THIC_DECAR
ID THIC_DECAR Reviewed; 638 AA.
AC Q478T2;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 13-SEP-2005, sequence version 1.
DT 03-AUG-2022, entry version 92.
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=Daro_3921;
OS Dechloromonas aromatica (strain RCB).
OC Bacteria; Proteobacteria; Betaproteobacteria; Rhodocyclales; Azonexaceae;
OC Dechloromonas.
OX NCBI_TaxID=159087;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=RCB;
RX PubMed=19650930; DOI=10.1186/1471-2164-10-351;
RA Salinero K.K., Keller K., Feil W.S., Feil H., Trong S., Di Bartolo G.,
RA Lapidus A.;
RT "Metabolic analysis of the soil microbe Dechloromonas aromatica str. RCB:
RT indications of a surprisingly complex life-style and cryptic anaerobic
RT pathways for aromatic degradation.";
RL BMC Genomics 10:351-351(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; CP000089; AAZ48649.1; -; Genomic_DNA.
DR RefSeq; WP_011289644.1; NC_007298.1.
DR AlphaFoldDB; Q478T2; -.
DR SMR; Q478T2; -.
DR STRING; 159087.Daro_3921; -.
DR PRIDE; Q478T2; -.
DR EnsemblBacteria; AAZ48649; AAZ48649; Daro_3921.
DR KEGG; dar:Daro_3921; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_4; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR UniPathway; UPA00060; -.
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; S-adenosyl-L-methionine;
KW Thiamine biosynthesis; Zinc.
FT CHAIN 1..638
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242254"
FT BINDING 243
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 272
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 301
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 337
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 357..359
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 398..401
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 437
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 441
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 464
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 505
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 585
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 588
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 593
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 638 AA; 70951 MW; F630D00AAAECE5E7 CRC64;
MNATEQFLAA NAHVDEAAVQ PLPNSRKIYV EGSRPDIRVP MREVSQDDTP TAFGGEKNPP
IYVYDCSGPY SDPAAKIDIR SGLPALRAQW IAERGDVEAL ADLSSEFGRQ RAADPKLDEL
RFPGLHRKPL RAKAGQNVSQ MHYARRGIIT PEMEYVAIRE NNNRRAYIES LKATGPMGNR
MADILGRQHK GQDFGASIPE EITPEFVRSE IARGRAIIPN NINHPESEPM IIGRNFLVKI
NANIGNSALG SSIQEEVEKM TWSIRWGGDT VMDLSTGKNI HETREWIIRN SPVPIGTVPI
YQALEKVNGK AEDLTWEIFR DTLIEQAEQG VDYFTIHAGV LLRYVPMTAN RLTGIVSRGG
SIMAKWCLAH HKESFLYTHF EEICEIMKAY DVAFSLGDGL RPGSIYDAND EAQLGELETL
GELTKIAWKH DVQVIIEGPG HVPMHMIKEN MDLQLKHCDE APFYTLGPLT TDIAPGYDHI
TSGIGAAMIG WYGTAMLCYV TPKEHLGLPD KDDVKEGIIT YKLAAHAADL AKGHPGAQIR
DNALSKARFE FRWDDQFNLG LDPDKAREFH DETLPKESAK VAHFCSMCGP HFCSMKITQE
VREFAAQQGL DEAAALEKGM EVKSVEFVKA GAEVYSKI
