THIC_YERPE
ID THIC_YERPE Reviewed; 681 AA.
AC Q8ZAQ2; Q0WAR9;
DT 01-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 128.
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};
GN OrderedLocusNames=YPO3739, y0491, YP_3102;
OS Yersinia pestis.
OC Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC Yersiniaceae; Yersinia.
OX NCBI_TaxID=632;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CO-92 / Biovar Orientalis;
RX PubMed=11586360; DOI=10.1038/35097083;
RA Parkhill J., Wren B.W., Thomson N.R., Titball R.W., Holden M.T.G.,
RA Prentice M.B., Sebaihia M., James K.D., Churcher C.M., Mungall K.L.,
RA Baker S., Basham D., Bentley S.D., Brooks K., Cerdeno-Tarraga A.-M.,
RA Chillingworth T., Cronin A., Davies R.M., Davis P., Dougan G., Feltwell T.,
RA Hamlin N., Holroyd S., Jagels K., Karlyshev A.V., Leather S., Moule S.,
RA Oyston P.C.F., Quail M.A., Rutherford K.M., Simmonds M., Skelton J.,
RA Stevens K., Whitehead S., Barrell B.G.;
RT "Genome sequence of Yersinia pestis, the causative agent of plague.";
RL Nature 413:523-527(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=KIM10+ / Biovar Mediaevalis;
RX PubMed=12142430; DOI=10.1128/jb.184.16.4601-4611.2002;
RA Deng W., Burland V., Plunkett G. III, Boutin A., Mayhew G.F., Liss P.,
RA Perna N.T., Rose D.J., Mau B., Zhou S., Schwartz D.C., Fetherston J.D.,
RA Lindler L.E., Brubaker R.R., Plano G.V., Straley S.C., McDonough K.A.,
RA Nilles M.L., Matson J.S., Blattner F.R., Perry R.D.;
RT "Genome sequence of Yersinia pestis KIM.";
RL J. Bacteriol. 184:4601-4611(2002).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=91001 / Biovar Mediaevalis;
RX PubMed=15368893; DOI=10.1093/dnares/11.3.179;
RA Song Y., Tong Z., Wang J., Wang L., Guo Z., Han Y., Zhang J., Pei D.,
RA Zhou D., Qin H., Pang X., Han Y., Zhai J., Li M., Cui B., Qi Z., Jin L.,
RA Dai R., Chen F., Li S., Ye C., Du Z., Lin W., Wang J., Yu J., Yang H.,
RA Wang J., Huang P., Yang R.;
RT "Complete genome sequence of Yersinia pestis strain 91001, an isolate
RT avirulent to humans.";
RL DNA Res. 11:179-197(2004).
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; AL590842; CAL22326.1; -; Genomic_DNA.
DR EMBL; AE009952; AAM84080.1; -; Genomic_DNA.
DR EMBL; AE017042; AAS63272.1; -; Genomic_DNA.
DR PIR; AC0455; AC0455.
DR RefSeq; WP_002210682.1; NZ_WUCM01000097.1.
DR RefSeq; YP_002348619.1; NC_003143.1.
DR AlphaFoldDB; Q8ZAQ2; -.
DR SMR; Q8ZAQ2; -.
DR IntAct; Q8ZAQ2; 6.
DR STRING; 214092.YPO3739; -.
DR PaxDb; Q8ZAQ2; -.
DR DNASU; 1145438; -.
DR EnsemblBacteria; AAM84080; AAM84080; y0491.
DR EnsemblBacteria; AAS63272; AAS63272; YP_3102.
DR GeneID; 66843296; -.
DR KEGG; ype:YPO3739; -.
DR KEGG; ypk:y0491; -.
DR KEGG; ypm:YP_3102; -.
DR PATRIC; fig|214092.21.peg.4256; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_6; -.
DR OMA; TWELFRD; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000000815; Chromosome.
DR Proteomes; UP000001019; Chromosome.
DR Proteomes; UP000002490; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
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; IBA:GO_Central.
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..681
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000152855"
FT REGION 1..29
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 658..681
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 254
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 283
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 312
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 348
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 368..370
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 409..412
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 448
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 452
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 475
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 516
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 596
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 599
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 604
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 681 AA; 75878 MW; F355A7ED8E147401 CRC64;
MSNNTTSLPA ENSSHPRKGT PIRKKQREEA QQFINTLQGV TFPNSQRIYL QGSRPDIQVP
MREIQLSPTQ IGGSKNEPRY EDNEAIPVYD TSGPYGDPQA KLDVHNGLPK LRAAWVADRQ
DTEALASVSS GFTQQRLADE GLDHLRFEHL PRPRKAATGQ CVTQLHYARQ GKITPEMEFI
ALRENMGRER IRGEVLLQQH PGQAFGAHLP ENITAEFVRQ EVAAGRAIIP ANINHPESEP
MIIGRNFLVK VNANIGNSAV TSSIEEEVEK LVWSTRWGAD TVMDLSTGRY IHETREWILR
NSPVPIGTVP IYQALEKVNG VAENLTWEMF RDTLLEQAEQ GVDYFTLHAG VLLRYVPMTA
KRLTGIVSRG GSIMAKWCLS HHQENFLYQH FREICQICAA YDVSLSLGDG LRPGSIQDAN
DEAQFAELHT LGELTKIAWE YDVQVMIEGP GHVPMQMIRR NMTEELEHCH EAPFYTLGPL
TTDIAPGYDH FTSGIGAAMI GWFGCAMLCY VTPKEHLGLP NKEDVKQGLI TYKIAAHAAD
LAKGHPGAQI RDNAMSKARF EFRWEDQFNL ALDPATARAY HDETLPQESG KVAHFCSMCG
PKFCSMKISQ EVRDYAAAQE QAAAQAQAAT PTTAAQPIDI TQPINMLQSG MEKMSAEFRS
RGSELYHRPA NLSAEANNEP T
