ID DXS2_ORYSJ Reviewed; 713 AA.
AC Q6YU51; A0A0N7KN22;
DT 13-JUN-2012, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 27-MAR-2024, entry version 127.
DE RecName: Full=Probable 1-deoxy-D-xylulose-5-phosphate synthase 2, chloroplastic;
DE Short=1-deoxyxylulose-5-phosphate synthase;
DE Short=DXP synthase;
DE Short=DXPS;
DE EC=2.2.1.7;
DE Flags: Precursor;
GN OrderedLocusNames=Os07g0190000, LOC_Os07g09190;
GN ORFNames=OsJ_23394, OSJNBb0002L09.31, OSJNBb0003E08.7;
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=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 [2]
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 [3]
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 [4]
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 [5]
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: Catalyzes the acyloin condensation reaction between C atoms 2
CC and 3 of pyruvate and glyceraldehyde 3-phosphate to yield 1-deoxy-D-
CC xylulose-5-phosphate (DXP). Is a limiting enzyme for plastidic
CC isoprenoid biosynthesis and essential for chloroplast development (By
CC similarity). {ECO:0000250}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-glyceraldehyde 3-phosphate + H(+) + pyruvate = 1-deoxy-D-
CC xylulose 5-phosphate + CO2; Xref=Rhea:RHEA:12605, ChEBI:CHEBI:15361,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:16526, ChEBI:CHEBI:57792,
CC ChEBI:CHEBI:59776; EC=2.2.1.7;
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 -!- COFACTOR:
CC Name=thiamine diphosphate; Xref=ChEBI:CHEBI:58937;
CC Evidence={ECO:0000250};
CC Note=Binds 1 thiamine pyrophosphate per subunit. {ECO:0000250};
CC -!- PATHWAY: Metabolic intermediate biosynthesis; 1-deoxy-D-xylulose 5-
CC phosphate biosynthesis; 1-deoxy-D-xylulose 5-phosphate from D-
CC glyceraldehyde 3-phosphate and pyruvate: step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast {ECO:0000250}.
CC -!- SIMILARITY: Belongs to the transketolase family. DXPS subfamily.
CC {ECO:0000305}.
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DR EMBL; AP005173; BAD31023.1; -; Genomic_DNA.
DR EMBL; AP005877; BAC84616.1; -; Genomic_DNA.
DR EMBL; AP008213; BAF21000.1; -; Genomic_DNA.
DR EMBL; AP014963; BAT00410.1; -; Genomic_DNA.
DR EMBL; CM000144; EEE66718.1; -; Genomic_DNA.
DR EMBL; AK100909; BAG94824.1; -; mRNA.
DR RefSeq; XP_015647944.1; XM_015792458.1.
DR AlphaFoldDB; Q6YU51; -.
DR SMR; Q6YU51; -.
DR STRING; 39947.Q6YU51; -.
DR PaxDb; 39947-Q6YU51; -.
DR EnsemblPlants; Os07t0190000-01; Os07t0190000-01; Os07g0190000.
DR GeneID; 4342614; -.
DR Gramene; Os07t0190000-01; Os07t0190000-01; Os07g0190000.
DR KEGG; osa:4342614; -.
DR eggNOG; KOG0523; Eukaryota.
DR HOGENOM; CLU_009227_1_4_1; -.
DR InParanoid; Q6YU51; -.
DR OMA; FAPQGMF; -.
DR OrthoDB; 3626892at2759; -.
DR PlantReactome; R-OSA-1119464; Methylerythritol phosphate pathway.
DR PlantReactome; R-OSA-1119594; Pyridoxal 5'-phosphate biosynthesis.
DR PlantReactome; R-OSA-1119629; Thiamine biosynthesis.
DR UniPathway; UPA00064; UER00091.
DR Proteomes; UP000000763; Chromosome 7.
DR Proteomes; UP000007752; Chromosome 7.
DR Proteomes; UP000059680; Chromosome 7.
DR Genevisible; Q6YU51; OS.
DR GO; GO:0009507; C:chloroplast; IEA:UniProtKB-SubCell.
DR GO; GO:0008661; F:1-deoxy-D-xylulose-5-phosphate synthase activity; IEA:UniProtKB-EC.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0016744; F:transketolase or transaldolase activity; IBA:GO_Central.
