RPE_ARATH
ID RPE_ARATH Reviewed; 281 AA.
AC Q9SAU2; C0Z3J9;
DT 16-OCT-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-MAY-2000, sequence version 1.
DT 03-AUG-2022, entry version 160.
DE RecName: Full=Ribulose-5-phosphate-3-epimerase, chloroplastic {ECO:0000303|PubMed:9843485};
DE Short=R5P3E {ECO:0000303|PubMed:9843485};
DE EC=5.1.3.1 {ECO:0000250|UniProtKB:Q43157};
DE AltName: Full=Pentose-5-phosphate 3-epimerase {ECO:0000305};
DE AltName: Full=Protein EMBRYO DEFECTIVE 2728 {ECO:0000303|PubMed:15266054};
DE Flags: Precursor;
GN Name=RPE {ECO:0000303|PubMed:9843485};
GN Synonyms=EMB2728 {ECO:0000303|PubMed:15266054};
GN OrderedLocusNames=At5g61410 {ECO:0000312|Araport:AT5G61410};
GN ORFNames=MFB13.19 {ECO:0000312|EMBL:BAB08496.1};
OS Arabidopsis thaliana (Mouse-ear cress).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX NCBI_TaxID=3702;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, DISRUPTION PHENOTYPE, INDUCTION BY
RP NEMATODES, TISSUE SPECIFICITY, AND DEVELOPMENTAL STAGE.
RC STRAIN=cv. Wassilewskija;
RX PubMed=9843485; DOI=10.1093/emboj/17.23.6799;
RA Favery B., Lecomte P., Gil N., Bechtold N., Bouchez D., Dalmasso A.,
RA Abad P.;
RT "RPE, a plant gene involved in early developmental steps of nematode
RT feeding cells.";
RL EMBO J. 17:6799-6811(1998).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=cv. Columbia;
RX PubMed=9628582; DOI=10.1093/dnares/5.1.41;
RA Sato S., Kaneko T., Kotani H., Nakamura Y., Asamizu E., Miyajima N.,
RA Tabata S.;
RT "Structural analysis of Arabidopsis thaliana chromosome 5. IV. Sequence
RT features of the regions of 1,456,315 bp covered by nineteen physically
RT assigned P1 and TAC clones.";
RL DNA Res. 5:41-54(1998).
RN [3]
RP GENOME REANNOTATION.
RC STRAIN=cv. Columbia;
RX PubMed=27862469; DOI=10.1111/tpj.13415;
RA Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA Town C.D.;
RT "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT genome.";
RL Plant J. 89:789-804(2017).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
RC STRAIN=cv. Columbia;
RX PubMed=14593172; DOI=10.1126/science.1088305;
RA Yamada K., Lim J., Dale J.M., Chen H., Shinn P., Palm C.J., Southwick A.M.,
RA Wu H.C., Kim C.J., Nguyen M., Pham P.K., Cheuk R.F., Karlin-Newmann G.,
RA Liu S.X., Lam B., Sakano H., Wu T., Yu G., Miranda M., Quach H.L.,
RA Tripp M., Chang C.H., Lee J.M., Toriumi M.J., Chan M.M., Tang C.C.,
RA Onodera C.S., Deng J.M., Akiyama K., Ansari Y., Arakawa T., Banh J.,
RA Banno F., Bowser L., Brooks S.Y., Carninci P., Chao Q., Choy N., Enju A.,
RA Goldsmith A.D., Gurjal M., Hansen N.F., Hayashizaki Y., Johnson-Hopson C.,
RA Hsuan V.W., Iida K., Karnes M., Khan S., Koesema E., Ishida J., Jiang P.X.,
RA Jones T., Kawai J., Kamiya A., Meyers C., Nakajima M., Narusaka M.,
RA Seki M., Sakurai T., Satou M., Tamse R., Vaysberg M., Wallender E.K.,
RA Wong C., Yamamura Y., Yuan S., Shinozaki K., Davis R.W., Theologis A.,
RA Ecker J.R.;
RT "Empirical analysis of transcriptional activity in the Arabidopsis
RT genome.";
RL Science 302:842-846(2003).
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 50-281.
