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Protein

Ribulose-phosphate 3-epimerase, cytoplasmic isoform

Gene

Os09g0505700

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: -Experimental evidence at protein leveli

Functioni

Catalyzes the reversible epimerization of D-ribulose 5-phosphate to D-xylulose 5-phosphate.

Catalytic activityi

D-ribulose 5-phosphate = D-xylulose 5-phosphate.

Cofactori

Co2+By similarity, Fe2+By similarity, Mn2+By similarity, Zn2+By similarityNote: Binds 1 divalent metal cation per subunit. Active with Co2+, Fe2+, Mn2+ and Zn2+.By similarity

Kineticsi

    1. Vmax=16000 µmol/min/mg enzyme1 Publication

    Pathwayi: pentose phosphate pathway

    This protein is involved in step 1 of the subpathway that synthesizes D-xylulose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage).
    Proteins known to be involved in this subpathway in this organism are:
    1. Ribulose-phosphate 3-epimerase, cytoplasmic isoform (Os09g0505700)
    This subpathway is part of the pathway pentose phosphate pathway, which is itself part of Carbohydrate degradation.
    View all proteins of this organism that are known to be involved in the subpathway that synthesizes D-xylulose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage), the pathway pentose phosphate pathway and in Carbohydrate degradation.

    Sites

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Binding sitei12SubstrateBy similarity1
    Metal bindingi37Divalent metal cation1
    Active sitei39Proton acceptorBy similarity1
    Metal bindingi39Divalent metal cation1
    Metal bindingi70Divalent metal cation1
    Binding sitei70SubstrateBy similarity1
    Active sitei179Proton donorBy similarity1
    Metal bindingi179Divalent metal cation1
    Binding sitei181Substrate; via amide nitrogenBy similarity1

    GO - Molecular functioni

    GO - Biological processi

    Keywordsi

    Molecular functionIsomerase
    Biological processCarbohydrate metabolism, Pentose shunt
    LigandCobalt, Iron, Manganese, Metal-binding, Zinc

    Enzyme and pathway databases

    BRENDAi5.1.3.1 4460
    ReactomeiR-OSA-71336 Pentose phosphate pathway (hexose monophosphate shunt)
    UniPathwayiUPA00115; UER00411

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribulose-phosphate 3-epimerase, cytoplasmic isoform (EC:5.1.3.1)
    Alternative name(s):
    Cyt-RPEase
    Pentose-5-phosphate 3-epimerase
    Short name:
    PPE
    RPEcyt
    Ribulose-5-phosphate-epimerase
    Gene namesi
    Ordered Locus Names:Os09g0505700, LOC_Os09g32810
    OrganismiOryza sativa subsp. japonica (Rice)
    Taxonomic identifieri39947 [NCBI]
    Taxonomic lineageiEukaryotaViridiplantaeStreptophytaEmbryophytaTracheophytaSpermatophytaMagnoliophytaLiliopsidaPoalesPoaceaeBOP cladeOryzoideaeOryzeaeOryzinaeOryzaOryza sativa
    Proteomesi
    • UP000059680 Componenti: Chromosome 9

    Subcellular locationi

    Extracellular region or secreted Cytosol Plasma membrane Cell wall Cytoskeleton Vacuole Chloroplast Endosome Peroxisome ER Golgi apparatus Nucleus Mitochondrion Manual annotation Automatic computational assertion Graphics by Christian Stolte; Source: COMPARTMENTS

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001715901 – 228Ribulose-phosphate 3-epimerase, cytoplasmic isoformAdd BLAST228