DR GO; GO:0052865; P:1-deoxy-D-xylulose 5-phosphate biosynthetic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0016114; P:terpenoid biosynthetic process; IEA:InterPro.
DR GO; GO:0009228; P:thiamine biosynthetic process; IEA:UniProtKB-KW.
DR CDD; cd02007; TPP_DXS; 1.
DR CDD; cd07033; TPP_PYR_DXS_TK_like; 1.
DR Gene3D; 3.40.50.920; -; 1.
DR Gene3D; 3.40.50.970; -; 2.
DR HAMAP; MF_00315; DXP_synth; 1.
DR InterPro; IPR005477; Dxylulose-5-P_synthase.
DR InterPro; IPR029061; THDP-binding.
DR InterPro; IPR009014; Transketo_C/PFOR_II.
DR InterPro; IPR005475; Transketolase-like_Pyr-bd.
DR InterPro; IPR020826; Transketolase_BS.
DR InterPro; IPR033248; Transketolase_C.
DR InterPro; IPR049557; Transketolase_CS.
DR NCBIfam; TIGR00204; dxs; 1.
DR PANTHER; PTHR43322; 1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED; 1.
DR PANTHER; PTHR43322:SF4; 1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE 2, CHLOROPLASTIC-RELATED; 1.
DR Pfam; PF13292; DXP_synthase_N; 1.
DR Pfam; PF02779; Transket_pyr; 1.
DR Pfam; PF02780; Transketolase_C; 1.
DR SMART; SM00861; Transket_pyr; 1.
DR SUPFAM; SSF52518; Thiamin diphosphate-binding fold (THDP-binding); 2.
DR SUPFAM; SSF52922; TK C-terminal domain-like; 1.
DR PROSITE; PS00801; TRANSKETOLASE_1; 1.
DR PROSITE; PS00802; TRANSKETOLASE_2; 1.
PE 2: Evidence at transcript level;
KW Chloroplast; Isoprene biosynthesis; Magnesium; Metal-binding; Plastid;
KW Reference proteome; Thiamine biosynthesis; Thiamine pyrophosphate;
KW Transferase; Transit peptide.
FT TRANSIT 1..30
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 31..713
FT /note="Probable 1-deoxy-D-xylulose-5-phosphate synthase 2,
FT chloroplastic"
FT /id="PRO_0000417594"
FT BINDING 140
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 181..183
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 212
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 213..214
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 241
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 241
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 362
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 444
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
SQ SEQUENCE 713 AA; 75809 MW; C97A9B600E5FD611 CRC64;
MALQASSSPS MFRAIPTNTN ASCRRKLQVR ASAAAAAANG GGDGKVMMRK EAASGAWKID
YSGEKPATPL LDTVNYPVHM KNLSTPELEQ LAAELRAEIV HTVSKTGGHL SSSLGVVELA
VALHHVFDTP EDKIIWDVGH QAYPHKILTG RRSRMHTIRQ TSGLAGFPKR DESAHDAFGA
GHSSTSISAA LGMAVARDLL GKKNHVISVI GDGAMTAGQA YEAMNNSGYL DSNMIVVLND
NKQVSLPTAT LDGPATPVGA LSKALTKLQS STKLRRLREA AKTVTKQIGG QAHEVAAKVD
EYARGMVSAS GSTLFEELGL YYIGPVDGHS VDDLVAIFNK VKSMPAPGPV LVHIVTEKGK
GYPPAEAAAD RMHGVVKFDP TTGRQFKSKC STLSYTQYFA EALIREAEAD DKVVGIHAAM
GGGTGLNYFH KRFPERCFDV GIAEQHAVTF AAGLAAEGLK PFCAIYSSFL QRGYDQVVHD
VDLQRLPVRF AMDRAGLVGA DGPTHCGAFD VAYMACLPNM VVMAPADEAE LMHMVATAAA
IDDRPSCFRF PRGNGIGAVL PPNHKGTPLE VGKGRVLVGG NRVALLGYGT MVQACMKAAE
ALKEHGIYVT VADARFCKPL DTGLIRELAA EHEVLVTVEE GSIGGFGSHV AHYLSLSGLL
DGPLKLRSMF LPDRYIDHGA PVDQLEEAGL TPRHIAATVL SLLGRPLEAL QLS
//
