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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)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei12 – 121SubstrateBy similarity
    Metal bindingi37 – 371Divalent metal cation
    Active sitei39 – 391Proton acceptorBy similarity
    Metal bindingi39 – 391Divalent metal cation
    Metal bindingi70 – 701Divalent metal cation
    Binding sitei70 – 701SubstrateBy similarity
    Active sitei179 – 1791Proton donorBy similarity
    Metal bindingi179 – 1791Divalent metal cation
    Binding sitei181 – 1811Substrate; via amide nitrogenBy similarity

    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)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 228228Ribulose-phosphate 3-epimerase, cytoplasmic isoformPRO_0000171590Add
    BLAST

    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

    1
    228
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi8 – 125Combined sources
    Helixi13 – 153Combined sources
    Helixi18 – 203Combined sources
    Helixi21 – 3010Combined sources
    Beta strandi34 – 4714Combined sources
    Helixi53 – 608Combined sources
    Beta strandi65 – 7410Combined sources
    Helixi76 – 794Combined sources
    Helixi80 – 867Combined sources
    Beta strandi89 – 946Combined sources
    Helixi95 – 973Combined sources
    Turni99 – 1013Combined sources
    Helixi102 – 11110Combined sources
    Beta strandi115 – 1206Combined sources
    Helixi126 – 1294Combined sources
    Helixi130 – 1345Combined sources
    Beta strandi135 – 1373Combined sources
    Beta strandi140 – 1478Combined sources
    Beta strandi149 – 1513Combined sources
    Helixi158 – 1603Combined sources
    Helixi161 – 17010Combined sources
    Beta strandi174 – 1818Combined sources
    Turni184 – 1863Combined sources
    Helixi187 – 1937Combined sources
    Beta strandi197 – 2015Combined sources
    Helixi202 – 2054Combined sources
    Helixi210 – 22314Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1H1YX-ray1.87A/B1-228[»]
    1H1ZX-ray3.40A/B1-228[»]
    ProteinModelPortaliQ9SE42.
    SMRiQ9SE42. Positions 6-224.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9SE42.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni150 – 1534Substrate bindingBy similarity
    Regioni201 – 2022Substrate bindingBy similarity

    Sequence similaritiesi

    Phylogenomic databases

    eggNOGiKOG3111. Eukaryota.
    COG0036. LUCA.
    HOGENOMiHOG000259349.
    InParanoidiQ9SE42.
    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)LengthDescriptionGraphical viewFeature identifierActions
    Sequence conflicti42 – 432DG → GR (PubMed:16100779).Curated

    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.

    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
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1H1YX-ray1.87A/B1-228[»]
    1H1ZX-ray3.40A/B1-228[»]
    ProteinModelPortaliQ9SE42.
    SMRiQ9SE42. Positions 6-224.
    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.

    Phylogenomic databases

    eggNOGiKOG3111. Eukaryota.
    COG0036. LUCA.
    HOGENOMiHOG000259349.
    InParanoidiQ9SE42.
    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: September 7, 2016
    This is version 90 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.