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Protein

Ribose-5-phosphate isomerase A

Gene

rpiA

Organism
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the interconversion between the ribose 5-P and ribulose 5-P involved in the pentose phosphate cycle and in the process of photosynthesis.1 Publication

Catalytic activityi

D-ribose 5-phosphate = D-ribulose 5-phosphate.UniRule annotation1 Publication

Enzyme regulationi

Inhibited by D-4-phosphoerythronic acid.1 Publication

Kineticsi

  1. KM=1.17 mM for ribose 5-P1 Publication

    pH dependencei

    Optimum pH is 6 (at 50 degrees Celsius).1 Publication

    Temperature dependencei

    Optimum temperature is over 95 degrees Celsius.1 Publication

    Pathwayi: pentose phosphate pathway

    This protein is involved in step 1 of the subpathway that synthesizes D-ribose 5-phosphate from D-ribulose 5-phosphate (non-oxidative stage).UniRule annotation
    Proteins known to be involved in this subpathway in this organism are:
    1. Ribose-5-phosphate isomerase A (rpiA)
    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-ribose 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
    Sitei85 – 851Plays a direct or indirect catalytic role
    Active sitei107 – 1071Proton acceptor1 Publication
    Binding sitei125 – 1251Substrate

    GO - Molecular functioni

    • ribose-5-phosphate isomerase activity Source: UniProtKB

    GO - Biological processi

    • pentose-phosphate shunt, non-oxidative branch Source: UniProtKB
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Enzyme and pathway databases

    BioCyciPHOR70601:GJWR-1382-MONOMER.
    BRENDAi5.3.1.6. 5244.
    UniPathwayiUPA00115; UER00412.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribose-5-phosphate isomerase AUniRule annotation (EC:5.3.1.6UniRule annotation)
    Alternative name(s):
    Phosphoriboisomerase AUniRule annotation
    Short name:
    PRIUniRule annotation
    Gene namesi
    Name:rpiAUniRule annotation
    Ordered Locus Names:PH1375
    OrganismiPyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
    Taxonomic identifieri70601 [NCBI]
    Taxonomic lineageiArchaeaEuryarchaeotaThermococciThermococcalesThermococcaceaePyrococcus
    Proteomesi
    • UP000000752 Componenti: Chromosome

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi85 – 851D → N: Strong decrease in the catalytic efficiency and increase in the binding affinity. 1 Publication
    Mutagenesisi100 – 1001R → A: 2-fold decrease in the catalytic efficiency and strong decrease in the binding affinity. 1 Publication
    Mutagenesisi107 – 1071E → Q: Loss of activity. 1 Publication
    Mutagenesisi125 – 1251K → A: 2-fold decrease in the catalytic efficiency and strong decrease in the binding affinity. 1 Publication
    Mutagenesisi168 – 1681D → N: Almost the same catalytic efficiency and binding affinity than wild-type. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 229229Ribose-5-phosphate isomerase APRO_0000158517Add
    BLAST

    Interactioni

    Subunit structurei

    Homotetramer.1 Publication

    Protein-protein interaction databases

    IntActiO50083. 1 interaction.
    MINTiMINT-1502514.
    STRINGi70601.PH1375.

    Structurei

    Secondary structure

    1
    229
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1412Combined sources
    Helixi15 – 173Combined sources
    Beta strandi23 – 264Combined sources
    Helixi30 – 4415Combined sources
    Beta strandi52 – 576Combined sources
    Helixi58 – 669Combined sources
    Helixi74 – 763Combined sources
    Beta strandi80 – 856Combined sources
    Beta strandi88 – 903Combined sources
    Helixi104 – 1129Combined sources
    Beta strandi114 – 1229Combined sources
    Helixi123 – 1253Combined sources
    Beta strandi136 – 1405Combined sources
    Helixi142 – 1443Combined sources
    Helixi145 – 1517Combined sources
    Helixi152 – 1554Combined sources
    Beta strandi158 – 1614Combined sources
    Beta strandi165 – 1706Combined sources
    Beta strandi178 – 1836Combined sources
    Helixi190 – 1989Combined sources
    Beta strandi203 – 2097Combined sources
    Beta strandi215 – 2206Combined sources
    Beta strandi223 – 2286Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1LK5X-ray1.75A/B/C/D1-229[»]
    1LK7X-ray2.00A/B/C/D1-229[»]
    ProteinModelPortaliO50083.
    SMRiO50083. Positions 1-229.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiO50083.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni28 – 314Substrate binding
    Regioni85 – 884Substrate binding
    Regioni98 – 1014Substrate binding

    Sequence similaritiesi

    Belongs to the ribose 5-phosphate isomerase family.UniRule annotation

    Phylogenomic databases

    eggNOGiarCOG01122. Archaea.
    COG0120. LUCA.
    HOGENOMiHOG000276369.
    KOiK01807.
    OMAiGACHVQE.

