THIC_PELPB
ID THIC_PELPB Reviewed; 544 AA.
AC B4SBF6;
DT 24-MAR-2009, integrated into UniProtKB/Swiss-Prot.
DT 23-SEP-2008, sequence version 1.
DT 03-AUG-2022, entry version 77.
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=Ppha_1778;
OS Pelodictyon phaeoclathratiforme (strain DSM 5477 / BU-1).
OC Bacteria; Chlorobi; Chlorobia; Chlorobiales; Chlorobiaceae;
OC Chlorobium/Pelodictyon group; Pelodictyon.
OX NCBI_TaxID=324925;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 5477 / BU-1;
RG US DOE Joint Genome Institute;
RA Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Dalin E., Tice H.,
RA Bruce D., Goodwin L., Pitluck S., Schmutz J., Larimer F., Land M.,
RA Hauser L., Kyrpides N., Mikhailova N., Liu Z., Li T., Zhao F., Overmann J.,
RA Bryant D.A., Richardson P.;
RT "Complete sequence of Pelodictyon phaeoclathratiforme BU-1.";
RL Submitted (JUN-2008) 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 -!- SIMILARITY: Belongs to the ThiC family. {ECO:0000255|HAMAP-
CC Rule:MF_00089}.
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DR EMBL; CP001110; ACF44010.1; -; Genomic_DNA.
DR RefSeq; WP_012508497.1; NC_011060.1.
DR AlphaFoldDB; B4SBF6; -.
DR SMR; B4SBF6; -.
DR STRING; 324925.Ppha_1778; -.
DR EnsemblBacteria; ACF44010; ACF44010; Ppha_1778.
DR KEGG; pph:Ppha_1778; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_10; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000002724; 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..544
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_1000093219"
FT BINDING 180
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 209
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 238
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 274
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 294..296
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 335..338
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 374
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 378
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 401
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 442
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 524
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 527
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 532
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 544 AA; 60840 MW; B89E2441FBB0FD61 CRC64;
MTNVTENITC PVKRIECIPP EKIYSKGTIF PLEVGMKRVK LSKTYFCNGQ EFSSLPLYDT
GGPYSDPSVS IDPEKGLPPI RKSWGFQRDE KAASSITQMH FARKGIITPE MEYVSIRENQ
QLEEWISSFS RGGAKVSPIT PEFVRQEIAE GRAIIPANIN HPELEPMIIG RKFRVKINAN
IGNSALGSSI EEEVEKAVWS CRWGADTVMD LSTGANIHQT REWILRNSPV PIGTVPMYQA
LEKAGGKAEA LTWELYRDTL IEQAEQGVDY FTIHAGILLE HLPFAEKRLT GIVSRGGSIM
AKWCKYHKEE NFLYTRFEEI CKILQRYDIA VSLGDALRPG SIIDANDEAQ FGELKVLGEL
TKVAWKYEVQ VMIEGPGHVP LHMIRENMDK ELAYCHEAPF YTLGPLITDI AAGYDHINSA
IGGALIASFG CSMLCYVTPK EHLGLPDRND VREGVIAHKV AAHGADLAKG NPVSWLQDEL
MSRARYSFAW EDQFNLSLDP EKIRAVHAQS MAARGHTEKN PHFCTMCGPD FCSMKKSKEA
AEQE
