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Protein

Ribose-5-phosphate isomerase A

Gene

rpiA

Organism
Escherichia coli (strain K12)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the first step of the non-oxidative branch of the pentose phosphate pathway. It catalyzes the reversible conversion of ribose-5-phosphate to ribulose 5-phosphate. Can also act on D-ribose-5-diphosphate and D-ribose-5-triphosphate as substrate.3 Publications

Catalytic activityi

D-ribose 5-phosphate = D-ribulose 5-phosphate.UniRule annotation2 Publications

Enzyme regulationi

Inhibited by arabinose-5-phosphate, D-erythrose-4-phosphate and D-erythronic acid.1 Publication

Kineticsi

Kcat is 2100 sec(-1) for ribose-5-phosphate.

  1. KM=3.1 mM for ribose-5-phosphate1 Publication
  2. KM=4.4 mM for D-ribose 5-phosphate (at 37 degrees Celsius)1 Publication

    Temperature dependencei

    After incubation at 45 degrees Celsius for 30 minutes RpiA retains 90% of its original activities.2 Publications

    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 B (rpiB), 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
    Active sitei103 – 1031Proton acceptorUniRule annotation1 Publication
    Binding sitei121 – 1211Substrate1 Publication

    GO - Molecular functioni

    • ribose-5-phosphate isomerase activity Source: EcoCyc

    GO - Biological processi

    • D-ribose metabolic process Source: EcoCyc
    • pentose-phosphate shunt, non-oxidative branch Source: UniProtKB-HAMAP
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Enzyme and pathway databases

    BioCyciEcoCyc:RIB5PISOMA-MONOMER.
    ECOL316407:JW5475-MONOMER.
    MetaCyc:RIB5PISOMA-MONOMER.
    BRENDAi5.3.1.6. 2026.
    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
    Synonyms:ygfC
    Ordered Locus Names:b2914, JW5475
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11443. rpiA.

    Subcellular locationi

    GO - Cellular componenti

    • cytosol Source: UniProtKB
    Complete GO annotation...

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi81 – 811D → A: Catalytic efficiency decreases by 10,000-fold, with no measurable effect on affinity binding. 1 Publication
    Mutagenesisi84 – 841D → A: Activity decreases by 250-fold, with little change on affinity binding. 1 Publication
    Mutagenesisi94 – 941K → A: Has a 1500-fold lower Catalytic efficiency than the wild-type, but affinity binding is increased by a factor of seven. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 219219Ribose-5-phosphate isomerase APRO_0000158412Add
    BLAST

    Proteomic databases

    EPDiP0A7Z0.
    PaxDbiP0A7Z0.
    PRIDEiP0A7Z0.

    2D gel databases

    SWISS-2DPAGEP0A7Z0.

    Expressioni

    Inductioni

    Constitutively expressed.3 Publications

    Interactioni

    Subunit structurei

    Homodimer.UniRule annotation1 Publication

    Protein-protein interaction databases

    BioGridi4259674. 21 interactions.
    DIPiDIP-10739N.
    STRINGi511145.b2914.

    Structurei

    Secondary structure

    1
    219
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi3 – 1311Combined sources
    Helixi14 – 163Combined sources
    Beta strandi24 – 263Combined sources
    Helixi32 – 409Combined sources
    Turni41 – 455Combined sources
    Beta strandi49 – 524Combined sources
    Helixi56 – 627Combined sources
    Helixi70 – 723Combined sources
    Beta strandi76 – 816Combined sources
    Beta strandi84 – 863Combined sources
    Beta strandi96 – 983Combined sources
    Helixi100 – 10910Combined sources
    Beta strandi110 – 1189Combined sources
    Helixi119 – 1213Combined sources
    Beta strandi124 – 1263Combined sources
    Beta strandi131 – 1355Combined sources
    Helixi137 – 1393Combined sources
    Helixi140 – 14910Combined sources
    Beta strandi153 – 1564Combined sources
    Beta strandi167 – 1737Combined sources
    Helixi179 – 1879Combined sources
    Beta strandi192 – 1987Combined sources
    Beta strandi204 – 2107Combined sources
    Beta strandi213 – 2175Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KS2X-ray1.50A/B1-219[»]
    1LKZX-ray2.50A/B1-219[»]
    1O8BX-ray1.25A/B1-219[»]
    ProteinModelPortaliP0A7Z0.
    SMRiP0A7Z0. Positions 2-219.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP0A7Z0.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni28 – 314Substrate binding1 Publication
    Regioni81 – 844Substrate binding1 Publication
    Regioni94 – 974Substrate binding1 Publication

