THIC_RHIEC
ID THIC_RHIEC Reviewed; 610 AA.
AC Q2K206; O34291;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 07-MAR-2006, sequence version 1.
DT 03-AUG-2022, 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=RHE_PB00082;
OS Rhizobium etli (strain CFN 42 / ATCC 51251).
OG Plasmid p42b.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Rhizobium.
OX NCBI_TaxID=347834;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=CE3;
RX PubMed=9371431; DOI=10.1128/jb.179.22.6887-6893.1997;
RA Miranda-Rios J., Morera C., Taboada H., Davalos A., Encarnacion S.,
RA Mora J., Soberon M.;
RT "Expression of thiamin biosynthetic genes (thiCOGE) and production of
RT symbiotic terminal oxidase cbb3 in Rhizobium etli.";
RL J. Bacteriol. 179:6887-6893(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CFN 42 / ATCC 51251;
RX PubMed=16505379; DOI=10.1073/pnas.0508502103;
RA Gonzalez V., Santamaria R.I., Bustos P., Hernandez-Gonzalez I.,
RA Medrano-Soto A., Moreno-Hagelsieb G., Janga S.C., Ramirez M.A.,
RA Jimenez-Jacinto V., Collado-Vides J., Davila G.;
RT "The partitioned Rhizobium etli genome: genetic and metabolic redundancy in
RT seven interacting replicons.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:3834-3839(2006).
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; AF004408; AAC45972.1; -; Genomic_DNA.
DR EMBL; CP000135; ABC93124.1; -; Genomic_DNA.
DR PIR; T44254; T44254.
DR RefSeq; WP_011427546.1; NC_007763.1.
DR AlphaFoldDB; Q2K206; -.
DR SMR; Q2K206; -.
DR EnsemblBacteria; ABC93124; ABC93124; RHE_PB00082.
DR GeneID; 61482657; -.
DR KEGG; ret:RHE_PB00082; -.
DR HOGENOM; CLU_013181_2_1_5; -.
DR OMA; TWELFRD; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000001936; Plasmid p42b.
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; Plasmid;
KW Reference proteome; S-adenosyl-L-methionine; Thiamine biosynthesis; Zinc.
FT CHAIN 1..610
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242294"
FT BINDING 216
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 245
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 274
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 310
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 330..332
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 371..374
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 410
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 414
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 437
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 478
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 558
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 561
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 566
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 CONFLICT 337..338
FT /note="AK -> PT (in Ref. 1; AAC45972)"
FT /evidence="ECO:0000305"
FT CONFLICT 434
FT /note="A -> G (in Ref. 1; AAC45972)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 610 AA; 67120 MW; 3BA2B1C89ECDCA3B CRC64;
MNIVAPQLTP VVTTGSLPAS TKIVKPGTLY PDLRVPMREI SLHPTSGEPP VTVYDSSGPY
TDPAHVISID AGLPRLRESW IKARGDVESY DGRIVKPEDN GFATGERLTP EFPVRNTPLK
AKAGRAVTQL AYARAGIVTP EMEFIAIREN LGRQAAKEAL ARDGESFGAH VPDFVTPEFV
RREVAEGRAI IPANINHPES EPMIIGRNFL VKINANIGNS AVTSSMAEEV EKMVWAIRWG
ADTVMDLSTG RNIHNIREWI IRNSPVPIGT VPLYQALEKV NGIAEDLTWE VYRDTLIEQA
EQGVDYFTIH AGVRLAYIPL TVNRVTGIVS RGGSIMAKWC LHHHKESFLY EHFEEICDIC
RAYDVSFSLG DGLRPGSIAD ANDAAQFAEL ETLGELTKIA WAKDCQVMIE GPGHVPMHKI
KENMDKQLEV CGEAPFYTLG PLTTDIAPGY DHITSGIGAA MIGWFGTAML CYVTPKEHLG
LPDRSDVKTG VITYKIAAHA ADLAKGHPAA RIRDDALSRA RFEFRWEDQF NLSLDPDTAR
SFHDETLPKE AHKVAHFCSM CGPKFCSMRI SHDIRAEAQK EGLEAMAAKY RDGGDLYMPV
AEVAKTPAGE
