DXS1_ORYSJ
ID DXS1_ORYSJ Reviewed; 720 AA.
AC O22567; A0A0P0WM75; Q0DI85; Q5TKB6; Q6I573;
DT 15-DEC-1998, integrated into UniProtKB/Swiss-Prot.
DT 21-MAR-2006, sequence version 2.
DT 03-AUG-2022, entry version 150.
DE RecName: Full=1-deoxy-D-xylulose-5-phosphate synthase 1, 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 Name=CLA1; OrderedLocusNames=Os05g0408900, LOC_Os05g33840;
GN ORFNames=OSJNBb0014K18.8, P0040B10.17;
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=16261349; DOI=10.1007/s00438-005-0039-y;
RA Cheng C.-H., Chung M.C., Liu S.-M., Chen S.-K., Kao F.Y., Lin S.-J.,
RA Hsiao S.-H., Tseng I.C., Hsing Y.-I.C., Wu H.-P., Chen C.-S., Shaw J.-F.,
RA Wu J., Matsumoto T., Sasaki T., Chen H.-C., Chow T.-Y.;
RT "A fine physical map of the rice chromosome 5.";
RL Mol. Genet. Genomics 274:337-345(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] (ISOFORMS 1 AND 2).
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).
RN [7]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 77-670 (ISOFORM 1).
RC TISSUE=Shoot;
RA Campos N., Lois L.M., Boronat A.;
RT "Nucleotide sequence of a rice cDNA encoding a transketolase-like protein
RT homologous to the Arabidopsis CLA1 gene product.";
RL (er) Plant Gene Register PGR97-169(1997).
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 stroma {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O22567-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O22567-2; Sequence=VSP_017655, VSP_017656;
CC -!- INDUCTION: By the mycorrhizal fungus G.intraradices colonization in
CC roots.
CC -!- SIMILARITY: Belongs to the transketolase family. DXPS subfamily.
CC {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=AAV59446.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR EMBL; AC137620; AAT58851.1; -; Genomic_DNA.
DR EMBL; AC137928; AAV59446.1; ALT_SEQ; Genomic_DNA.
DR EMBL; AP008211; BAF17438.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS93978.1; -; Genomic_DNA.
DR EMBL; AP014961; BAS93980.1; -; Genomic_DNA.
DR EMBL; CM000142; EEE63700.1; -; Genomic_DNA.
DR EMBL; AK064944; BAG89290.1; -; mRNA.
DR EMBL; AK104851; BAG96994.1; -; mRNA.
DR EMBL; AK106750; -; NOT_ANNOTATED_CDS; mRNA.
DR EMBL; AF024512; AAB88295.1; -; mRNA.
DR PIR; T02208; T02208.
DR RefSeq; XP_015640505.1; XM_015785019.1. [O22567-1]
DR AlphaFoldDB; O22567; -.
DR SMR; O22567; -.
DR STRING; 4530.OS05T0408900-03; -.
DR PaxDb; O22567; -.
DR PRIDE; O22567; -.
DR EnsemblPlants; Os05t0408900-01; Os05t0408900-01; Os05g0408900. [O22567-2]
DR EnsemblPlants; Os05t0408900-02; Os05t0408900-02; Os05g0408900. [O22567-2]
DR EnsemblPlants; Os05t0408900-03; Os05t0408900-03; Os05g0408900. [O22567-1]
DR EnsemblPlants; Os05t0408900-04; Os05t0408900-04; Os05g0408900. [O22567-1]
DR GeneID; 4338768; -.
DR Gramene; Os05t0408900-01; Os05t0408900-01; Os05g0408900. [O22567-2]
DR Gramene; Os05t0408900-02; Os05t0408900-02; Os05g0408900. [O22567-2]
DR Gramene; Os05t0408900-03; Os05t0408900-03; Os05g0408900. [O22567-1]
DR Gramene; Os05t0408900-04; Os05t0408900-04; Os05g0408900. [O22567-1]
DR KEGG; osa:4338768; -.
DR eggNOG; KOG0523; Eukaryota.
