THIC_SPHAL
ID THIC_SPHAL Reviewed; 630 AA.
AC Q1GQJ3;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 27-JUN-2006, sequence version 1.
DT 03-AUG-2022, entry version 90.
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=Sala_2370;
OS Sphingopyxis alaskensis (strain DSM 13593 / LMG 18877 / RB2256)
OS (Sphingomonas alaskensis).
OC Bacteria; Proteobacteria; Alphaproteobacteria; Sphingomonadales;
OC Sphingomonadaceae; Sphingopyxis.
OX NCBI_TaxID=317655;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 13593 / LMG 18877 / RB2256;
RX PubMed=19805210; DOI=10.1073/pnas.0903507106;
RA Lauro F.M., McDougald D., Thomas T., Williams T.J., Egan S., Rice S.,
RA DeMaere M.Z., Ting L., Ertan H., Johnson J., Ferriera S., Lapidus A.,
RA Anderson I., Kyrpides N., Munk A.C., Detter C., Han C.S., Brown M.V.,
RA Robb F.T., Kjelleberg S., Cavicchioli R.;
RT "The genomic basis of trophic strategy in marine bacteria.";
RL Proc. Natl. Acad. Sci. U.S.A. 106:15527-15533(2009).
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; CP000356; ABF54079.1; -; Genomic_DNA.
DR RefSeq; WP_011542654.1; NC_008048.1.
DR AlphaFoldDB; Q1GQJ3; -.
DR SMR; Q1GQJ3; -.
DR STRING; 317655.Sala_2370; -.
DR EnsemblBacteria; ABF54079; ABF54079; Sala_2370.
DR KEGG; sal:Sala_2370; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_5; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000006578; 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..630
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_1000004806"
FT REGION 1..22
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 97..120
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 224
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 253
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 282
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 318
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 338..340
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 379..382
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 418
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 422
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 445
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 486
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00089"
FT BINDING 566
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"
FT BINDING 574
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 630 AA; 69436 MW; B88742F57DE26726 CRC64;
MADIDSRLDT TQATPIGVTT GPIRGSRKIH VASPTGSGIR VAMREILLEP SSGEPPVRVY
DTSGPYTDPD ATIDIAQGLP ELRASWIRAR GDVEEVAQRE VRPEDNGQLG PDRSGGVPAF
PNVRKKVLRA KPGANVSQMH YARRGIITPE MEYVATRENL GRERLAEYVR DGQDWGASIP
DYVTPEFVRD EVARGRAIIP SNINHPESEP MAIGRNFLVK INANIGNSAV ASDVAAEVDK
MVWSIRWGAD TVMDLSTGRN IHDTREWILR NSPVPIGTVP IYQALEKVGG IAEELTWEIF
RDTLIEQAEQ GVDYFTIHAG VRLPYVPLAA KRVTGIVSRG GSIMAKWCLA HHRESFLYDH
FDEITEIMKA YDIAYSLGDG LRPGSIADAN DEAQFAELYT LGELTRRAWA QDVQVMIEGP
GHVPMHKIKE NMDKQLEACG EAPFYTLGPL TTDIAPGYDH ITSGIGAAMI GWYGTAMLCY
VTPKEHLGLP DRDDVKVGVV TYKLAAHAAD LAKGHPAAQV RDDALSKARF EFRWRDQFNL
SLDPDTAEQY HDQTLPAEGA KTAHFCSMCG PKFCSMKISQ EVREFAKLQN QDSAGFIAAE
EAEKGMAEMS QVYEDTGREL YMGAGGREHD