    Family and domain databases

    HAMAPiMF_00170. Rib_5P_isom_A.
    InterProiIPR004788. Ribose5P_isomerase_typA.
    IPR020672. Ribose5P_isomerase_typA_subgr.
    [Graphical view]
    PANTHERiPTHR11934. PTHR11934. 1 hit.
    PfamiPF06026. Rib_5-P_isom_A. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00021. rpiA. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    O50083-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MNVEEMKKIA AKEALKFIED DMVIGLGTGS TTAYFIKLLG EKLKRGEISD
    60 70 80 90 100
    IVGVPTSYQA KLLAIEHDIP IASLDQVDAI DVAVDGADEV DPNLNLIKGR
    110 120 130 140 150
    GAALTMEKII EYRAGTFIVL VDERKLVDYL CQKMPVPIEV IPQAWKAIIE
    160 170 180 190 200
    ELSIFNAKAE LRMGVNKDGP VITDNGNFII DAKFPRIDDP LDMEIELNTI
    210 220
    PGVIENGIFA DIADIVIVGT REGVKKLER
    Length:229
    Mass (Da):25,162
    Last modified:June 1, 1998 - v1
    Checksum:i0E35BCB9F608D93C
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000001 Genomic DNA. Translation: BAA30481.1.
    PIRiA71010.
    RefSeqiWP_010885464.1. NC_000961.1.

    Genome annotation databases

    EnsemblBacteriaiBAA30481; BAA30481; BAA30481.
    GeneIDi1443702.
    KEGGipho:PH1375.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    BA000001 Genomic DNA. Translation: BAA30481.1.
    PIRiA71010.
    RefSeqiWP_010885464.1. NC_000961.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1LK5X-ray1.75A/B/C/D1-229[»]
    1LK7X-ray2.00A/B/C/D1-229[»]
    ProteinModelPortaliO50083.
    SMRiO50083. Positions 1-229.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    IntActiO50083. 1 interaction.
    MINTiMINT-1502514.
    STRINGi70601.PH1375.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiBAA30481; BAA30481; BAA30481.
    GeneIDi1443702.
    KEGGipho:PH1375.

    Phylogenomic databases

    eggNOGiarCOG01122. Archaea.
    COG0120. LUCA.
    HOGENOMiHOG000276369.
    KOiK01807.
    OMAiGACHVQE.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00412.
    BioCyciPHOR70601:GJWR-1382-MONOMER.
    BRENDAi5.3.1.6. 5244.

    Miscellaneous databases

    EvolutionaryTraceiO50083.

    Family and domain databases

    HAMAPiMF_00170. Rib_5P_isom_A.
    InterProiIPR004788. Ribose5P_isomerase_typA.
    IPR020672. Ribose5P_isomerase_typA_subgr.
    [Graphical view]
    PANTHERiPTHR11934. PTHR11934. 1 hit.
    PfamiPF06026. Rib_5-P_isom_A. 1 hit.
    [Graphical view]
    TIGRFAMsiTIGR00021. rpiA. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3.
    2. "A hyperthermostable D-ribose-5-phosphate isomerase from Pyrococcus horikoshii characterization and three-dimensional structure."
      Ishikawa K., Matsui I., Payan F., Cambillau C., Ishida H., Kawarabayasi Y., Kikuchi H., Roussel A.
      Structure 10:877-886(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.75 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-85; ARG-100; GLU-107; LYS-125 AND ASP-168, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, SUBUNIT.

    Entry informationi

    Entry nameiRPIA_PYRHO
    AccessioniPrimary (citable) accession number: O50083
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: May 30, 2000
    Last sequence update: June 1, 1998
    Last modified: December 9, 2015
    This is version 107 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome

    Documents

    1. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    2. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    3. 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.