THIC_NOCFA
ID THIC_NOCFA Reviewed; 547 AA.
AC Q5YNS3;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 23-NOV-2004, sequence version 1.
DT 03-AUG-2022, entry version 103.
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=NFA_53160;
OS Nocardia farcinica (strain IFM 10152).
OC Bacteria; Actinobacteria; Corynebacteriales; Nocardiaceae; Nocardia.
OX NCBI_TaxID=247156;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=IFM 10152;
RX PubMed=15466710; DOI=10.1073/pnas.0406410101;
RA Ishikawa J., Yamashita A., Mikami Y., Hoshino Y., Kurita H., Hotta K.,
RA Shiba T., Hattori M.;
RT "The complete genomic sequence of Nocardia farcinica IFM 10152.";
RL Proc. Natl. Acad. Sci. U.S.A. 101:14925-14930(2004).
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; AP006618; BAD60168.1; -; Genomic_DNA.
DR RefSeq; WP_011211850.1; NC_006361.1.
DR AlphaFoldDB; Q5YNS3; -.
DR SMR; Q5YNS3; -.
DR STRING; 247156.NFA_53160; -.
DR EnsemblBacteria; BAD60168; BAD60168; NFA_53160.
DR GeneID; 61135891; -.
DR KEGG; nfa:NFA_53160; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_11; -.
DR OMA; TWELFRD; -.
DR BioCyc; NFAR247156:NFA_RS26380-MON; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000006820; 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..547
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242279"
FT BINDING 150
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 179
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 208
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 244
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 264..266
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 305..308
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 344
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 348
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 371
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 412
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 492
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 495
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 500
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 547 AA; 59777 MW; E1FA6C6558B24AA4 CRC64;
MASADRVTAP VDTVTTGPIE GSVKHYREVD GLRIPVRRIN LTNGETFDVY DTSGPYTDEN
ATIDLEAGLP KLRDSWDKPT VAGPRTQLAW ARAGIVTPEM RFIAAREGVE PELVRAEVAA
GRAVIPANHN HPELEPTIIG KKFLVKINAN IGNSAVSSSI AEEVEKMVWA TRWGADTIMD
LSTGKNIHET REWILRNSPV PVGTVPIYQA LEKVNGDPAA LTWEIYRDTV IEQAEQGVDY
MTVHAGVLLR YVPLTAKRVT GIVSRGGSIM AAWCLAHHRE SFLYTHFEEL CEILARYDVT
FSLGDGLRPG SVADANDEAQ FAELRTLGEL TKIAKSHGVQ VMIEGPGHVP MHKIVENVRL
EEELCEEAPF YTLGPLATDI APAYDHITSA IGAAIIAQAG TAMLCYVTPK EHLGLPNRDD
VKTGVITYKI AAHAADLAKG HPHAQQRDDA LSKARFEFRW RDQFALSLDP DTAREYHDET
MPAEPAKTAH FCSMCGPKFC SMRISADVRE YAEANNLTDV AAIEAGMAAK SAEFAESGGK
VYLPVVS
