THIC_ALBFT
ID THIC_ALBFT Reviewed; 624 AA.
AC Q21XR6;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 18-APR-2006, 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}; OrderedLocusNames=Rfer_1708;
OS Albidiferax ferrireducens (strain ATCC BAA-621 / DSM 15236 / T118)
OS (Rhodoferax ferrireducens).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Comamonadaceae; Rhodoferax.
OX NCBI_TaxID=338969;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-621 / DSM 15236 / T118;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Pitluck S., Brettin T., Bruce D.,
RA Han C., Tapia R., Gilna P., Kiss H., Schmutz J., Larimer F., Land M.,
RA Kyrpides N., Ivanova N., Richardson P.;
RT "Complete sequence of chromosome of Rhodoferax ferrireducens DSM 15236.";
RL Submitted (FEB-2006) 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; CP000267; ABD69437.1; -; Genomic_DNA.
DR RefSeq; WP_011464005.1; NC_007908.1.
DR AlphaFoldDB; Q21XR6; -.
DR SMR; Q21XR6; -.
DR STRING; 338969.Rfer_1708; -.
DR PRIDE; Q21XR6; -.
DR EnsemblBacteria; ABD69437; ABD69437; Rfer_1708.
DR KEGG; rfr:Rfer_1708; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_4; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000008332; Chromosome.
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..624
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242295"
FT REGION 75..99
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 226
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 255
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 284
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 320
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 340..342
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 381..384
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 420
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 424
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 447
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 488
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 568
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 571
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 576
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 624 AA; 69040 MW; 0F7C68198073CC6F CRC64;
MNAPDKFSQL MSLTREPLPA SRKIYVPGTQ ADIQVPMREI MQSNGEAVVV YDTSGPYTDP
NANIDVRQGL PSVRSPWIES RGDTESYTGR TPFALDDGLK NGDSESLASL RVQAAGLQRT
PRRAKAGANV SQMHYARSGI ITPEMEYVAI RENQKLAWME QYLGNAEREA RLAGNSFGAN
IPKIMTPEFV RDEVARGRAI IPANINHPEV EPMVIGRNFL VKINANIGNS AVTSSIEEEV
EKLVWSMRWG ADTVMDLSTG RNIHTTRDWI LRNSPVPIGT VPIYQALEKV GGVAEDLTWA
IFRDTLIEQA EQGVDYFTVH AGVRLAFIHL TANRMTGIVS RGGSIMAKWC IAHHKENFIY
SHFDEMTEIL KAYDVSYSLG DGLRPGSGAD ANDEAQFAEL RTLGELTQQA WQQDVQVMIE
GPGHVPMHMV QANMTEQLKA CHEAPFYTLG PLTTDIAPGY DHITSGIGAA MIGWFGTAML
CYVTPKEHLG LPDRDDVKVG IITYKIAAHV ADVAKGHPGV RARDDALSKA RFEFRWMDQF
NLSLDPDTAR NFHDETLPKD SSKVAHFCSM CGPKFCSMKI SQEVRDYAKT RGVSEEQALQ
SGMQTKSEEF RLAGGEMYIP ISPA
