THIC_NOVAD
ID THIC_NOVAD Reviewed; 626 AA.
AC Q2G7A9;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 21-MAR-2006, 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=Saro_1824;
OS Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG
OS 56034 / CIP 105152 / NBRC 16084 / F199).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Novosphingobium.
OX NCBI_TaxID=279238;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 /
RC F199;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C., Glavina T.,
RA Hammon N., Israni S., Pitluck S., Chain P., Malfatti S., Shin M.,
RA Vergez L., Schmutz J., Larimer F., Land M., Kyrpides N., Ivanova N.,
RA Fredrickson J., Balkwill D., Romine M.F., Richardson P.;
RT "Complete sequence of Novosphingobium aromaticivorans DSM 12444.";
RL Submitted (JAN-2006) 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; CP000248; ABD26264.1; -; Genomic_DNA.
DR RefSeq; WP_011445474.1; NC_007794.1.
DR AlphaFoldDB; Q2G7A9; -.
DR SMR; Q2G7A9; -.
DR STRING; 279238.Saro_1824; -.
DR PRIDE; Q2G7A9; -.
DR EnsemblBacteria; ABD26264; ABD26264; Saro_1824.
DR KEGG; nar:Saro_1824; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_5; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000009134; 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..626
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242280"
FT REGION 92..117
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 219
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 248
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 277
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 313
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 333..335
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 374..377
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 413
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 417
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 440
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 481
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 561
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 564
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 569
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 626 AA; 69212 MW; 993E6B2B1F469E2A CRC64;
MADINSKLEI GVTTGPIRGS RKIHVESARF PGLTVAMREI QLEPSSGEPP VRVYDTSGPY
TDPKVTIDIA AGLPTLRRDW IMARGDVEEY DAREVKPEDN GLKGPDRSAG VPPFPNVVKR
PLRAKAGQNV SQMHYARRGI ITPEMEYVAI RENLGRKQAK EAMIRDGQDW GASIPDYVTP
EFVRDEVARG RAIIPSNINH PESEPMAIGR NFLVKINANI GNSAVASDVA SEVDKMVWSI
RWGADTVMDL STGRNIHDTR EWILRNSPVP IGTVPIYQAL EKVGGVAEDL TWEVFRDTLI
EQAEQGVDYF TIHAGVRLPY IPLAAKRMTG IVSRGGSIMA KWCLAHHKES FLYENFDEIT
EIMKAYDVAY SLGDGLRPGS IYDANDEAQF AELYTLGELT KRAWEQDVQV MIEGPGHVPM
HKIKENMTKQ LEACGEAPFY TLGPLVTDIA PGYDHITSGI GAAQIGWYGT AMLCYVTPKE
HLGLPDRDDV KVGVVTYKLA AHAADLAKGH PAAQARDDAL SKARFEFRWR DQFNLSLDPE
TAEQYHDQTL PAEGAKTAHF CSMCGPKFCS MKISQEVRDF AAKQNAGIET FVANEAEAEA
GMKAMSDKYD EMGRELYIGA GGREHD
