RPE1_ORYSJ
ID RPE1_ORYSJ Reviewed; 228 AA.
AC Q9SE42; B7EGE3; Q0J0L5;
DT 01-MAR-2005, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 117.
DE RecName: Full=Ribulose-phosphate 3-epimerase, cytoplasmic isoform;
DE EC=5.1.3.1 {ECO:0000250|UniProtKB:Q96AT9};
DE AltName: Full=Cyt-RPEase;
DE AltName: Full=Pentose-5-phosphate 3-epimerase;
DE Short=PPE;
DE AltName: Full=RPEcyt;
DE AltName: Full=Ribulose-5-phosphate-epimerase;
GN OrderedLocusNames=Os09g0505700, LOC_Os09g32810;
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 [MRNA], SUBCELLULAR LOCATION, SUBUNIT, TISSUE
RP SPECIFICITY, AND BIOPHYSICOCHEMICAL PROPERTIES.
RC STRAIN=cv. Nipponbare;
RX PubMed=10625676; DOI=10.1074/jbc.275.2.1294;
RA Kopriva S., Koprivova A., Suess K.-H.;
RT "Identification, cloning, and properties of cytosolic D-ribulose-5-
RT phosphate 3-epimerase from higher plants.";
RL J. Biol. Chem. 275:1294-1299(2000).
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 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).
RN [6]
RP X-RAY CRYSTALLOGRAPHY (1.87 ANGSTROMS) IN COMPLEX WITH ZINC, COFACTOR,
RP ACTIVE SITE, AND SUBUNIT.
RX PubMed=12547196; DOI=10.1016/s0022-2836(02)01374-8;
RA Jelakovic S., Kopriva S., Suess K.-H., Schulz G.E.;
RT "Structure and catalytic mechanism of the cytosolic D-ribulose-5-phosphate
RT 3-epimerase from rice.";
RL J. Mol. Biol. 326:127-135(2003).
CC -!- FUNCTION: Catalyzes the reversible epimerization of D-ribulose 5-
CC phosphate to D-xylulose 5-phosphate. {ECO:0000250|UniProtKB:Q96AT9}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=D-ribulose 5-phosphate = D-xylulose 5-phosphate;
CC Xref=Rhea:RHEA:13677, ChEBI:CHEBI:57737, ChEBI:CHEBI:58121;
CC EC=5.1.3.1; Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC -!- COFACTOR:
CC Name=Co(2+); Xref=ChEBI:CHEBI:48828;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Name=Fe(2+); Xref=ChEBI:CHEBI:29033;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000250|UniProtKB:Q96AT9};
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000269|PubMed:12547196};
CC Note=Binds 1 divalent metal cation per subunit. Active with Co(2+),
CC Fe(2+), Mn(2+) and Zn(2+). {ECO:0000269|PubMed:12547196};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC Vmax=16000 umol/min/mg enzyme {ECO:0000269|PubMed:10625676};
CC -!- PATHWAY: Carbohydrate degradation; pentose phosphate pathway; D-
CC xylulose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage):
CC step 1/1.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:10625676,
CC ECO:0000269|PubMed:12547196}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000269|PubMed:10625676}.
CC -!- TISSUE SPECIFICITY: Predominantly accumulates in roots and seedlings.
CC {ECO:0000269|PubMed:10625676}.
CC -!- SIMILARITY: Belongs to the ribulose-phosphate 3-epimerase family.
CC {ECO:0000305}.
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DR EMBL; AF189365; AAF01048.1; -; mRNA.
DR EMBL; AC108753; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP008215; BAF25518.2; -; Genomic_DNA.
DR EMBL; AP014965; BAT08853.1; -; Genomic_DNA.
DR EMBL; AK069451; BAG91440.1; -; mRNA.
DR RefSeq; XP_015611665.1; XM_015756179.1.
DR PDB; 1H1Y; X-ray; 1.87 A; A/B=1-228.
DR PDB; 1H1Z; X-ray; 3.40 A; A/B=1-228.
DR PDBsum; 1H1Y; -.
DR PDBsum; 1H1Z; -.
DR AlphaFoldDB; Q9SE42; -.
DR SMR; Q9SE42; -.
DR STRING; 4530.OS09T0505700-02; -.
DR PaxDb; Q9SE42; -.
DR PRIDE; Q9SE42; -.
DR EnsemblPlants; Os09t0505700-02; Os09t0505700-02; Os09g0505700.
DR GeneID; 4347508; -.
DR Gramene; Os09t0505700-02; Os09t0505700-02; Os09g0505700.