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiENOG4105E66. Bacteria.
    COG0120. LUCA.
    HOGENOMiHOG000276368.
    InParanoidiP0A7Z0.
    KOiK01807.
    OMAiGACHVQE.
    OrthoDBiEOG67MF61.
    PhylomeDBiP0A7Z0.

    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.

    P0A7Z0-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MTQDELKKAV GWAALQYVQP GTIVGVGTGS TAAHFIDALG TMKGQIEGAV
    60 70 80 90 100
    SSSDASTEKL KSLGIHVFDL NEVDSLGIYV DGADEINGHM QMIKGGGAAL
    110 120 130 140 150
    TREKIIASVA EKFICIADAS KQVDILGKFP LPVEVIPMAR SAVARQLVKL
    160 170 180 190 200
    GGRPEYRQGV VTDNGNVILD VHGMEILDPI AMENAINAIP GVVTVGLFAN
    210
    RGADVALIGT PDGVKTIVK
    Length:219
    Mass (Da):22,860
    Last modified:June 7, 2005 - v1
    Checksum:iB53C49CC3DB188BC
    GO

    Sequence cautioni

    The sequence CAA47309.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73026 Genomic DNA. Translation: CAA51509.1.
    X66836 Genomic DNA. Translation: CAA47309.1. Different initiation.
    U28377 Genomic DNA. Translation: AAA69081.1.
    U00096 Genomic DNA. Translation: AAC75951.1.
    AP009048 Genomic DNA. Translation: BAE76978.1.
    M64630 Genomic DNA. Translation: AAA73015.1.
    PIRiA65076.
    RefSeqiNP_417389.1. NC_000913.3.
    WP_000189743.1. NZ_LN832404.1.

    Genome annotation databases

    EnsemblBacteriaiAAC75951; AAC75951; b2914.
    BAE76978; BAE76978; BAE76978.
    GeneIDi947407.
    KEGGiecj:JW5475.
    eco:b2914.
    PATRICi32121242. VBIEscCol129921_3009.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X73026 Genomic DNA. Translation: CAA51509.1.
    X66836 Genomic DNA. Translation: CAA47309.1. Different initiation.
    U28377 Genomic DNA. Translation: AAA69081.1.
    U00096 Genomic DNA. Translation: AAC75951.1.
    AP009048 Genomic DNA. Translation: BAE76978.1.
    M64630 Genomic DNA. Translation: AAA73015.1.
    PIRiA65076.
    RefSeqiNP_417389.1. NC_000913.3.
    WP_000189743.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1KS2X-ray1.50A/B1-219[»]
    1LKZX-ray2.50A/B1-219[»]
    1O8BX-ray1.25A/B1-219[»]
    ProteinModelPortaliP0A7Z0.
    SMRiP0A7Z0. Positions 2-219.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4259674. 21 interactions.
    DIPiDIP-10739N.
    STRINGi511145.b2914.

    2D gel databases

    SWISS-2DPAGEP0A7Z0.

    Proteomic databases

    EPDiP0A7Z0.
    PaxDbiP0A7Z0.
    PRIDEiP0A7Z0.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC75951; AAC75951; b2914.
    BAE76978; BAE76978; BAE76978.
    GeneIDi947407.
    KEGGiecj:JW5475.
    eco:b2914.
    PATRICi32121242. VBIEscCol129921_3009.

    Organism-specific databases

    EchoBASEiEB1413.
    EcoGeneiEG11443. rpiA.

