MTH1201) [ 128 ]. CO 2 reduction to formate is their only means of generating formate. Accordingly, formate-dehydrogenase-negative mutants of M. marburgensis require formate for growth on H 2 and...”

D7DS15 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase from Methanococcus voltae (strain ATCC BAA-1334 / A3)
Aligns to 174:361 / 361 (52.1%), covers 99.5% of PF06973, 281.7 bits

• Proteomic Analysis of Methanococcus voltae Grown in the Presence of Mineral and Nonmineral Sources of Iron and Sulfur
  Steward, Microbiology spectrum 2022
  • “...transporter-related proteins Extracellular solute-binding protein family 1 D7DV05 2.89244 2.05020 5-Formaminoimidazole-4-carboxamide-1-(beta)- d -ribofuranosyl 5-monophosphate synthetase D7DS15 11.55548 5.51428 ABC transporter-related protein D7DTS1 0.06359 0.01663 3.8233 0.0023623 ABC transporter-related protein D7DR50 0.23008 0.55915 2.43019 0.0003957 ABC transporter-related protein D7DT53 21.68802 15.94546 Formate/nitrite transporter D7DTM1 1.57738 1.21316 Substrate-binding...”

PF0421 hypothetical protein from Pyrococcus furiosus DSM 3638
Aligns to 189:380 / 380 (50.5%), covers 100.0% of PF06973, 272.1 bits

• Impact of growth mode, phase, and rate on the metabolic state of the extremely thermophilic archaeon Pyrococcus furiosus
  Khatibi, Biotechnology and bioengineering 2017
  • “...14 Energy metabolism PF0477 extracellular alpha amylase 3 17 50 Purines, pyrimidines, nucleosides, and nucleotides PF0421 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5-monophosphate synthetase --- 19 29 PF0422 phosphoribosylamine-glycine ligase --- 13 12 PF0426 phosphoribosylaminoimidazole carboxylase --- 7 8 PF0427 phosphoribosylaminoimidazole carboxylase 2 4 8 PF0430 phosphoribosylglycinamide formyltransferase 2 36 16...”
• Purine biosynthesis in archaea: variations on a theme
  Brown, Biology direct 2011
  • “...AICAR formyltransferase originally designated PurP [ 8 ]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have no AICAR formyltransferase activity previously [ 66 ], although activity under different conditions or with different substrates cannot be ruled out. Crude...”
• Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
  Zhang, Biochemistry 2008
  • “...P. furiosus, for example, has two purP genes (Pf0421 and Pf1517). In preliminary studies, neither P. furiosus gene product showed detectable FAICAR synthetase...”
  • “...Author Manuscript subgroups; and the second P. furiosus PurP (Pf0421) belongs to group 3. No gene product from group 2 or group 3 has been functionally...”

PAB1272 hypothetical protein from Pyrococcus abyssi GE5
Aligns to 189:380 / 380 (50.5%), covers 100.0% of PF06973, 270.6 bits

• Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
  Gao, BMC genomics 2007
  • “...Archaea. Of these proteins, 11 proteins (viz. PAB0654, PAB0950, PAB1135, PAB1906, PAB7388, PAB0547, PAB0552, PAB0623, PAB1272, PAB1429 and PAB1721) are mainly missing in the 4 Thermoplasmata species. Thermoplasmata are thermoacidophilic archaea which lack cell envelope [ 19 , 55 , 63 ](see Table 1 ). Some...”
  • “...[NP_127373] CDD5727 PAB0552 [NP_126501] Hjr CDD29957 PAB1135 [NP_127406] CDD8168 PAB0623 [NP_126611] CDD9586 PAB1241 [NP_127355] CDD9682 PAB1272 [NP_127310] COG1759 PAB1387 [NP_127161] flaJ COG1955 PAB1429 [NP_127105] COG2433 PAB1715 [NP_126667] CDD9801 PAB1721 [NP_126657] COG2248 PAB1906 [NP_126377] CDD2531 PAB2342 2 [NP_125707] CDD15774 PAB7094 [NP_126085] Alba CDD25844 PAB7309 [NP_126897] CDD2523 These...”

TK0203 hypothetical protein from Thermococcus kodakaraensis KOD1
Aligns to 189:380 / 380 (50.5%), covers 100.0% of PF06973, 267.6 bits

• Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis
  Sanders, Frontiers in microbiology 2021
  • “...component Purine metabolism 9.18 TK0204 Phosphoribosylamine-glycine ligase Purine metabolism 8.97 TK1392 NADH oxidase Metabolsim 8.74 TK0203 Phosphoribosyl formylglycinamidine cyclo-ligase Purine metabolism 8.43 TK1356 ATPase, AAA superfamily Unknown, viral region 4 8.41 TK0835 Phosphoribosy laminoimidazole carboxylase, ATPase subunit Purine metabolism 7 60 TK1393 Anaerobic glycerol 3-phosphate dehydrogenase...”
• An archaeal histone is required for transformation of Thermococcus kodakarensis
  Čuboňováa, Journal of bacteriology 2012
  • “...TK0475 TK0268 TK0269 TK0270 TK0271 TK1893 TK0835 TK0204 TK0203 TK1895 TK0010 TK2147 TK1002 TK1287 TK2138 TK1737 TK0766 TK1605 TK1961 TK1459 TK0252 Aspartate...”
  • “...(histone B) TK0264 TK2195 TK2196 TK0766 TK0157 TK0202 TK0203 TK0204 TK0190 TK0191 TK0192 TK0193 TK0194 TK0835 TK0207 TK0603 TK0604 TK1090 TK0561 TK1352 TK1583...”

SSO0239 Conserved hypothetical protein from Sulfolobus solfataricus P2
Aligns to 171:356 / 356 (52.2%), covers 99.5% of PF06973, 263.6 bits

• Dynamic metabolic adjustments and genome plasticity are implicated in the heat shock response of the extremely thermoacidophilic archaeon Sulfolobus solfataricus
  Tachdjian, Journal of bacteriology 2006
  • “...SSO0458 SSO1082 SSO1108 SSO1110 SSO2138 SSO2897 SSO3242 SSO0200 SSO0239 SSO0618 SSO0669 SSO1952 SSO2131 SSO5522 SSO10340 SSO2827 24.3 4.0 32.0 3.2 4.0 4.9 4.0...”

MCP_2462 5-formaminoimidazole-4-carboxamide-1-(beta)-D- ribofuranosyl 5'-monophosphate synthetase from Methanocella paludicola SANAE
Aligns to 175:362 / 362 (51.9%), covers 99.5% of PF06973, 261.7 bits

• Purine biosynthesis in archaea: variations on a theme
  Brown, Biology direct 2011
  • “...of the Methanococcales, Methanobacteriales, and Methanocella sp . RC-I, and one of the PurP-like proteins (MCP_2462) from Methanocella paludicola . As each of these organisms (except for M. paludicola ) has a single PurP with high similarity to M. jannaschii PurP and no PurH1, all are...”

PURP_PYRFU / Q8U0R7 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5'-monophosphate synthetase; 5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5'-monophosphate--formate ligase; EC 6.3.4.23 from Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1) (see paper)
2r86A / Q8U0R7 Crystal structure of purp from pyrococcus furiosus complexed with atp (see paper)
PF1517 hypothetical protein from Pyrococcus furiosus DSM 3638
Aligns to 150:334 / 334 (55.4%), covers 100.0% of PF06973, 258.9 bits

• function: Catalyzes the ATP- and formate-dependent formylation of 5- aminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (AICAR) to 5-formaminoimidazole-4-carboxamide-1-beta-d-ribofuranosyl 5'-monophosphate (FAICAR) in the absence of folates.
  catalytic activity: 5-amino-1-(5-phospho-beta-D-ribosyl)imidazole-4-carboxamide + ATP + formate = 5-formamido-1-(5-phospho-D-ribosyl)imidazole-4- carboxamide + ADP + phosphate (RHEA:24836)
  cofactor: Mg(2+) Mn(2+) (Binds 1 Mg(2+) or Mn(2+) ion per subunit.)
  subunit: Homotrimer and homohexamer.
• Ligands: phosphate ion; adenosine-5'-triphosphate (2r86A)
• Purine biosynthesis in archaea: variations on a theme
  Brown, Biology direct 2011
  • “...cluster Ia, is the formate-dependent AICAR formyltransferase originally designated PurP [ 8 ]. Pyrococcus furiosus PF1517, in cluster Ib, and PF0421, in cluster II, have been reported to have no AICAR formyltransferase activity previously [ 66 ], although activity under different conditions or with different substrates...”
• Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii
  Zhang, Biochemistry 2008
  • “...also report structures from three crystal forms of a PF1517 (PfPurP), one of two PurP orthologs found in Pyrococcus furiosus. Although the MjPurP and PfPurP...”
  • “...Purification of PfPurP Pyrococcus furiosus purP gene at loci Pf1517 was amplified by PCR from genomic DNA and subcloned into pT7-7 vector. The gene containing...”
• Impact of substrate glycoside linkage and elemental sulfur on bioenergetics of and hydrogen production by the hyperthermophilic archaeon Pyrococcus furiosus
  Chou, Applied and environmental microbiology 2007
  • “...vs maltose 4.1 2.5 2.1 2.3 PF0426 PF1516 PF1517 4.3 2.3 4.8 4.0 2.4 3.1 SAICAR synthase Glutamine phosphoribosylpyrophosphate amidotransferase NCAIR synthetase...”