DR KEGG; osa:4347508; -.
DR eggNOG; KOG3111; Eukaryota.
DR HOGENOM; CLU_054856_0_1_1; -.
DR InParanoid; Q9SE42; -.
DR OMA; WLQVDGG; -.
DR OrthoDB; 1554029at2759; -.
DR BRENDA; 5.1.3.1; 4460.
DR PlantReactome; R-OSA-1119519; Calvin cycle.
DR SABIO-RK; Q9SE42; -.
DR UniPathway; UPA00115; UER00411.
DR EvolutionaryTrace; Q9SE42; -.
DR Proteomes; UP000000763; Chromosome 9.
DR Proteomes; UP000059680; Chromosome 9.
DR ExpressionAtlas; Q9SE42; baseline and differential.
DR Genevisible; Q9SE42; OS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0004750; F:D-ribulose-phosphate 3-epimerase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IBA:GO_Central.
DR GO; GO:0044262; P:cellular carbohydrate metabolic process; IBA:GO_Central.
DR GO; GO:0009052; P:pentose-phosphate shunt, non-oxidative branch; IBA:GO_Central.
DR CDD; cd00429; RPE; 1.
DR Gene3D; 3.20.20.70; -; 1.
DR HAMAP; MF_02227; RPE; 1.
DR InterPro; IPR013785; Aldolase_TIM.
DR InterPro; IPR026019; Ribul_P_3_epim.
DR InterPro; IPR000056; Ribul_P_3_epim-like.
DR InterPro; IPR011060; RibuloseP-bd_barrel.
DR PANTHER; PTHR11749; PTHR11749; 1.
DR Pfam; PF00834; Ribul_P_3_epim; 1.
DR PIRSF; PIRSF001461; RPE; 1.
DR SUPFAM; SSF51366; SSF51366; 1.
DR TIGRFAMs; TIGR01163; rpe; 1.
DR PROSITE; PS01085; RIBUL_P_3_EPIMER_1; 1.
DR PROSITE; PS01086; RIBUL_P_3_EPIMER_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Cobalt; Cytoplasm; Iron; Isomerase;
KW Manganese; Metal-binding; Pentose shunt; Reference proteome; Zinc.
FT CHAIN 1..228
FT /note="Ribulose-phosphate 3-epimerase, cytoplasmic isoform"
FT /id="PRO_0000171590"
FT ACT_SITE 39
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT ACT_SITE 179
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 12
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 37
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:12547196,
FT ECO:0007744|PDB:1H1Z"
FT BINDING 39
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:12547196,
FT ECO:0007744|PDB:1H1Z"
FT BINDING 70
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:12547196,
FT ECO:0007744|PDB:1H1Z"
FT BINDING 70
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 150..153
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 179..181
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 179
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|PubMed:12547196,
FT ECO:0007744|PDB:1H1Z"
FT BINDING 201..202
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT CONFLICT 42..43
FT /note="DG -> GR (in Ref. 2; AC108753)"
FT /evidence="ECO:0000305"
FT STRAND 8..12
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 13..15
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 18..20
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 21..30
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 34..47
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 53..60
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 65..74
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 76..79
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 80..86
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 89..94
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 95..97
FT /evidence="ECO:0007829|PDB:1H1Y"
FT TURN 99..101
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 102..111
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 115..120
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 126..129
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 130..134
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 135..137
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 140..147
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 149..151
FT /evidence="ECO:0007829|PDB:1H1Z"
FT HELIX 158..160
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 161..170
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 174..181
FT /evidence="ECO:0007829|PDB:1H1Y"
FT TURN 184..186
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 187..193
FT /evidence="ECO:0007829|PDB:1H1Y"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 202..205
FT /evidence="ECO:0007829|PDB:1H1Y"
FT HELIX 210..223
FT /evidence="ECO:0007829|PDB:1H1Y"
SQ SEQUENCE 228 AA; 24291 MW; ED2FD8F9F230226B CRC64;
MAAAAAAKIA PSMLSSDFAN LAAEADRMVR LGADWLHMDI MDGHFVPNLT IGAPVIQSLR
KHTKAYLDCH LMVTNPSDYV EPLAKAGASG FTFHIEVSRD NWQELIQSIK AKGMRPGVSL
RPGTPVEEVF PLVEAENPVE LVLVMTVEPG FGGQKFMPEM MEKVRALRKK YPSLDIEVDG
GLGPSTIDVA ASAGANCIVA GSSIFGAAEP GEVISALRKS VEGSQNKS