RC STRAIN=cv. Columbia; TISSUE=Flower, and Silique;
RX PubMed=19423640; DOI=10.1093/dnares/dsp009;
RA Iida K., Fukami-Kobayashi K., Toyoda A., Sakaki Y., Kobayashi M., Seki M.,
RA Shinozaki K.;
RT "Analysis of multiple occurrences of alternative splicing events in
RT Arabidopsis thaliana using novel sequenced full-length cDNAs.";
RL DNA Res. 16:155-164(2009).
RN [6]
RP FUNCTION [LARGE SCALE ANALYSIS], AND DISRUPTION PHENOTYPE [LARGE SCALE
RP ANALYSIS].
RC STRAIN=cv. Columbia;
RX PubMed=15266054; DOI=10.1104/pp.104.045179;
RA Tzafrir I., Pena-Muralla R., Dickerman A., Berg M., Rogers R., Hutchens S.,
RA Sweeney T.C., McElver J., Aux G., Patton D., Meinke D.;
RT "Identification of genes required for embryo development in Arabidopsis.";
RL Plant Physiol. 135:1206-1220(2004).
CC -!- FUNCTION: Essential protein required during embryogenesis
CC (PubMed:15266054). Catalyzes the reversible epimerization of D-ribulose
CC 5-phosphate to D-xylulose 5-phosphate (By similarity). Essential for
CC the early steps of nematode feeding sites (NFS, multinucleated root
CC cells) formation induced by the root-knot nematodes Heterodera
CC schachtii, Meloidogyne incognita, M.javanica and M.hapla
CC (PubMed:9843485). {ECO:0000250|UniProtKB:Q43157,
CC ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:9843485}.
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:Q43157};
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:0000250|UniProtKB:Q96AT9};
CC Note=Binds 1 divalent metal cation per subunit. Active with Co(2+),
CC Fe(2+), Mn(2+) and Zn(2+). {ECO:0000250|UniProtKB:Q96AT9};
CC -!- PATHWAY: Carbohydrate biosynthesis; Calvin cycle.
CC {ECO:0000250|UniProtKB:Q43157}.
CC -!- SUBUNIT: Homooctamer. {ECO:0000250|UniProtKB:Q43157}.
CC -!- SUBCELLULAR LOCATION: Plastid, chloroplast thylakoid membrane
CC {ECO:0000250|UniProtKB:Q43157}.
CC -!- TISSUE SPECIFICITY: Present in roots, seeds and flowers
CC (PubMed:9843485). Accumulates in nematode feeding sites (NFS)
CC (PubMed:9843485). {ECO:0000269|PubMed:9843485}.
CC -!- DEVELOPMENTAL STAGE: During root development, expressed in the
CC meristems, in part of the elongation zone, in which cells divide and
CC expand, and initiation sites of lateral roots (PubMed:9843485). In
CC mature embryos from dry seeds, observed in the zone corresponding to
CC the root apical meristem and in cotyledons (PubMed:9843485).
CC {ECO:0000269|PubMed:9843485}.
CC -!- INDUCTION: Induced by both root-knot and cyst nematodes when nematode
CC feeding sites (NFS, giant cells) are developped and form galls.
CC {ECO:0000269|PubMed:9843485}.
CC -!- DISRUPTION PHENOTYPE: Defective embryo arrested at cotyledon stage
CC (PubMed:15266054). Reduced germination capacity, leading to the
CC development of some dwarf seedlings unable to grow on soil
CC (PubMed:9843485). Reduced sensitivity to nematodes associated with
CC reduced number of cysts and limited number of galls upon infection with
CC Meloidogyne incognita and Heterodera schachtii (PubMed:9843485).
CC {ECO:0000269|PubMed:15266054, ECO:0000269|PubMed:9843485}.
CC -!- SIMILARITY: Belongs to the ribulose-phosphate 3-epimerase family.
CC {ECO:0000305}.
CC -!- WEB RESOURCE: Name=Seed defective Arabidopsis mutants;
CC URL="http://seedgenes.org/MutantList";
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DR EMBL; AF015274; AAD09954.1; -; mRNA.
DR EMBL; AB010073; BAB08496.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97463.1; -; Genomic_DNA.
DR EMBL; CP002688; AED97464.1; -; Genomic_DNA.
DR EMBL; AY045855; AAK76529.1; -; mRNA.
