ID THIC_RHORT Reviewed; 621 AA. AC Q2RST7; DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot. DT 24-JAN-2006, sequence version 1. DT 02-OCT-2024, entry version 103. DE RecName: Full=Phosphomethylpyrimidine synthase {ECO:0000255|HAMAP-Rule:MF_00089}; DE EC=4.1.99.17 {ECO:0000255|HAMAP-Rule:MF_00089}; DE AltName: Full=Hydroxymethylpyrimidine phosphate synthase {ECO:0000255|HAMAP-Rule:MF_00089}; DE Short=HMP-P synthase {ECO:0000255|HAMAP-Rule:MF_00089}; DE Short=HMP-phosphate synthase {ECO:0000255|HAMAP-Rule:MF_00089}; DE Short=HMPP synthase {ECO:0000255|HAMAP-Rule:MF_00089}; DE AltName: Full=Thiamine biosynthesis protein ThiC {ECO:0000255|HAMAP-Rule:MF_00089}; GN Name=thiC {ECO:0000255|HAMAP-Rule:MF_00089}; OrderedLocusNames=Rru_A2008; OS Rhodospirillum rubrum (strain ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / OS NCIMB 8255 / S1). OC Bacteria; Pseudomonadota; Alphaproteobacteria; Rhodospirillales; OC Rhodospirillaceae; Rhodospirillum. OX NCBI_TaxID=269796; RN [1] RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA]. RC STRAIN=ATCC 11170 / ATH 1.1.1 / DSM 467 / LMG 4362 / NCIMB 8255 / S1; RX PubMed=21886856; DOI=10.4056/sigs.1804360; RA Munk A.C., Copeland A., Lucas S., Lapidus A., Del Rio T.G., Barry K., RA Detter J.C., Hammon N., Israni S., Pitluck S., Brettin T., Bruce D., RA Han C., Tapia R., Gilna P., Schmutz J., Larimer F., Land M., Kyrpides N.C., RA Mavromatis K., Richardson P., Rohde M., Goeker M., Klenk H.P., Zhang Y., RA Roberts G.P., Reslewic S., Schwartz D.C.; RT "Complete genome sequence of Rhodospirillum rubrum type strain (S1)."; RL Stand. Genomic Sci. 4:293-302(2011). CC -!- FUNCTION: Catalyzes the synthesis of the hydroxymethylpyrimidine CC phosphate (HMP-P) moiety of thiamine from aminoimidazole ribotide (AIR) CC in a radical S-adenosyl-L-methionine (SAM)-dependent reaction. CC {ECO:0000255|HAMAP-Rule:MF_00089}. CC -!- CATALYTIC ACTIVITY: CC Reaction=5-amino-1-(5-phospho-beta-D-ribosyl)imidazole + S-adenosyl-L- CC methionine = 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine + 5'- CC deoxyadenosine + CO + formate + 3 H(+) + L-methionine; CC Xref=Rhea:RHEA:24840, ChEBI:CHEBI:15378, ChEBI:CHEBI:15740, CC ChEBI:CHEBI:17245, ChEBI:CHEBI:17319, ChEBI:CHEBI:57844, CC ChEBI:CHEBI:58354, ChEBI:CHEBI:59789, ChEBI:CHEBI:137981; CC EC=4.1.99.17; Evidence={ECO:0000255|HAMAP-Rule:MF_00089}; CC -!- COFACTOR: CC Name=[4Fe-4S] cluster; Xref=ChEBI:CHEBI:49883; CC Evidence={ECO:0000255|HAMAP-Rule:MF_00089}; CC Note=Binds 1 [4Fe-4S] cluster per subunit. The cluster is coordinated CC with 3 cysteines and an exchangeable S-adenosyl-L-methionine. CC {ECO:0000255|HAMAP-Rule:MF_00089}; CC -!- PATHWAY: Cofactor biosynthesis; thiamine diphosphate biosynthesis. CC {ECO:0000255|HAMAP-Rule:MF_00089}. CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00089}. CC -!- SIMILARITY: Belongs to the ThiC family. {ECO:0000255|HAMAP- CC Rule:MF_00089}. CC --------------------------------------------------------------------------- CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms CC Distributed under the Creative Commons Attribution (CC BY 4.0) License CC --------------------------------------------------------------------------- DR EMBL; CP000230; ABC22808.1; -; Genomic_DNA. DR RefSeq; WP_011389761.1; NC_007643.1. DR RefSeq; YP_427095.1; NC_007643.1. DR AlphaFoldDB; Q2RST7; -. DR SMR; Q2RST7; -. DR STRING; 269796.Rru_A2008; -. DR