THIC_NEIG1
ID THIC_NEIG1 Reviewed; 633 AA.
AC Q5F588;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 15-MAR-2005, sequence version 1.
DT 03-AUG-2022, entry version 94.
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=NGO2041;
OS Neisseria gonorrhoeae (strain ATCC 700825 / FA 1090).
OC Bacteria; Proteobacteria; Betaproteobacteria; Neisseriales; Neisseriaceae;
OC Neisseria.
OX NCBI_TaxID=242231;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700825 / FA 1090;
RA Lewis L.A., Gillaspy A.F., McLaughlin R.E., Gipson M., Ducey T.F.,
RA Ownbey T., Hartman K., Nydick C., Carson M.B., Vaughn J., Thomson C.,
RA Song L., Lin S., Yuan X., Najar F., Zhan M., Ren Q., Zhu H., Qi S.,
RA Kenton S.M., Lai H., White J.D., Clifton S., Roe B.A., Dyer D.W.;
RT "The complete genome sequence of Neisseria gonorrhoeae.";
RL Submitted (MAR-2003) 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; AE004969; AAW90649.1; -; Genomic_DNA.
DR RefSeq; WP_003686973.1; NC_002946.2.
DR RefSeq; YP_209061.1; NC_002946.2.
DR AlphaFoldDB; Q5F588; -.
DR SMR; Q5F588; -.
DR STRING; 242231.NGO_2041; -.
DR EnsemblBacteria; AAW90649; AAW90649; NGO_2041.
DR KEGG; ngo:NGO_2041; -.
DR PATRIC; fig|242231.10.peg.2456; -.
DR HOGENOM; CLU_013181_2_1_4; -.
DR OMA; TWELFRD; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000000535; 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..633
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242275"
FT BINDING 245
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 303
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 339
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 359..361
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 400..403
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 439
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 443
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 466
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 507
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
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 590
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 595
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 633 AA; 71367 MW; 324571B4402CBB2A CRC64;
MTTPKKTAKI SGNEARELSD LSEDIGIRFK YQNSERVYLQ GSRDDIRVPL REIRQDDTYT
AQGTEANPPI PVYDTSGAYG DPAAHIDLKQ GLPHIRTAWL DERGDTEILP KLSSEYGIER
AHDPKTAHLR FNQITRPRRA KAGRNVTQLH YARQGIITPE MEFAAIRERM KLDELFRRPE
YAKLLKQHTG QSFGANIPTR PDQITPEFVR QEIAAGRAII PANINHPELE PMIIGRNFRV
KINGNLGNSA VTSSLTEEVE KMVWSLRWGA DTIMDLSTGA HIHETREWII RNAPVPIGTV
PIYQTLEKTG GIAEDLTWDL FRDTLIEQAE QGVDYFTIHA GVLLRYVPMT ANRLTGIVSR
GGSIMAKWCL AHHRENFLYT HFDEICEIMK AYDVSFSLGD GLRPGCIADA NDESQFAELH
TLGELTDKAW KHDVQVMIEG PGHVPLQRVK ENMTEELQHC FEAPFYTLGP LVTDIAPGYD
HITSGIGAAN IGWYGTAMLC YVTPKEHLGL PDKEDVRTGI ITYKLAAHAA DLAKGWPGAQ
LRDNALSKAR FEFRWRDQFR LSLDPERAES FHDETLPAEG AKIAHFCSMC GPKFCSMKIT
QEVRDYADKQ KAQRQGMEEK AVEFVKKGAK IYS
