THIC_PSESM
ID THIC_PSESM Reviewed; 629 AA.
AC Q87VG1;
DT 24-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 107.
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=PSPTO_4976;
OS Pseudomonas syringae pv. tomato (strain ATCC BAA-871 / DC3000).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=223283;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-871 / DC3000;
RX PubMed=12928499; DOI=10.1073/pnas.1731982100;
RA Buell C.R., Joardar V., Lindeberg M., Selengut J., Paulsen I.T.,
RA Gwinn M.L., Dodson R.J., DeBoy R.T., Durkin A.S., Kolonay J.F., Madupu R.,
RA Daugherty S.C., Brinkac L.M., Beanan M.J., Haft D.H., Nelson W.C.,
RA Davidsen T.M., Zafar N., Zhou L., Liu J., Yuan Q., Khouri H.M.,
RA Fedorova N.B., Tran B., Russell D., Berry K.J., Utterback T.R.,
RA Van Aken S.E., Feldblyum T.V., D'Ascenzo M., Deng W.-L., Ramos A.R.,
RA Alfano J.R., Cartinhour S., Chatterjee A.K., Delaney T.P., Lazarowitz S.G.,
RA Martin G.B., Schneider D.J., Tang X., Bender C.L., White O., Fraser C.M.,
RA Collmer A.;
RT "The complete genome sequence of the Arabidopsis and tomato pathogen
RT Pseudomonas syringae pv. tomato DC3000.";
RL Proc. Natl. Acad. Sci. U.S.A. 100:10181-10186(2003).
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; AE016853; AAO58404.1; -; Genomic_DNA.
DR RefSeq; NP_794709.1; NC_004578.1.
DR RefSeq; WP_011105255.1; NC_004578.1.
DR AlphaFoldDB; Q87VG1; -.
DR SMR; Q87VG1; -.
DR STRING; 223283.PSPTO_4976; -.
DR PRIDE; Q87VG1; -.
DR EnsemblBacteria; AAO58404; AAO58404; PSPTO_4976.
DR GeneID; 1186661; -.
DR KEGG; pst:PSPTO_4976; -.
DR PATRIC; fig|223283.9.peg.5091; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_6; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR PhylomeDB; Q87VG1; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000002515; 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..629
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000152827"
FT REGION 1..24
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 233
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 262
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 291
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 327
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 347..349
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 388..391
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 427
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 431
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 454
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 495
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 575
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 578
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 583
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 629 AA; 69627 MW; EB80EDC67D1B7E36 CRC64;
MSTKPKNAAH LSESAQVDSG SVQPFTRSQK IYVQGSRPDI RVPMREVTLD VTPTDFGGEI
NAPVTVYDTS GPYTDPNVII DVRKGLADVR SPWIDSRNDT ERLPGLSSHF GQQRLSDAEL
TALRFAHVRN PRRAKAGANV SQMHYARQGI ITAEMEYVAI RENMKLQEAR AAGLLTQQHA
GHSFGASIPK EITAEFVREE IARGRAIIPA NINHVELEPM IIGRNFLVKI NGNIGNSALG
SSIEEEVAKL TWGIRWGSDT VMDLSTGKHI HETREWIIRN SPVPIGTVPI YQALEKVGGA
AEDLTWELFR DTLIEQAEQG VDYFTIHAGV LLRYVPLTAK RVTGIVSRGG SIMAKWCLAH
HQENFLYTHF EDICEIMKAY DVSFSLGDGL RPGSIADAND AAQFGELETL GELTKIAWKH
DLQTMIEGPG HVPMQLIKEN MDKQLECCDE APFYTLGPLT TDIAPGYDHI TSGIGAAMIG
WFGCAMLCYV TPKEHLGLPN KDDVKTGIIT YKIAAHAADL AKGHPGAQIR DNALSKARFE
FRWEDQFNLG LDPDTARSYH DETLPKDSAK VAHFCSMCGP KFCSMKITQE VREYAANQRI
EAVDVDVARG LAEQAERFKQ EGSQLYKKV
