THIC_FRACC
ID THIC_FRACC Reviewed; 652 AA.
AC Q2JG22;
DT 27-JUN-2006, integrated into UniProtKB/Swiss-Prot.
DT 07-MAR-2006, sequence version 1.
DT 03-AUG-2022, entry version 95.
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};
GN OrderedLocusNames=Francci3_0383;
OS Frankia casuarinae (strain DSM 45818 / CECT 9043 / CcI3).
OC Bacteria; Actinobacteria; Frankiales; Frankiaceae; Frankia.
OX NCBI_TaxID=106370;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=DSM 45818 / CECT 9043 / CcI3;
RX PubMed=17151343; DOI=10.1101/gr.5798407;
RA Normand P., Lapierre P., Tisa L.S., Gogarten J.P., Alloisio N.,
RA Bagnarol E., Bassi C.A., Berry A.M., Bickhart D.M., Choisne N., Couloux A.,
RA Cournoyer B., Cruveiller S., Daubin V., Demange N., Francino M.P.,
RA Goltsman E., Huang Y., Kopp O.R., Labarre L., Lapidus A., Lavire C.,
RA Marechal J., Martinez M., Mastronunzio J.E., Mullin B.C., Niemann J.,
RA Pujic P., Rawnsley T., Rouy Z., Schenowitz C., Sellstedt A., Tavares F.,
RA Tomkins J.P., Vallenet D., Valverde C., Wall L.G., Wang Y., Medigue C.,
RA Benson D.R.;
RT "Genome characteristics of facultatively symbiotic Frankia sp. strains
RT reflect host range and host plant biogeography.";
RL Genome Res. 17:7-15(2007).
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; CP000249; ABD09770.1; -; Genomic_DNA.
DR AlphaFoldDB; Q2JG22; -.
DR SMR; Q2JG22; -.
DR STRING; 106370.Francci3_0383; -.
DR PRIDE; Q2JG22; -.
DR EnsemblBacteria; ABD09770; ABD09770; Francci3_0383.
DR KEGG; fra:Francci3_0383; -.
DR eggNOG; COG0422; Bacteria.
DR HOGENOM; CLU_013181_2_1_11; -.
DR OMA; TWELFRD; -.
DR OrthoDB; 505395at2; -.
DR PhylomeDB; Q2JG22; -.
DR UniPathway; UPA00060; -.
DR Proteomes; UP000001937; 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..652
FT /note="Phosphomethylpyrimidine synthase"
FT /id="PRO_0000242263"
FT REGION 1..45
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 118..166
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 136..150
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
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 652 AA; 69061 MW; 8237FA7832EC1537 CRC64;
MVSRTDRSSS STSKAVTSSP STSSLSSAAS SPSVSSSSSS SSVSAAGMTA VSTGPLTGSR
KTWLVGADPD LRVPMREIVL TTGDTVVVYD TSGPYTDPGV TIDVRRGLPA TRDSWIAQRG
DTAPDERRTV PGTGASGPGT LGSGTPGSGT PGSGPLGLGG TDLDGRVRVP RRAVPGRPSI
TQLGYARRGQ ITREMEFVAL REGLPVETVR AEIAAGRAVL PANVNHPESE PMAIGRAFLV
KINANLGNSA VTSSIEEEVE KMVWATRWGA DTVMDLSTGS DIALTREWII RNAPVPVGTV
PIYQALEKVG GRPEKLSWEV YRDTVIEQCE QGVDYMTVHA GVLLRYVPLT ARRRTGIVSR
GGSILASWCL AHHEENFLYT HFAELCEIFA AYDVTFSLGD GLRPGSIADA NDEAQLAELA
TLGELTQVAW EHDVQVMIEG PGHVPMNKIE ENVQLQRELC HDAPFYTLGP LTTDIAPGYD
HITSAIGAAM IGWAGTAMLC YVTPKEHLGL PDRDDVKAGV IAYKIAAHAA DLAKGHPGAQ
AWDDALSDAR FEFRWADQFH LALDPDTARA FHDETLPAPA AKSAHFCSMC GPHFCSMKIS
HQVRAHAGGD GLDPAGHGAD PAGDEAVTAG LREKAAEFNA AGNRIYLPVA NS