DR EMBL; AY091381; AAM14320.1; -; mRNA.
DR EMBL; AK319163; BAH57278.1; -; mRNA.
DR RefSeq; NP_200949.1; NM_125534.4.
DR RefSeq; NP_851240.1; NM_180909.3.
DR AlphaFoldDB; Q9SAU2; -.
DR SMR; Q9SAU2; -.
DR IntAct; Q9SAU2; 1.
DR STRING; 3702.AT5G61410.1; -.
DR PaxDb; Q9SAU2; -.
DR PRIDE; Q9SAU2; -.
DR ProMEX; Q9SAU2; -.
DR ProteomicsDB; 174983; -.
DR EnsemblPlants; AT5G61410.1; AT5G61410.1; AT5G61410.
DR EnsemblPlants; AT5G61410.2; AT5G61410.2; AT5G61410.
DR GeneID; 836262; -.
DR Gramene; AT5G61410.1; AT5G61410.1; AT5G61410.
DR Gramene; AT5G61410.2; AT5G61410.2; AT5G61410.
DR KEGG; ath:AT5G61410; -.
DR Araport; AT5G61410; -.
DR TAIR; locus:2163228; AT5G61410.
DR eggNOG; KOG3111; Eukaryota.
DR HOGENOM; CLU_054856_1_1_1; -.
DR InParanoid; Q9SAU2; -.
DR OMA; CDLILIM; -.
DR OrthoDB; 1554029at2759; -.
DR PhylomeDB; Q9SAU2; -.
DR BioCyc; ARA:AT5G61410-MON; -.
DR UniPathway; UPA00116; -.
DR PRO; PR:Q9SAU2; -.
DR Proteomes; UP000006548; Chromosome 5.
DR ExpressionAtlas; Q9SAU2; baseline and differential.
DR GO; GO:0048046; C:apoplast; HDA:TAIR.
DR GO; GO:0009507; C:chloroplast; HDA:TAIR.
DR GO; GO:0009941; C:chloroplast envelope; HDA:TAIR.
DR GO; GO:0009570; C:chloroplast stroma; HDA:TAIR.
DR GO; GO:0009535; C:chloroplast thylakoid membrane; IEA:UniProtKB-SubCell.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0009536; C:plastid; HDA:TAIR.
DR GO; GO:0010319; C:stromule; IDA:TAIR.
DR GO; GO:0009579; C:thylakoid; HDA:TAIR.
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 GO; GO:0019253; P:reductive pentose-phosphate cycle; IEA:UniProtKB-UniPathway.
DR GO; GO:0009409; P:response to cold; IEP:TAIR.
DR GO; GO:0009624; P:response to nematode; IMP:TAIR.
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 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 2: Evidence at transcript level;
KW Chloroplast; Isomerase; Membrane; Metal-binding; Plastid;
KW Reference proteome; Thylakoid; Transit peptide.
FT TRANSIT 1..45
FT /note="Chloroplast"
FT /evidence="ECO:0000255"
FT CHAIN 46..281
FT /note="Ribulose-5-phosphate-3-epimerase, chloroplastic"
FT /evidence="ECO:0000255"
FT /id="PRO_0000448241"
FT ACT_SITE 90
FT /note="Proton acceptor"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT ACT_SITE 232
FT /note="Proton donor"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 63
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 88
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 90
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 121
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 121
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 199..202
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 232..234
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 232
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000250|UniProtKB:P32719"
FT BINDING 254..256
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:P32719"
SQ SEQUENCE 281 AA; 30009 MW; 0F4FEE6549F6FE70 CRC64;
MSTSAASLCC SSTQVNGFGL RPERSLLYQP TSFSFSRRRT HGIVKASSRV DRFSKSDIIV
SPSILSANFA KLGEQVKAVE LAGCDWIHVD VMDGRFVPNI TIGPLVVDAL RPVTDLPLDV
HLMIVEPEQR VPDFIKAGAD IVSVHCEQQS TIHLHRTVNQ IKSLGAKAGV VLNPGTPLSA
IEYVLDMVDL VLIMSVNPGF GGQSFIESQV KKISDLRKMC AEKGVNPWIE VDGGVTPANA
YKVIEAGANA LVAGSAVFGA KDYAEAIKGI KASKRPAAVA V
