TPS1_ORYSJ
ID TPS1_ORYSJ Reviewed; 548 AA.
AC Q2QWK9; A0A0P0Y7Y2; Q0IPK3;
DT 28-NOV-2012, integrated into UniProtKB/Swiss-Prot.
DT 11-JUL-2006, sequence version 2.
DT 03-AUG-2022, entry version 105.
DE RecName: Full=Probable thiamine biosynthetic bifunctional enzyme, chloroplastic;
DE Includes:
DE RecName: Full=Thiamine-phosphate synthase;
DE Short=TP synthase;
DE Short=TPS;
DE EC=2.5.1.3 {ECO:0000250|UniProtKB:Q5M731};
DE AltName: Full=Thiamine-phosphate pyrophosphorylase;
DE Short=TMP pyrophosphorylase;
DE Short=TMP-PPase;
DE Includes:
DE RecName: Full=Hydroxymethylpyrimidine kinase;
DE Short=HMP kinase;
DE EC=2.7.1.49 {ECO:0000250|UniProtKB:P30137};
DE Flags: Precursor;
GN OrderedLocusNames=Os12g0192500, LOC_Os12g09000; ORFNames=OsJ_35490;
OS Oryza sativa subsp. japonica (Rice).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; Liliopsida; Poales; Poaceae; BOP clade;
OC Oryzoideae; Oryzeae; Oryzinae; Oryza; Oryza sativa.
OX NCBI_TaxID=39947;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16188032; DOI=10.1186/1741-7007-3-20;
RG The rice chromosomes 11 and 12 sequencing consortia;
RT "The sequence of rice chromosomes 11 and 12, rich in disease resistance
RT genes and recent gene duplications.";
RL BMC Biol. 3:20-20(2005).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=16100779; DOI=10.1038/nature03895;
RG International rice genome sequencing project (IRGSP);
RT "The map-based sequence of the rice genome.";
RL Nature 436:793-800(2005).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=18089549; DOI=10.1093/nar/gkm978;
RG The rice annotation project (RAP);
RT "The rice annotation project database (RAP-DB): 2008 update.";
RL Nucleic Acids Res. 36:D1028-D1033(2008).
RN [4]
RP GENOME REANNOTATION.
RC STRAIN=cv. Nipponbare;
RX PubMed=24280374; DOI=10.1186/1939-8433-6-4;
RA Kawahara Y., de la Bastide M., Hamilton J.P., Kanamori H., McCombie W.R.,
RA Ouyang S., Schwartz D.C., Tanaka T., Wu J., Zhou S., Childs K.L.,
RA Davidson R.M., Lin H., Quesada-Ocampo L., Vaillancourt B., Sakai H.,
RA Lee S.S., Kim J., Numa H., Itoh T., Buell C.R., Matsumoto T.;
RT "Improvement of the Oryza sativa Nipponbare reference genome using next
RT generation sequence and optical map data.";
RL Rice 6:4-4(2013).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=15685292; DOI=10.1371/journal.pbio.0030038;
RA Yu J., Wang J., Lin W., Li S., Li H., Zhou J., Ni P., Dong W., Hu S.,
RA Zeng C., Zhang J., Zhang Y., Li R., Xu Z., Li S., Li X., Zheng H., Cong L.,
RA Lin L., Yin J., Geng J., Li G., Shi J., Liu J., Lv H., Li J., Wang J.,
RA Deng Y., Ran L., Shi X., Wang X., Wu Q., Li C., Ren X., Wang J., Wang X.,
RA Li D., Liu D., Zhang X., Ji Z., Zhao W., Sun Y., Zhang Z., Bao J., Han Y.,
RA Dong L., Ji J., Chen P., Wu S., Liu J., Xiao Y., Bu D., Tan J., Yang L.,
RA Ye C., Zhang J., Xu J., Zhou Y., Yu Y., Zhang B., Zhuang S., Wei H.,
RA Liu B., Lei M., Yu H., Li Y., Xu H., Wei S., He X., Fang L., Zhang Z.,
RA Zhang Y., Huang X., Su Z., Tong W., Li J., Tong Z., Li S., Ye J., Wang L.,
RA Fang L., Lei T., Chen C.-S., Chen H.-C., Xu Z., Li H., Huang H., Zhang F.,
RA Xu H., Li N., Zhao C., Li S., Dong L., Huang Y., Li L., Xi Y., Qi Q.,
RA Li W., Zhang B., Hu W., Zhang Y., Tian X., Jiao Y., Liang X., Jin J.,
RA Gao L., Zheng W., Hao B., Liu S.-M., Wang W., Yuan L., Cao M.,
RA McDermott J., Samudrala R., Wang J., Wong G.K.-S., Yang H.;
RT "The genomes of Oryza sativa: a history of duplications.";
RL PLoS Biol. 3:266-281(2005).
