THIC_PSEPK
ID THIC_PSEPK Reviewed; 626 AA.
AC Q88DA5;
DT 24-OCT-2003, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 106.
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=PP_4922;
OS Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950
OS / KT2440).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Pseudomonadales;
OC Pseudomonadaceae; Pseudomonas.
OX NCBI_TaxID=160488;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440;
RX PubMed=12534463; DOI=10.1046/j.1462-2920.2002.00366.x;
RA Nelson K.E., Weinel C., Paulsen I.T., Dodson R.J., Hilbert H.,
RA Martins dos Santos V.A.P., Fouts D.E., Gill S.R., Pop M., Holmes M.,
RA Brinkac L.M., Beanan M.J., DeBoy R.T., Daugherty S.C., Kolonay J.F.,
RA Madupu R., Nelson W.C., White O., Peterson J.D., Khouri H.M., Hance I.,
RA Chris Lee P., Holtzapple E.K., Scanlan D., Tran K., Moazzez A.,
RA Utterback T.R., Rizzo M., Lee K., Kosack D., Moestl D., Wedler H.,
RA Lauber J., Stjepandic D., Hoheisel J., Straetz M., Heim S., Kiewitz C.,
RA Eisen J.A., Timmis K.N., Duesterhoeft A., Tuemmler B., Fraser C.M.;
RT "Complete genome sequence and comparative analysis of the metabolically
RT versatile Pseudomonas putida KT2440.";
RL Environ. Microbiol. 4:799-808(2002).
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; AE015451; AAN70489.1; -; Genomic_DNA.
DR RefSeq; NP_747025.1; NC_002947.4.
DR RefSeq; WP_010955502.1; NC_002947.4.
DR AlphaFoldDB; Q88DA5; -.
DR SMR; Q88DA5; -.
DR STRING; 160488.PP_4922; -.
DR EnsemblBacteria; AAN70489; AAN70489; PP_4922.
DR KEGG; ppu:PP_4922; -.
DR PATRIC; fig|160488.4.peg.5257; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_6; -.
DR OMA; TWELFRD; -.
DR PhylomeDB; Q88DA5; -.
DR BioCyc; PPUT160488:G1G01-5264-MON; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000000556; 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..626
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000152826"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 232
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 261
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 290
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 326
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 346..348
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 387..390
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 426
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 430
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 453
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 494
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 574
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 577
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 582
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 626 AA; 69727 MW; E22CBAAE6B8D6313 CRC64;
MTKQEKAINL SESAQVDQQS VQPFPRSRKV YVEGSRPDIR VPMREISLDD TPTDFGGESN
APVLVYDTSG PYTDPDVIID VRKGLPDVRS AWIEARGDTE RLEGLSSDFG QQRLNDAELA
KLRFAHVRNP RRAKAGANVS QMHYARQGII TAEMEYVAIR ENMKLQEARA AGLLNEQHAG
HSFGANIPKE ITPEFVRQEI ARGRAIIPAN INHPEVEPMI IGRNFLVKIN GNIGNSALGS
SIEEEVAKLT WGIRWGSDTV MDLSTGKHIH ETREWIIRNS PVPIGTVPIY QALEKVNGVA
EDLTWELFRD TLIEQAEQGV DYFTIHAGVL LRYVPLTAKR VTGIVSRGGS IMAKWCLAHH
KENFLYTHFD EICEIMKAYD VSFSLGDGLR PGSIADANDA AQFGELETLG ELTKIAWKHD
VQCMIEGPGH VPMQLIKENM DKQLECCDEA PFYTLGPLTT DIAPGYDHIT SGIGAAMIGW
FGCAMLCYVT PKEHLGLPNK DDVKTGIITY KIAAHAADLA KGHPGAQIRD NALSKARFEF
RWEDQFNLGL DPDTARAFHD ETLPKESAKV AHFCSMCGPK FCSMKITQEV REYAAKIEAV
DVTVEQGMRE QAERFRQEGS QLYHKV