    Proteomic databases

    PaxDbiQ9SE42

    Expressioni

    Tissue specificityi

    Predominantly accumulates in roots and seedlings.1 Publication

    Gene expression databases

    ExpressionAtlasiQ9SE42 baseline and differential
    GenevisibleiQ9SE42 OS

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi39947.LOC_Os09g32810.1

    Structurei

    Secondary structure

    1228
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi8 – 12Combined sources5
    Helixi13 – 15Combined sources3
    Helixi18 – 20Combined sources3
    Helixi21 – 30Combined sources10
    Beta strandi34 – 47Combined sources14
    Helixi53 – 60Combined sources8
    Beta strandi65 – 74Combined sources10
    Helixi76 – 79Combined sources4
    Helixi80 – 86Combined sources7
    Beta strandi89 – 94Combined sources6
    Helixi95 – 97Combined sources3
    Turni99 – 101Combined sources3
    Helixi102 – 111Combined sources10
    Beta strandi115 – 120Combined sources6
    Helixi126 – 129Combined sources4
    Helixi130 – 134Combined sources5
    Beta strandi135 – 137Combined sources3
    Beta strandi140 – 147Combined sources8
    Beta strandi149 – 151Combined sources3
    Helixi158 – 160Combined sources3
    Helixi161 – 170Combined sources10
    Beta strandi174 – 181Combined sources8
    Turni184 – 186Combined sources3
    Helixi187 – 193Combined sources7
    Beta strandi197 – 201Combined sources5
    Helixi202 – 205Combined sources4
    Helixi210 – 223Combined sources14

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1H1YX-ray1.87A/B1-228[»]
    1H1ZX-ray3.40A/B1-228[»]
    ProteinModelPortaliQ9SE42
    SMRiQ9SE42
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9SE42

    Family & Domainsi

    Region

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Regioni150 – 153Substrate bindingBy similarity4
    Regioni201 – 202Substrate bindingBy similarity2

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG3111 Eukaryota
    COG0036 LUCA
    HOGENOMiHOG000259349
    InParanoidiQ9SE42
    KOiK01783
    OMAiISVHYES
    OrthoDBiEOG09360LI4

    Family and domain databases

    CDDicd00429 RPE, 1 hit
    Gene3Di3.20.20.70, 1 hit
    InterProiView protein in InterPro
    IPR013785 Aldolase_TIM
    IPR026019 Ribul_P_3_epim
    IPR000056 Ribul_P_3_epim-like
    IPR011060 RibuloseP-bd_barrel
    PANTHERiPTHR11749 PTHR11749, 1 hit
    PfamiView protein in Pfam
    PF00834 Ribul_P_3_epim, 1 hit
    PIRSFiPIRSF001461 RPE, 1 hit
    SUPFAMiSSF51366 SSF51366, 1 hit
    TIGRFAMsiTIGR01163 rpe, 1 hit
    PROSITEiView protein in PROSITE
    PS01085 RIBUL_P_3_EPIMER_1, 1 hit
    PS01086 RIBUL_P_3_EPIMER_2, 1 hit

    Sequencei

    Sequence statusi: Complete.

    Q9SE42-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MAAAAAAKIA PSMLSSDFAN LAAEADRMVR LGADWLHMDI MDGHFVPNLT
    60 70 80 90 100
    IGAPVIQSLR KHTKAYLDCH LMVTNPSDYV EPLAKAGASG FTFHIEVSRD
    110 120 130 140 150
    NWQELIQSIK AKGMRPGVSL RPGTPVEEVF PLVEAENPVE LVLVMTVEPG
    160 170 180 190 200
    FGGQKFMPEM MEKVRALRKK YPSLDIEVDG GLGPSTIDVA ASAGANCIVA
    210 220
    GSSIFGAAEP GEVISALRKS VEGSQNKS
    Length:228
    Mass (Da):24,291
    Last modified:May 1, 2000 - v1
    Checksum:iED2FD8F9F230226B
    GO

    Experimental Info

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Sequence conflicti42 – 43DG → GR (PubMed:16100779).Curated2

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AF189365 mRNA Translation: AAF01048.1
    AC108753 Genomic DNA No translation available.
    AP008215 Genomic DNA Translation: BAF25518.2
    AP014965 Genomic DNA Translation: BAT08853.1
    AK069451 mRNA Translation: BAG91440.1
    RefSeqiXP_015611665.1, XM_015756179.1
    UniGeneiOs.8665

    Genome annotation databases

    EnsemblPlantsiOs09t0505700-02; Os09t0505700-02; Os09g0505700
    GeneIDi4347508
    GrameneiOs09t0505700-02; Os09t0505700-02; Os09g0505700
    KEGGiosa:4347508

    Similar proteinsi

    Entry informationi

    Entry nameiRPE1_ORYSJ
    AccessioniPrimary (citable) accession number: Q9SE42
    Secondary accession number(s): B7EGE3, Q0J0L5
    Entry historyiIntegrated into UniProtKB/Swiss-Prot: March 1, 2005
    Last sequence update: May 1, 2000
    Last modified: February 28, 2018
    This is version 95 of the entry and version 1 of the sequence. See complete history.
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome
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    Main funding by: National Institutes of Health