DR HOGENOM; CLU_009227_1_4_1; -.
DR InParanoid; O22567; -.
DR OMA; QVGYHAQ; -.
DR OrthoDB; 354970at2759; -.
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 5.
DR Proteomes; UP000007752; Chromosome 5.
DR Proteomes; UP000059680; Chromosome 5.
DR Genevisible; O22567; OS.
DR GO; GO:0009507; C:chloroplast; IBA:GO_Central.
DR GO; GO:0009570; C:chloroplast stroma; 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:0015995; P:chlorophyll biosynthetic process; IBA:GO_Central.
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 Gene3D; 3.40.50.920; -; 1.
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; IPR005474; Transketolase_N.
DR PANTHER; PTHR43322; PTHR43322; 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; SSF52518; 2.
DR SUPFAM; SSF52922; SSF52922; 1.
DR TIGRFAMs; TIGR00204; dxs; 1.
DR PROSITE; PS00801; TRANSKETOLASE_1; 1.
DR PROSITE; PS00802; TRANSKETOLASE_2; 1.
PE 2: Evidence at transcript level;
KW Alternative splicing; Chloroplast; Isoprene biosynthesis; Magnesium;
KW Metal-binding; Plastid; Reference proteome; Thiamine biosynthesis;
KW Thiamine pyrophosphate; Transferase; Transit peptide.
FT TRANSIT 1..51
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 52..720
FT /note="1-deoxy-D-xylulose-5-phosphate synthase 1,
FT chloroplastic"
FT /id="PRO_0000189180"
FT REGION 35..74
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 142
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 183..185
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 214
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 215..216
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 243
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /evidence="ECO:0000250"
FT BINDING 243
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 364
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT BINDING 446
FT /ligand="thiamine diphosphate"
FT /ligand_id="ChEBI:CHEBI:58937"
FT /evidence="ECO:0000250"
FT VAR_SEQ 285..305
FT /note="GVTKQIGGSVHELAAKVDEYA -> VRPHKRSTLTLDCPLPRKARE (in
FT isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_017655"
FT VAR_SEQ 306..720
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:12869764"
FT /id="VSP_017656"
SQ SEQUENCE 720 AA; 77304 MW; FB70C11EAF6C8BB5 CRC64;
MALTTFSISR GGFVGALPQE GHFAPAAAEL SLHKLQSRPH KARRRSSSSI SASLSTEREA
AEYHSQRPPT PLLDTVNYPI HMKNLSLKEL QQLADELRSD VIFHVSKTGG HLGSSLGVVE
LTVALHYVFN TPQDKILWDV GHQSYPHKIL TGRRDKMPTM RQTNGLSGFT KRSESEYDSF
GTGHSSTTIS AALGMAVGRD LKGGKNNVVA VIGDGAMTAG QAYEAMNNAG YLDSDMIVIL
NDNKQVSLPT ATLDGPAPPV GALSSALSKL QSSRPLRELR EVAKGVTKQI GGSVHELAAK
VDEYARGMIS GSGSTLFEEL GLYYIGPVDG HNIDDLITIL REVKSTKTTG PVLIHVVTEK
GRGYPYAERA ADKYHGVAKF DPATGKQFKS PAKTLSYTNY FAEALIAEAE QDNRVVAIHA
AMGGGTGLNY FLRRFPNRCF DVGIAEQHAV TFAAGLACEG LKPFCAIYSS FLQRGYDQVV
HDVDLQKLPV RFAMDRAGLV GADGPTHCGA FDVTYMACLP NMVVMAPSDE AELCHMVATA
AAIDDRPSCF RYPRGNGIGV PLPPNYKGVP LEVGKGRVLL EGERVALLGY GSAVQYCLAA
ASLVERHGLK VTVADARFCK PLDQTLIRRL ASSHEVLLTV EEGSIGGFGS HVAQFMALDG
LLDGKLKWRP LVLPDRYIDH GSPADQLAEA GLTPSHIAAT VFNVLGQARE ALAIMTVPNA