RN [6]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Nipponbare;
RX PubMed=12869764; DOI=10.1126/science.1081288;
RG The rice full-length cDNA consortium;
RT "Collection, mapping, and annotation of over 28,000 cDNA clones from
RT japonica rice.";
RL Science 301:376-379(2003).
CC -!- FUNCTION: Essential for thiamine biosynthesis. Bifunctional enzyme that
CC catalyzes the phosphorylation of hydroxymethylpyrimidine phosphate
CC (HMP-P) to HMP-PP and condenses 4-methyl-5-(beta-hydroxyethyl)thiazole
CC monophosphate (THZ-P) and 2-methyl-4-amino-5-hydroxymethyl pyrimidine
CC pyrophosphate (HMP-PP) to form thiamine monophosphate (TMP).
CC {ECO:0000250|UniProtKB:Q5M731}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl
CC phosphate + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 2
CC H(+) = CO2 + diphosphate + thiamine phosphate; Xref=Rhea:RHEA:47844,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:33019,
CC ChEBI:CHEBI:37575, ChEBI:CHEBI:57841, ChEBI:CHEBI:62899; EC=2.5.1.3;
CC Evidence={ECO:0000250|UniProtKB:Q5M731};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=2-(2-carboxy-4-methylthiazol-5-yl)ethyl phosphate + 4-amino-2-
CC methyl-5-(diphosphooxymethyl)pyrimidine + 2 H(+) = CO2 + diphosphate
CC + thiamine phosphate; Xref=Rhea:RHEA:47848, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:16526, ChEBI:CHEBI:33019, ChEBI:CHEBI:37575,
CC ChEBI:CHEBI:57841, ChEBI:CHEBI:62890; EC=2.5.1.3;
CC Evidence={ECO:0000250|UniProtKB:Q5M731};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine + 4-methyl-
CC 5-(2-phosphooxyethyl)-thiazole + H(+) = diphosphate + thiamine
CC phosphate; Xref=Rhea:RHEA:22328, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:33019, ChEBI:CHEBI:37575, ChEBI:CHEBI:57841,
CC ChEBI:CHEBI:58296; EC=2.5.1.3;
CC Evidence={ECO:0000250|UniProtKB:Q5M731};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=4-amino-5-hydroxymethyl-2-methylpyrimidine + ATP = 4-amino-2-
CC methyl-5-(phosphooxymethyl)pyrimidine + ADP + H(+);
CC Xref=Rhea:RHEA:23096, ChEBI:CHEBI:15378, ChEBI:CHEBI:16892,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:58354, ChEBI:CHEBI:456216;
CC EC=2.7.1.49; Evidence={ECO:0000250|UniProtKB:P30137};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Note=Binds 1 Mg(2+) ion per subunit. {ECO:0000250};
CC -!- PATHWAY: Cofactor biosynthesis; thiamine diphosphate biosynthesis;
CC thiamine phosphate from 4-amino-2-methyl-5-diphosphomethylpyrimidine
CC and 4-methyl-5-(2-phosphoethyl)-thiazole: step 1/1.
CC -!- PATHWAY: Cofactor biosynthesis; thiamine diphosphate biosynthesis; 4-
CC amino-2-methyl-5-diphosphomethylpyrimidine from 5-amino-1-(5-phospho-D-
CC ribosyl)imidazole: step 2/3.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the thiamine-phosphate synthase family.
CC {ECO:0000305}.
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DR EMBL; DP000011; ABA96049.2; -; Genomic_DNA.
DR EMBL; AP008218; BAF29362.2; -; Genomic_DNA.
DR EMBL; AP014968; BAT16214.1; -; Genomic_DNA.
DR EMBL; CM000149; EEE52897.1; -; Genomic_DNA.
DR EMBL; AK066087; BAG89812.1; -; mRNA.
DR RefSeq; XP_015618273.1; XM_015762787.1.
DR AlphaFoldDB; Q2QWK9; -.
DR SMR; Q2QWK9; -.
DR STRING; 4530.OS12T0192500-02; -.
DR PaxDb; Q2QWK9; -.
DR PRIDE; Q2QWK9; -.
DR EnsemblPlants; Os12t0192500-02; Os12t0192500-02; Os12g0192500.
DR GeneID; 4351707; -.
DR Gramene; Os12t0192500-02; Os12t0192500-02; Os12g0192500.
DR KEGG; osa:4351707; -.
DR eggNOG; KOG2598; Eukaryota.
DR HOGENOM; CLU_018272_7_0_1; -.
DR InParanoid; Q2QWK9; -.
DR OMA; GHIFPTN; -.
DR OrthoDB; 1245353at2759; -.
DR PlantReactome; R-OSA-1119629; Thiamine biosynthesis.
DR UniPathway; UPA00060; UER00137.
DR UniPathway; UPA00060; UER00141.
DR Proteomes; UP000000763; Chromosome 12.
DR Proteomes; UP000007752; Chromosome 12.
DR Proteomes; UP000059680; Chromosome 12.
DR ExpressionAtlas; Q2QWK9; baseline and differential.
