THIC_BORPA
ID THIC_BORPA Reviewed; 637 AA.
AC Q7W1Q0;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-OCT-2003, sequence version 1.
DT 03-AUG-2022, entry version 92.
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=BPP0301;
OS Bordetella parapertussis (strain 12822 / ATCC BAA-587 / NCTC 13253).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Alcaligenaceae; Bordetella.
OX NCBI_TaxID=257311;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=12822 / ATCC BAA-587 / NCTC 13253;
RX PubMed=12910271; DOI=10.1038/ng1227;
RA Parkhill J., Sebaihia M., Preston A., Murphy L.D., Thomson N.R.,
RA Harris D.E., Holden M.T.G., Churcher C.M., Bentley S.D., Mungall K.L.,
RA Cerdeno-Tarraga A.-M., Temple L., James K.D., Harris B., Quail M.A.,
RA Achtman M., Atkin R., Baker S., Basham D., Bason N., Cherevach I.,
RA Chillingworth T., Collins M., Cronin A., Davis P., Doggett J., Feltwell T.,
RA Goble A., Hamlin N., Hauser H., Holroyd S., Jagels K., Leather S.,
RA Moule S., Norberczak H., O'Neil S., Ormond D., Price C., Rabbinowitsch E.,
RA Rutter S., Sanders M., Saunders D., Seeger K., Sharp S., Simmonds M.,
RA Skelton J., Squares R., Squares S., Stevens K., Unwin L., Whitehead S.,
RA Barrell B.G., Maskell D.J.;
RT "Comparative analysis of the genome sequences of Bordetella pertussis,
RT Bordetella parapertussis and Bordetella bronchiseptica.";
RL Nat. Genet. 35:32-40(2003).
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; BX640423; CAE40042.1; -; Genomic_DNA.
DR RefSeq; WP_003807441.1; NC_002928.3.
DR AlphaFoldDB; Q7W1Q0; -.
DR SMR; Q7W1Q0; -.
DR EnsemblBacteria; CAE40042; CAE40042; BPP0301.
DR GeneID; 56481016; -.
DR KEGG; bpa:BPP0301; -.
DR HOGENOM; CLU_013181_2_1_4; -.
DR OMA; TWELFRD; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000001421; 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..637
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000152788"
FT BINDING 242
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 271
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 300
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 336
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 356..358
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 397..400
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 436
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 440
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 463
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 504
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 584
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 587
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 592
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 637 AA; 70996 MW; 52D6DCB90E807DBE CRC64;
MNANPKFLAA TAEVDAAAVA PLPKSRKVYE TGSRPDIRVP FREIEQADTP TMFGGEKNPP
LTVYDTSGPY TDPQASIDIR RGLPALRRAW IEERGDTEVL DGPTSDYGKE RLTDPKLTAM
RFDLQRPPRR ARAGANVTQM HYARRGIVTP EMEFIALREN LRREHYLETL RASGPDGEKL
AKRLLRQHPG QSFGAALPSA ITPEFVREEV ARGRAIIPAN INHPEIEPMI IGRNFLVKIN
ANIGNSAVSS GIGEEVEKMT WAIRWGGDTV MDLSTGKHIH ETREWIIRNS PVPIGTVPIY
QALEKVDGKA EELTWEIFRD TLIEQAEQGV DYFTIHAGVR LPFIPMTADR MTGIVSRGGS
IMAKWCLAHH KESFLYERFE EICEIMKAYD VSFSLGDGLR PGSGYDANDE AQFAELKTLG
ELTQVAWKHD VQVMIEGPGH VPMQMIKENM ELQLKHCDEA PFYTLGPLTT DIAPGYDHIT
SGIGAALIGW YGTAMLCYVT PKEHLGLPNK KDVKDGIITY KIAAHAADLA KGHPGAAIRD
NALSKARFEF RWDDQFNLGL DPDTAKEFHD ETLPKDSMKV AHFCSMCGPH FCSMKITQDV
RDYAAAQGVS EKDALQQGMQ EKAVEFVKKG AEVYHRT
