THIC_SHEPC
ID THIC_SHEPC Reviewed; 712 AA.
AC A4Y6R2;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 29-MAY-2007, sequence version 1.
DT 03-AUG-2022, entry version 89.
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=Sputcn32_1922;
OS Shewanella putrefaciens (strain CN-32 / ATCC BAA-453).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Shewanellaceae; Shewanella.
OX NCBI_TaxID=319224;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=CN-32 / ATCC BAA-453;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Chain P., Malfatti S., Shin M., Vergez L., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Mikhailova N., Romine M.F., Fredrickson J.,
RA Tiedje J., Richardson P.;
RT "Complete sequence of Shewanella putrefaciens CN-32.";
RL Submitted (APR-2007) to the EMBL/GenBank/DDBJ databases.
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; CP000681; ABP75645.1; -; Genomic_DNA.
DR RefSeq; WP_011919272.1; NC_009438.1.
DR AlphaFoldDB; A4Y6R2; -.
DR SMR; A4Y6R2; -.
DR STRING; 319224.Sputcn32_1922; -.
DR PRIDE; A4Y6R2; -.
DR GeneID; 45042382; -.
DR KEGG; spc:Sputcn32_1922; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_6; -.
DR OMA; TWELFRD; -.
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..712
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_1000004802"
FT REGION 14..49
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 19..45
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
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 341
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 377
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 397..399
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 438..441
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 477
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 481
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 504
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 545
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 625
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 628
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 633
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 712 AA; 78310 MW; 9DA16FD839F525AA CRC64;
MSSSNQNLAI AANAIDITAP ESTIPNKSKV PNKSAESSQS TVPKAPSRRE IRAQAQAFID
TLAPLQHTNS QKVYLEGSSA DIRVGMRQIL QTDTLVGGTD DAPIMEKNPP IRVYDCAGPY
SDPEADINVR LGLVKLRQNW ILARKDTEQL PCATSDFTQQ RLADDGLDHL RFEAGSSAIV
RPRRALQGKR VSQLHYARQG IITPEMEYVA IRENMALAEV QDEILNRKAK GEAFGALVGE
PITAEFVRAE VARGRAIIPL NINHPEAEPM IIGRNFLVKV NANIGNSAVT SSIEEEVEKL
VWSTRWGADT VMDLSTGRYI HETREWIIRN SPVPIGTVPI YQALEKVNGV AEDLTWEVFR
DTLIEQAEQG VDYFTIHAGV LLRYVPMTAK RVTGIVSRGG SIMAKWCLSH HKENFLYSHF
REICELCVAY DVSLSLGDGM RPGSIADAND AAQFAELETL GELVKIAWEY DVQTIIEGPG
HIPMQLIKEN MDKQLAHCGE APFYTLGPQI TDIAPGYDHF TSGIGAAMIA WYGCAMLCYV
TPKEHLGLPN KQDVKQGLIA YKIAAHAADV AKGHPSAQIR DNALAKARFE FRWEDQYNLG
LDPETARAYH DESLPQESAK VAHFCSMCGP KFCSMKITQD VRAYAAGLEA AQTKAEQVEA
AAQAMQVTIK TPQELEAAMA LKSAQFAASG AEIYQVIDKH VKDKLVAEAE EA