PAB0547 hypothetical protein from Pyrococcus abyssi GE5
Aligns to 153:337 / 337 (54.9%), covers 99.5% of PF06973, 254.2 bits

• Phylogenomic analysis of proteins that are distinctive of Archaea and its main subgroups and the origin of methanogenesis
  Gao, BMC genomics 2007
  • “...characteristics of most Archaea. Of these proteins, 11 proteins (viz. PAB0654, PAB0950, PAB1135, PAB1906, PAB7388, PAB0547, PAB0552, PAB0623, PAB1272, PAB1429 and PAB1721) are mainly missing in the 4 Thermoplasmata species. Thermoplasmata are thermoacidophilic archaea which lack cell envelope [ 19 , 55 , 63 ](see Table...”
  • “...COG1685 PAB7388 [NP_127197] Ribosomal_LX CDD2437 PAB0654 [NP_126650] CDD8168 PAB0469.1n [NP_877631] CDD8674 PAB0950 [NP_127106] TFIIE CDD480 PAB0547 [NP_126484] COG1759 PAB1112 [NP_127373] CDD5727 PAB0552 [NP_126501] Hjr CDD29957 PAB1135 [NP_127406] CDD8168 PAB0623 [NP_126611] CDD9586 PAB1241 [NP_127355] CDD9682 PAB1272 [NP_127310] COG1759 PAB1387 [NP_127161] flaJ COG1955 PAB1429 [NP_127105] COG2433 PAB1715 [NP_126667]...”

2r84B / Q8U0R7 Crystal structure of purp from pyrococcus furiosus complexed with amp and aicar (see paper)
Aligns to 142:313 / 313 (55.0%), covers 89.4% of PF06973, 249.5 bits

• Ligands: adenosine monophosphate; aminoimidazole 4-carboxamide ribonucleotide (2r84B)

AF0256 conserved hypothetical protein from Archaeoglobus fulgidus DSM 4304
Aligns to 174:373 / 373 (53.6%), covers 100.0% of PF06973, 188.9 bits

• Purine biosynthesis in archaea: variations on a theme
  Brown, Biology direct 2011
  • “...both purP -like genes to purine biosynthesis. The A. fulgidus cluster II purP -like gene (AF0256) is clustered with guaA1 (not shown), while the cluster Ib gene has no apparent linkage to purine biosynthesis. Pyrococcus abyssi and P. furiosus ' purP -like genes are both near...”

TEU_09520 formate--phosphoribosylaminoimidazolecarboxamide ligase from Thermococcus eurythermalis
Aligns to 147:310 / 310 (52.9%), covers 87.8% of PF06973, 147.9 bits

• Cross-Stress Adaptation in a Piezophilic and Hyperthermophilic Archaeon From Deep Sea Hydrothermal Vent
  Zhao, Frontiers in microbiology 2020
  • “...in molybdopterin biosynthesis were up-expressed under alkali stress. Moreover, DEPs involved in purine-containing compound biosynthesis (TEU_09520, TEU_00750, and TEU_09080) and nucleoside transport (TEU_08830), which provided the components for molybdopterin, were also up-expressed ( Supplementary Data S4 ). These results showed the importance and increased requirement of...”

2pbzA / Q5JD28 Crystal structure of an imp biosynthesis protein purp from thermococcus kodakaraensis
Aligns to 129:293 / 293 (56.3%), covers 91.5% of PF06973, 145.6 bits

• Ligand: adenosine-5'-triphosphate (2pbzA)

TK0431 hypothetical protein from Thermococcus kodakaraensis KOD1
Aligns to 148:310 / 310 (52.6%), covers 88.3% of PF06973, 143.8 bits

• Extended Archaeal Histone-Based Chromatin Structure Regulates Global Gene Expression in Thermococcus kodakarensis
  Sanders, Frontiers in microbiology 2021
  • “...Methyl-accepting chemotaxis protein Environmental information processing 5.19 TK0637 Chemotaxis protein CheC Environmental information processing 5.07 TK0431 5-formaminoimidazole-4-carboxamide-1-(beta)-D-ribofuranosyl 5-monophosphate synthetase Purine metabolism 4.51 TK0638 Methyl-accepting chemotaxis protein Environmental information processing 4.43 TK0432 Phosphonbosylam inoimidazole-succinocarboxamide synthase Purine metaboism 4.26 TK1139 ATPase, AAA superfamily unknown 4.23 TK0051 Protein- L...”
• Purine biosynthesis in archaea: variations on a theme
  Brown, Biology direct 2011
  • “...one protein closely related to the cluster Ib proteins of other Thermococci and one protein (TK0431 and the split TK1267 and TK1266) that is only distantly related to other PurP proteins in cluster I. The "extra" T. kodakaraensis gene product has been crystallized without substrates (PDB...”
  • “...the loop from 161-165 for all the archaea studied. In this regard, the divergent sequences TK0431 and TGAM_1266-7 are members of cluster I. Figure 6 WebLOGOs for the combined cluster Ia/Ib P-loop (top) and corresponding cluster II loop region (bottom) . At this time, only a...”

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