DR Genevisible; Q2QWK9; OS.
DR GO; GO:0009507; C:chloroplast; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008902; F:hydroxymethylpyrimidine kinase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0008972; F:phosphomethylpyrimidine kinase activity; IBA:GO_Central.
DR GO; GO:0004789; F:thiamine-phosphate diphosphorylase activity; IEA:UniProtKB-EC.
DR GO; GO:0016310; P:phosphorylation; IEA:UniProtKB-KW.
DR GO; GO:0009228; P:thiamine biosynthetic process; IBA:GO_Central.
DR GO; GO:0009229; P:thiamine diphosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR CDD; cd01169; HMPP_kinase; 1.
DR CDD; cd00564; TMP_TenI; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR Gene3D; 3.40.1190.20; -; 1.
DR HAMAP; MF_00097; TMP_synthase; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR045029; HMP/HMP-P_kinase.
DR InterPro; IPR004399; HMP/HMP-P_kinase_dom.
DR InterPro; IPR013749; PM/HMP-P_kinase-1.
DR InterPro; IPR029056; Ribokinase-like.
DR InterPro; IPR036206; ThiamineP_synth_sf.
DR InterPro; IPR022998; ThiamineP_synth_TenI.
DR InterPro; IPR034291; TMP_synthase.
DR PANTHER; PTHR20858; PTHR20858; 1.
DR Pfam; PF08543; Phos_pyr_kin; 1.
DR Pfam; PF02581; TMP-TENI; 1.
DR SUPFAM; SSF51391; SSF51391; 1.
DR SUPFAM; SSF53613; SSF53613; 1.
DR TIGRFAMs; TIGR00097; HMP-P_kinase; 1.
DR TIGRFAMs; TIGR00693; thiE; 1.
PE 2: Evidence at transcript level;
KW ATP-binding; Chloroplast; Kinase; Magnesium; Metal-binding;
KW Multifunctional enzyme; Nucleotide-binding; Plastid; Reference proteome;
KW Thiamine biosynthesis; Transferase; Transit peptide.
FT TRANSIT 1..47
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 48..548
FT /note="Probable thiamine biosynthetic bifunctional enzyme,
FT chloroplastic"
FT /id="PRO_0000420254"
FT REGION 1..40
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..25
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 372..376
FT /ligand="4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine"
FT /ligand_id="ChEBI:CHEBI:57841"
FT /evidence="ECO:0000250"
FT BINDING 404
FT /ligand="4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine"
FT /ligand_id="ChEBI:CHEBI:57841"
FT /evidence="ECO:0000250"
FT BINDING 405
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 424
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 443
FT /ligand="4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine"
FT /ligand_id="ChEBI:CHEBI:57841"
FT /evidence="ECO:0000250"
FT BINDING 469..471
FT /ligand="2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-
FT ylidene]ethyl phosphate"
FT /ligand_id="ChEBI:CHEBI:62899"
FT /evidence="ECO:0000250"
FT BINDING 472
FT /ligand="4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine"
FT /ligand_id="ChEBI:CHEBI:57841"
FT /evidence="ECO:0000250"
FT BINDING 499
FT /ligand="2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-
FT ylidene]ethyl phosphate"
FT /ligand_id="ChEBI:CHEBI:62899"
FT /evidence="ECO:0000250"
FT BINDING 522..523
FT /ligand="2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-
FT ylidene]ethyl phosphate"
FT /ligand_id="ChEBI:CHEBI:62899"
FT /evidence="ECO:0000250"
SQ SEQUENCE 548 AA; 57804 MW; 9B5204B75835A72E CRC64;
MAAAPQQSVH PSLPSSTSTL RLLISSSPRR PPPPPPRARR YNRLAASASA AREMPWPHVL
TVAGSDSGGG AGIQADIKAC AALGAYCSSV VTAVTAQNTA GVQGIHVVPE EFIREQLNSV
LSDMSVDVVK TGMLPSIGVV RVLCESLKKF PVKALVVDPV MVSTSGDTLS ESSTLSVYRD
ELFAMADIVT PNVKEASRLL GGVSLRTVSD MRNAAESIYK FGPKHVLVKG GDMLESSDAT
DVFFDGKEFI ELHAHRIKTH NTHGTGCTLA SCIASELAKG ATMLHAVQVA KNFVESALHH
SKDLVVGNGP QGPFDHLFKL KCPPYNVGSQ PSFKPDQLFL YAVTDSGMNK KWGRSIKEAV
QAAIEGGATI VQLREKDSET REFLEAAKAC MEICKSSGVP LLINDRVDIA LACNADGVHV
GQLDMSAHEV RELLGPGKII GVSCKTPAQA QQAWNDGADY IGCGGVFPTS TKANNPTLGF
DGLKTVCLAS KLPVVAIGGI NASNAGSVME LGLPNLKGVA VVSALFDRPS VVAETRNMKS
ILTNTSRT