EnsemblBacteria; ABC22808; ABC22808; Rru_A2008. DR KEGG; rru:Rru_A2008; -. DR PATRIC; fig|269796.9.peg.2092; -. DR eggNOG; COG0422; Bacteria. DR HOGENOM; CLU_013181_2_1_5; -. DR PhylomeDB; Q2RST7; -. DR UniPathway; UPA00060; -. DR Proteomes; UP000001929; Chromosome. DR GO; GO:0051539; F:4 iron, 4 sulfur cluster binding; IEA:UniProtKB-KW. DR GO; GO:0016830; F:carbon-carbon lyase activity; IEA:InterPro. DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule. DR GO; GO:0009228; P:thiamine biosynthetic process; IEA:UniProtKB-KW. DR GO; GO:0009229; P:thiamine diphosphate biosynthetic process; IEA:UniProtKB-UniRule. DR Gene3D; 6.10.250.620; -; 1. DR Gene3D; 3.20.20.540; Radical SAM ThiC family, central domain; 1. DR HAMAP; MF_00089; ThiC; 1. DR InterPro; IPR037509; ThiC. DR InterPro; IPR025747; ThiC-associated_dom. DR InterPro; IPR038521; ThiC/Bza_core_dom. DR InterPro; IPR002817; ThiC/BzaA/B. DR NCBIfam; TIGR00190; thiC; 1. DR PANTHER; PTHR30557:SF1; PHOSPHOMETHYLPYRIMIDINE SYNTHASE, CHLOROPLASTIC; 1. DR PANTHER; PTHR30557; THIAMINE BIOSYNTHESIS PROTEIN THIC; 1. DR Pfam; PF13667; ThiC-associated; 1. DR Pfam; PF01964; ThiC_Rad_SAM; 1. DR SFLD; SFLDF00407; phosphomethylpyrimidine_syntha; 1. DR SFLD; SFLDG01114; phosphomethylpyrimidine_syntha; 1. DR SFLD; SFLDS00113; Radical_SAM_Phosphomethylpyrim; 1. PE 3: Inferred from homology; KW 4Fe-4S; Iron; Iron-sulfur; Lyase; Metal-binding; Reference proteome; KW S-adenosyl-L-methionine; Thiamine biosynthesis; Zinc. FT CHAIN 1..621 FT /note="Phosphomethylpyrimidine synthase" FT /id="PRO_0000242298" FT REGION 1..29 FT /note="Disordered" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT COMPBIAS 1..19 FT /note="Polar residues" FT /evidence="ECO:0000256|SAM:MobiDB-lite" FT BINDING 215 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 244 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 273 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 309 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 329..331 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 370..373 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 409 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 413 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 436 FT /ligand="substrate" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 477 FT /ligand="Zn(2+)" FT /ligand_id="ChEBI:CHEBI:29105" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 557 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 560 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" FT BINDING 565 FT /ligand="[4Fe-4S] cluster" FT /ligand_id="ChEBI:CHEBI:49883" FT /ligand_note="4Fe-4S-S-AdoMet" FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089" SQ SEQUENCE 621 AA; 66602 MW; 73ED29E7D7D1C7F9 CRC64; MTAPFLSSLS PTSPLASATA PFPGSRKVYA RPADAPHLRV PFREIILSDP GEAPVRVADP SGPYSDPEAT IDLRQGLARH RASWASARGN STVTAGRPAP SEGDFEAFPL TYAPLRRRDE TPFTQLEYAR AGVITDEMIY VATRENLGRD SAVAGACARL AGGEAFGAAL PAHVTPEFVR AEIAAGRAII PANINHPELE PTIIGRNFLV KVNANIGNSA LGSSIEDEVA KLVWAIRWGA DTVMDLSTGK AIHATREWIL RNSPVPIGTV PLYQALEKVG GDATRLDWAV FEDTLIEQCE QGVDYFTIHA GVRLAHIPLT ASRTTGIVSR GGSILAKWCL SHHRENFLYE RFADICAILR RYDVAFSLGD GLRPGSVADA NDAAQFAELD TLGALTAVAW EHGCQVMVEG PGHVPMHKIK ANMDRQLATC GEAPFYTLGP LTTDIAPGHD HITSAIGAAM IGWFGTAMLC YVTPKEHLGL PDRADVKAGV IAYKLAAHAA DIAKGHPAAQ LRDDAISRAR FDFRWSDQFN LGLDPEGARA FHDETLPHAA HKTAHFCSMC GPKFCSMKIS HDIRDGALEG ADALTQAGLD QMSATFRASG GEVHLDAQAL DALAWEGKPA R //