THIC_NITEU
ID THIC_NITEU Reviewed; 632 AA.
AC Q82Y50;
DT 24-MAY-2004, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 102.
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=NE0038;
OS Nitrosomonas europaea (strain ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC
OS 14298).
OC Bacteria; Proteobacteria; Betaproteobacteria; Nitrosomonadales;
OC Nitrosomonadaceae; Nitrosomonas.
OX NCBI_TaxID=228410;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 19718 / CIP 103999 / KCTC 2705 / NBRC 14298;
RX PubMed=12700255; DOI=10.1128/jb.185.9.2759-2773.2003;
RA Chain P., Lamerdin J.E., Larimer F.W., Regala W., Lao V., Land M.L.,
RA Hauser L., Hooper A.B., Klotz M.G., Norton J., Sayavedra-Soto L.A.,
RA Arciero D.M., Hommes N.G., Whittaker M.M., Arp D.J.;
RT "Complete genome sequence of the ammonia-oxidizing bacterium and obligate
RT chemolithoautotroph Nitrosomonas europaea.";
RL J. Bacteriol. 185:2759-2773(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; AL954747; CAD83949.1; -; Genomic_DNA.
DR AlphaFoldDB; Q82Y50; -.
DR SMR; Q82Y50; -.
DR STRING; 228410.NE0038; -.
DR EnsemblBacteria; CAD83949; CAD83949; NE0038.
DR KEGG; neu:NE0038; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_4; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR PhylomeDB; Q82Y50; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000001416; 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..632
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000152819"
FT BINDING 237
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 266
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 295
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 331
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 351..353
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 392..395
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 431
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 435
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 458
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 499
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 579
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 582
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"
SQ SEQUENCE 632 AA; 71042 MW; B3E1BFDFA79CBBD3 CRC64;
MKTPVSKLEK FTNDNARVDT AAVQPLPNSR KIYIQGSRAD IQVPMREITQ SDTATGRGAE
KNPPIYVYDT SGPYTDPDTR IDIRHGLPPL REKWIDERGD TEILTGLSSS YSLKRLQDPA
LTKMRFNLMR PVRHARNGAN VTQMHYARRG IITPEMEFIA LRENQRRERV ADLASNELLN
RQHPGQSFGA IIQEWITPEF VRDEVACGRA IIPANINHPE TEPMIIGRNF LVKINANIGN
SALGSSIQDE VEKMTWAIRW GGDTVMDLST GKNIHETREW IIRNSPVPIG TVPIYQALEK
VDGKAEELTW EIFRDTLIEQ AEQGVDYFTI HAGVRLPFIP MTAKRMTGIV SRGGSIMAKW
CLAHHQESFL YTHFEDICEI MKAYDVSFSL GDGLRPGSIY DANDEAQFAE LKTLGELTEI
AWKHDVQVMI EGPGHVPMHL IRENMDLQLK YCHEAPFYTL GPLTTDIAPG YDHITSAIGA
AMIGWYGTAM LCYVTPKEHL GLPDKDDVKD GIITYKIAAH AADLAKGHPG AQVRDNALSK
ARFEFRWNDQ FNLSLDPDKA REFHDETLPQ EGAKLAHFCS MCGPNFCSMK ITQDVRDYAA
QQGISETVAL QEGMARKANE FIEKGGELYS KQ
