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Protein

Ribose-5-phosphate isomerase B

Gene

rpiB

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

Functioni

In addition to its activity on D-ribose 5-phosphate it probably also has activity on D-allose 6-phosphate.4 Publications

Catalytic activityi

D-ribose 5-phosphate = D-ribulose 5-phosphate.
D-allose 6-phosphate = D-allulose 6-phosphate.

Enzyme regulationi

Inhibited by iodoacetate and glucose 6-phosphate.2 Publications

Kineticsi

  1. KM=0.83 mM for D-ribose 5-phosphate (at 37 degrees Celsius)(PubMed: 1104357)3 Publications
  2. KM=1.23 mM for D-ribose 5-phosphate (PubMed: 18640127)3 Publications
  3. KM=0.5 mM for D-allose 6-phosphate (PubMed: 18640127)3 Publications

    Temperature dependencei

    After incubation at 45 degrees Celsius for 30 minutes RpiB retains 65% of its original activities. At 60 degrees Celsius RpiB is rapidly inactivated.3 Publications

    Pathway: 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).
    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), 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
    Binding sitei10 – 101Substrate
    Binding sitei17 – 171Substrate
    Active sitei66 – 661Proton acceptor1 Publication
    Active sitei99 – 991Proton donor1 Publication
    Binding sitei110 – 1101Substrate
    Binding sitei133 – 1331Substrate
    Binding sitei137 – 1371Substrate

    GO - Molecular functioni

    • allose 6-phosphate isomerase activity Source: EcoCyc
    • ribose-5-phosphate isomerase activity Source: EcoCyc

    GO - Biological processi

    • D-allose catabolic process Source: EcoCyc
    • pentose-phosphate shunt Source: UniProtKB-UniPathway
    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism

    Enzyme and pathway databases

    BioCyciEcoCyc:RIB5PISOMB-MONOMER.
    ECOL316407:JW4051-MONOMER.
    MetaCyc:RIB5PISOMB-MONOMER.
    SABIO-RKP37351.
    UniPathwayiUPA00115; UER00412.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    Ribose-5-phosphate isomerase B (EC:5.3.1.6)
    Alternative name(s):
    Phosphoriboisomerase B
    Gene namesi
    Name:rpiB
    Synonyms:yjcA
    Ordered Locus Names:b4090, JW4051
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    ProteomesiUP000000318 Componenti: Chromosome UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG11827. rpiB.

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi99 – 991H → N: Strongly reduced enzyme activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 149149Ribose-5-phosphate isomerase BPRO_0000208163Add
    BLAST

    Proteomic databases

    PaxDbiP37351.
    PRIDEiP37351.

    Expressioni

    Inductioni

    Induced by ribose and repressed by RpiR.2 Publications

    Interactioni

    Subunit structurei

    Homodimer, and homotetramer.1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    rplJP0A7J31EBI-557460,EBI-546827

    Protein-protein interaction databases

    DIPiDIP-10740N.
    IntActiP37351. 3 interactions.
    MINTiMINT-1235144.
    STRINGi511145.b4090.

    Structurei

    Secondary structure

    1
    149
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi3 – 86Combined sources
    Helixi12 – 154Combined sources
    Helixi16 – 2510Combined sources
    Beta strandi29 – 324Combined sources
    Beta strandi37 – 393Combined sources
    Helixi43 – 5513Combined sources
    Beta strandi58 – 6912Combined sources
    Helixi70 – 778Combined sources
    Beta strandi84 – 863Combined sources
    Helixi90 – 10011Combined sources
    Beta strandi104 – 1085Combined sources
    Turni109 – 1113Combined sources
    Helixi114 – 12613Combined sources
    Helixi134 – 14512Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NN4X-ray2.20A/B/C/D1-149[»]
    2VVRX-ray2.10A/B/C/D/E/F1-149[»]
    ProteinModelPortaliP37351.
    SMRiP37351. Positions 1-147.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP37351.

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni67 – 726Substrate bindingBy similarity

    Sequence similaritiesi

    Belongs to the LacAB/RpiB family.Curated

    Phylogenomic databases

    eggNOGiCOG0698.
    HOGENOMiHOG000226301.
    InParanoidiP37351.
    KOiK01808.
    OMAiMAKEHNN.
    OrthoDBiEOG679TJ4.
    PhylomeDBiP37351.

    Family and domain databases

    Gene3Di3.40.1400.10. 1 hit.
    InterProiIPR004785. RpiB.
    IPR003500. RpiB_LacA_LacB.
    [Graphical view]
    PANTHERiPTHR30345. PTHR30345. 1 hit.
    PfamiPF02502. LacAB_rpiB. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005384. RpiB_LacA_B. 1 hit.
    SUPFAMiSSF89623. SSF89623. 1 hit.
    TIGRFAMsiTIGR01120. rpiB. 1 hit.
    TIGR00689. rpiB_lacA_lacB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P37351-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MKKIAFGCDH VGFILKHEIV AHLVERGVEV IDKGTWSSER TDYPHYASQV
    60 70 80 90 100
    ALAVAGGEVD GGILICGTGV GISIAANKFA GIRAVVCSEP YSAQLSRQHN
    110 120 130 140
    DTNVLAFGSR VVGLELAKMI VDAWLGAQYE GGRHQQRVEA ITAIEQRRN
    Length:149
    Mass (Da):16,073
    Last modified:February 1, 1995 - v2
    Checksum:iBE610B5F995CEEB6
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X82203 Genomic DNA. Translation: CAA57688.1.
    U14003 Genomic DNA. Translation: AAA96989.1.
    U00096 Genomic DNA. Translation: AAC77051.1.
    AP009048 Genomic DNA. Translation: BAE78093.1.
    D90227 Genomic DNA. Translation: BAA21501.1.
    PIRiJC6054.
    RefSeqiNP_418514.1. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC77051; AAC77051; b4090.
    BAE78093; BAE78093; BAE78093.
    GeneIDi948602.
    KEGGiecj:Y75_p3978.
    eco:b4090.
    PATRICi32123739. VBIEscCol129921_4218.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    X82203 Genomic DNA. Translation: CAA57688.1.
    U14003 Genomic DNA. Translation: AAA96989.1.
    U00096 Genomic DNA. Translation: AAC77051.1.
    AP009048 Genomic DNA. Translation: BAE78093.1.
    D90227 Genomic DNA. Translation: BAA21501.1.
    PIRiJC6054.
    RefSeqiNP_418514.1. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1NN4X-ray2.20A/B/C/D1-149[»]
    2VVRX-ray2.10A/B/C/D/E/F1-149[»]
    ProteinModelPortaliP37351.
    SMRiP37351. Positions 1-147.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    DIPiDIP-10740N.
    IntActiP37351. 3 interactions.
    MINTiMINT-1235144.
    STRINGi511145.b4090.

