THIC_RHORT
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 03-AUG-2022, entry version 95.
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; Proteobacteria; 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}.
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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 PRIDE; Q2RST7; -.
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 OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
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-UniRule.
DR GO; GO:0009229; P:thiamine diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR Gene3D; 3.20.20.540; -; 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 PANTHER; PTHR30557; PTHR30557; 1.
DR Pfam; PF13667; ThiC-associated; 1.
DR Pfam; PF01964; ThiC_Rad_SAM; 1.
DR SFLD; SFLDF00407; phosphomethylpyrimidine_syntha; 1.
DR TIGRFAMs; TIGR00190; thiC; 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
