THIC_PORG3
ID THIC_PORG3 Reviewed; 587 AA.
AC B2RH34;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 01-JUL-2008, sequence version 1.
DT 03-AUG-2022, entry version 80.
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=PGN_0160;
OS Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM
OS 12257 / NCTC 11834 / 2561).
OC Bacteria; Bacteroidetes; Bacteroidia; Bacteroidales; Porphyromonadaceae;
OC Porphyromonas.
OX NCBI_TaxID=431947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561;
RX PubMed=18524787; DOI=10.1093/dnares/dsn013;
RA Naito M., Hirakawa H., Yamashita A., Ohara N., Shoji M., Yukitake H.,
RA Nakayama K., Toh H., Yoshimura F., Kuhara S., Hattori M., Hayashi T.,
RA Nakayama K.;
RT "Determination of the genome sequence of Porphyromonas gingivalis strain
RT ATCC 33277 and genomic comparison with strain W83 revealed extensive genome
RT rearrangements in P. gingivalis.";
RL DNA Res. 15:215-225(2008).
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 -!- SIMILARITY: Belongs to the ThiC family. {ECO:0000255|HAMAP-
CC Rule:MF_00089}.
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DR EMBL; AP009380; BAG32679.1; -; Genomic_DNA.
DR RefSeq; WP_012457290.1; NZ_CP025930.1.
DR AlphaFoldDB; B2RH34; -.
DR SMR; B2RH34; -.
DR STRING; 431947.PGN_0160; -.
DR EnsemblBacteria; BAG32679; BAG32679; PGN_0160.
DR GeneID; 29255410; -.
DR KEGG; pgn:PGN_0160; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_10; -.
DR OMA; TWELFRD; -.
DR BioCyc; PGIN431947:G1G2V-178-MON; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000008842; 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; S-adenosyl-L-methionine;
KW Thiamine biosynthesis; Zinc.
FT CHAIN 1..587
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_1000093222"
FT BINDING 218
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 247
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 276
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 332..334
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 373..376
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 412
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 416
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 439
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 480
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 560
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 563
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 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"
SQ SEQUENCE 587 AA; 66795 MW; 8843C56020CF3C14 CRC64;
MKEFKVTTGP LPGSEKIYVE GERFPFLRVP MRRIRMSDTI LENGEREKNE DVVVYDTSGP
YTDTSYEVNL HRGVPKIREQ WIEDRGDTLR LEGLSSEYGR MRQSDASLEE LRYEHVCTRP
RAAKDGCATQ LYYARQGIVT PEMEFVAIRE NQLIDQVRTR YRAEEGEPLG AVIPRKITPE
FVRDEIAAGR AILPANINHP ESEPMIIGRN FLVKINANIG NSPISSTIEE EVEKAVWAIR
WGADTVMDLS TGDHIHETRE WIIRNSPVPI GTVPLYQTLE KVQGDVTKLN WEIFRDTLIE
QAEQGVDYFT IHAGLRWHHV PLTLRRLTGI VSRGGSIIAN WCTTHKRESF IYEHFEEICR
ILAHYDVAIS LGDGLRPGCI HDANDAAQIA ELKTLGELTE IAWKYNVQTI IEGPGHVPMH
KIRENMEIQL EACHGAPFYT LGPLVSDVAS GYDHITSAIG AAQIGWFGTA MLCYVTQKEH
LGLPNREDVR EGVVTYKLAA HAADLAKGHP TAYWRDYMMS KARFEFRWKD QFHLSLDPEK
AIQFHDATLP DEGHKEAHFC SMCGEHFCSM RANKNFRKLL NEEAVSK