    Phylogenomic databases

    eggNOGiENOG4105E66. Bacteria.
    COG0120. LUCA.
    HOGENOMiHOG000276368.
    InParanoidiP0A7Z0.
    KOiK01807.
    OMAiGACHVQE.
    OrthoDBiEOG67MF61.
    PhylomeDBiP0A7Z0.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00412.
    BioCyciEcoCyc:RIB5PISOMA-MONOMER.
    ECOL316407:JW5475-MONOMER.
    MetaCyc:RIB5PISOMA-MONOMER.
    BRENDAi5.3.1.6. 2026.

    Miscellaneous databases

    EvolutionaryTraceiP0A7Z0.
    PROiP0A7Z0.

    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. "Escherichia coli rpiA gene encoding ribose phosphate isomerase A."
      Hove-Jensen B., Maigaard M.
      J. Bacteriol. 175:5628-5635(1993) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], PROTEIN SEQUENCE OF 1-10.
      Strain: K12.
    2. Roy I., Leadlay P.F.
      Submitted (JUN-1992) to the EMBL/GenBank/DDBJ databases
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
      Strain: K12.
    3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    4. "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655 and W3110."
      Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S., Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.
      Mol. Syst. Biol. 2:E1-E5(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    5. "The tdh and serA operons of Escherichia coli: mutational analysis of the regulatory elements of leucine-responsive genes."
      Rex J.H., Aronson B.D., Somerville R.L.
      J. Bacteriol. 173:5944-5953(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 154-219.
      Strain: K12.
    6. "Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12."
      Link A.J., Robison K., Church G.M.
      Electrophoresis 18:1259-1313(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROTEIN SEQUENCE OF 1-12.
      Strain: K12 / EMG2.
    7. Cited for: PROTEIN SEQUENCE OF 1-4.
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    8. "Regulation of ribose metabolism in Escherichia coli. II. Evidence for two ribose-5-phosphate isomerase activities."
      David J., Wiesmeyer H.
      Biochim. Biophys. Acta 208:56-67(1970) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    9. "The regulation of ribose-5-phosphate isomerisation in Escherichia coli K12."
      Skinner A.J., Cooper R.A.
      FEBS Lett. 12:293-296(1971) [PubMed] [Europe PMC] [Abstract]
      Cited for: INDUCTION.
    10. "Two ribose-5-phosphate isomerases from Escherichia coli K12: partial characterisation of the enzymes and consideration of their possible physiological roles."
      Essenberg M.K., Cooper R.A.
      Eur. J. Biochem. 55:323-332(1975) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION.
    11. "Crystal structure of D-ribose-5-phosphate isomerase (RpiA) from Escherichia coli."
      Rangarajan E.S., Sivaraman J., Matte A., Cygler M.
      Proteins 48:737-740(2002) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.50 ANGSTROMS).
    12. "Structure of Escherichia coli ribose-5-phosphate isomerase: a ubiquitous enzyme of the pentose phosphate pathway and the Calvin cycle."
      Zhang R.G., Andersson C.E., Savchenko A., Skarina T., Evdokimova E., Beasley S., Arrowsmith C.H., Edwards A.M., Joachimiak A., Mowbray S.L.
      Structure 11:31-42(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.25 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS, FUNCTION, CATALYTIC ACTIVITY, MUTAGENESIS OF ASP-81; ASP-84 AND LYS-94, ACTIVE SITE, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME REGULATION, REACTION MECHANISM, SUBSTRATE SPECIFICITY, INDUCTION, SUBUNIT.

    Entry informationi

    Entry nameiRPIA_ECOLI
    AccessioniPrimary (citable) accession number: P0A7Z0
    Secondary accession number(s): P27252, Q2M9S8
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: June 7, 2005
    Last sequence update: June 7, 2005
    Last modified: April 13, 2016
    This is version 93 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, Direct protein sequencing, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    2. PATHWAY comments
      Index of metabolic and biosynthesis pathways
    3. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    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.