THIC_AGRVS
ID THIC_AGRVS Reviewed; 610 AA.
AC B9K253;
DT 28-JUL-2009, integrated into UniProtKB/Swiss-Prot.
DT 24-MAR-2009, sequence version 1.
DT 03-AUG-2022, entry version 73.
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=Avi_5917;
OS Agrobacterium vitis (strain S4 / ATCC BAA-846) (Rhizobium vitis (strain
OS S4)).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Hyphomicrobiales;
OC Rhizobiaceae; Rhizobium/Agrobacterium group; Agrobacterium.
OX NCBI_TaxID=311402;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=S4 / ATCC BAA-846;
RX PubMed=19251847; DOI=10.1128/jb.01779-08;
RA Slater S.C., Goldman B.S., Goodner B., Setubal J.C., Farrand S.K.,
RA Nester E.W., Burr T.J., Banta L., Dickerman A.W., Paulsen I., Otten L.,
RA Suen G., Welch R., Almeida N.F., Arnold F., Burton O.T., Du Z., Ewing A.,
RA Godsy E., Heisel S., Houmiel K.L., Jhaveri J., Lu J., Miller N.M.,
RA Norton S., Chen Q., Phoolcharoen W., Ohlin V., Ondrusek D., Pride N.,
RA Stricklin S.L., Sun J., Wheeler C., Wilson L., Zhu H., Wood D.W.;
RT "Genome sequences of three Agrobacterium biovars help elucidate the
RT evolution of multichromosome genomes in bacteria.";
RL J. Bacteriol. 191:2501-2511(2009).
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; CP000634; ACM38951.1; -; Genomic_DNA.
DR RefSeq; WP_012654193.1; NC_011988.1.
DR AlphaFoldDB; B9K253; -.
DR SMR; B9K253; -.
DR STRING; 311402.Avi_5917; -.
DR EnsemblBacteria; ACM38951; ACM38951; Avi_5917.
DR KEGG; avi:Avi_5917; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_5; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000001596; Chromosome 2.
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..610
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_1000118497"
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"
SQ SEQUENCE 610 AA; 67130 MW; F415DB0DBE9EA3A7 CRC64;
MNIAPQFPTP EVTTGTLPAS AKVHIAGEIH PQIRVPMRQI TLHPTSGEPP VNVYDSSGPY
TDPNATIAID AGLPRIRAEW VVARGDVEPY AGRHVKPEDN GFASGEKLTP EFPVRNAPLR
AKPGQAVTQL AYARAGIVTP EMEFIAIREN IGRKAAKDAL IRDGESFGAS IPDYVTPEFV
RQEVAMGRAI IPANINHPEA EPMIIGRNFL VKINANIGNS AVTSSMAEEV EKMVWAIRWG
ADTVMDLSTG RNIHNIRDWI IRNSPVPIGT VPLYQALEKV HGIAENLTWD VFRDTLIEQA
EQGVDYFTIH AGVRLSYIHL TVNRVTGIVS RGGSIMAKWC LHHHKESFLY EHFDEICDIC
RAYDVSFSLG DGLRPGSIAD ANDAAQFAEL ETLGELTKIA WAKDCQVMIE GPGHVPMHKI
KENMDKQLKT CGEAPFYTLG PLTTDIAPGY DHITSGIGAA MIGWYGTAML CYVTPKEHLG
LPDRNDVKTG VITYKIAAHA ADLAKGHPAA QVRDDALSRA RFEFRWEDQF NLSLDPDTAR
SFHDETLPKE AHKVAHFCSM CGPKFCSMRI SHDIRAEAQK EGLEAMAAKY RDGGDLYMPV
SDEEKPSVGE
