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Protein

Ribulose-phosphate 3-epimerase, cytoplasmic isoform

Gene

Os09g0505700

Organism
Oryza sativa subsp. japonica (Rice)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-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

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism, Pentose shunt

    Keywords - Ligandi

    Cobalt, 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 cladeOryzoideaeOryzeaeOryzinaeOryza
    Proteomesi
    • UP000059680 Componenti: Chromosome 9

    Subcellular locationi

    • Cytoplasm 1 Publication

    GO - Cellular componenti

    Complete GO annotation...

    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.
    OMAiKTIDVCA.
    OrthoDBiEOG09360LI4.

    Family and domain databases

    CDDicd00429. RPE. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR026019. Ribul_P_3_epim.
    IPR000056. Ribul_P_3_epim-like.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PANTHERiPTHR11749. PTHR11749. 1 hit.
    PfamiPF00834. Ribul_P_3_epim. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001461. RPE. 1 hit.
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR01163. rpe. 1 hit.
    PROSITEiPS01085. RIBUL_P_3_EPIMER_1. 1 hit.
    PS01086. RIBUL_P_3_EPIMER_2. 1 hit.
    [Graphical view]

    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.

    Cross-referencesi

    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.

    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...

    Protein-protein interaction databases

    STRINGi39947.LOC_Os09g32810.1.

    Proteomic databases

    PaxDbiQ9SE42.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblPlantsiOS09T0505700-02; OS09T0505700-02; OS09G0505700.
    GeneIDi4347508.
    GrameneiOS09T0505700-02; OS09T0505700-02; OS09G0505700.
    KEGGiosa:4347508.

    Phylogenomic databases

    eggNOGiKOG3111. Eukaryota.
    COG0036. LUCA.
    HOGENOMiHOG000259349.
    InParanoidiQ9SE42.
    KOiK01783.
    OMAiKTIDVCA.
    OrthoDBiEOG09360LI4.

    Enzyme and pathway databases

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

    Miscellaneous databases

    EvolutionaryTraceiQ9SE42.

    Gene expression databases

    ExpressionAtlasiQ9SE42. baseline and differential.
    GenevisibleiQ9SE42. OS.

    Family and domain databases

    CDDicd00429. RPE. 1 hit.
    Gene3Di3.20.20.70. 1 hit.
    InterProiIPR013785. Aldolase_TIM.
    IPR026019. Ribul_P_3_epim.
    IPR000056. Ribul_P_3_epim-like.
    IPR011060. RibuloseP-bd_barrel.
    [Graphical view]
    PANTHERiPTHR11749. PTHR11749. 1 hit.
    PfamiPF00834. Ribul_P_3_epim. 1 hit.
    [Graphical view]
    PIRSFiPIRSF001461. RPE. 1 hit.
    SUPFAMiSSF51366. SSF51366. 1 hit.
    TIGRFAMsiTIGR01163. rpe. 1 hit.
    PROSITEiPS01085. RIBUL_P_3_EPIMER_1. 1 hit.
    PS01086. RIBUL_P_3_EPIMER_2. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Entry informationi

    Entry nameiRPE1_ORYSJ
    AccessioniPrimary (citable) accession number: Q9SE42
    Secondary accession number(s): B7EGE3, Q0J0L5
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: March 1, 2005
    Last sequence update: May 1, 2000
    Last modified: November 2, 2016
    This is version 92 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programPlant Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. Oryza sativa (rice)
      Index of Oryza sativa entries and their corresponding gene designations
    4. SIMILARITY comments
      Index of protein domains and families

    Similar proteinsi

    Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
    100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
    90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
    50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.