    Proteomic databases

    PaxDbiP37351.
    PRIDEiP37351.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC77051; AAC77051; b4090.
    BAE78093; BAE78093; BAE78093.
    GeneIDi948602.
    KEGGiecj:Y75_p3978.
    eco:b4090.
    PATRICi32123739. VBIEscCol129921_4218.

    Organism-specific databases

    EchoBASEiEB1774.
    EcoGeneiEG11827. rpiB.

    Phylogenomic databases

    eggNOGiCOG0698.
    HOGENOMiHOG000226301.
    InParanoidiP37351.
    KOiK01808.
    OMAiMAKEHNN.
    OrthoDBiEOG679TJ4.
    PhylomeDBiP37351.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00412.
    BioCyciEcoCyc:RIB5PISOMB-MONOMER.
    ECOL316407:JW4051-MONOMER.
    MetaCyc:RIB5PISOMB-MONOMER.
    SABIO-RKP37351.

    Miscellaneous databases

    EvolutionaryTraceiP37351.
    PROiP37351.

    Family and domain databases

    Gene3Di3.40.1400.10. 1 hit.
    InterProiIPR004785. RpiB.
    IPR003500. RpiB_LacA_LacB.
    [Graphical view]
    PANTHERiPTHR30345. PTHR30345. 1 hit.
    PfamiPF02502. LacAB_rpiB. 1 hit.
    [Graphical view]
    PIRSFiPIRSF005384. RpiB_LacA_B. 1 hit.
    SUPFAMiSSF89623. SSF89623. 1 hit.
    TIGRFAMsiTIGR01120. rpiB. 1 hit.
    TIGR00689. rpiB_lacA_lacB. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. "Ribose catabolism of Escherichia coli: characterization of the rpiB gene encoding ribose phosphate isomerase B and of the rpiR gene, which is involved in regulation of rpiB expression."
      Soerensen K.I., Hove-Jensen B.
      J. Bacteriol. 178:1003-1011(1996) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, INDUCTION.
      Strain: K12.
    2. "Analysis of the Escherichia coli genome VI: DNA sequence of the region from 92.8 through 100 minutes."
      Burland V.D., Plunkett G. III, Sofia H.J., Daniels D.L., Blattner F.R.
      Nucleic Acids Res. 23:2105-2119(1995) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    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. "Molecular analysis of the cryptic and functional phn operons for phosphonate use in Escherichia coli K-12."
      Makino K., Kim S.K., Shinagawa H., Amemura M., Nakata A.
      J. Bacteriol. 173:2665-2672(1991) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 82-149.
      Strain: K12.
    6. "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, ENZYME REGULATION.
    7. "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, ENZYME REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, INDUCTION.
    8. "Intrinsic and extrinsic approaches for detecting genes in a bacterial genome."
      Borodovsky M., Rudd K.E., Koonin E.V.
      Nucleic Acids Res. 22:4756-4767(1994) [PubMed] [Europe PMC] [Abstract]
      Cited for: IDENTIFICATION.
    9. "The D-allose operon of Escherichia coli K-12."
      Kim C., Song S., Park C.
      J. Bacteriol. 179:7631-7637(1997) [PubMed] [Europe PMC] [Abstract]
      Cited for: PROBABLE ADDITIONAL FUNCTION.
    10. "The 2.2 A resolution structure of RpiB/AlsB from Escherichia coli illustrates a new approach to the ribose-5-phosphate isomerase reaction."
      Zhang R.G., Andersson C.E., Skarina T., Evdokimova E., Edwards A.M., Joachimiak A., Savchenko A., Mowbray S.L.
      J. Mol. Biol. 332:1083-1094(2003) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.20 ANGSTROMS), CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT.
    11. "D-ribose-5-phosphate isomerase B from Escherichia coli is also a functional D-allose-6-phosphate isomerase, while the Mycobacterium tuberculosis enzyme is not."
      Roos A.K., Mariano S., Kowalinski E., Salmon L., Mowbray S.L.
      J. Mol. Biol. 382:667-679(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, MUTAGENESIS OF HIS-99, ACTIVE SITE.

    Entry informationi

    Entry nameiRPIB_ECOLI
    AccessioniPrimary (citable) accession number: P37351
    Secondary accession number(s): O32564, Q2M6L3
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 1, 1994
    Last sequence update: February 1, 1995
    Last modified: June 24, 2015
    This is version 128 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    3D-structure, Complete proteome, 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

    External Data

    Dasty 3

    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 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.