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Protein

Ribose-5-phosphate isomerase B

Gene

rpiB

Organism
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Has isomerase activity towards D-ribose 5-phosphate, but not towards D-allose 6-phosphate.1 Publication

Catalytic activityi

D-ribose 5-phosphate = D-ribulose 5-phosphate.1 Publication

Kineticsi

  1. KM=1.0 mM for D-ribose 5-phosphate1 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).
    Proteins known to be involved in this subpathway in this organism are:
    1. Ribose-5-phosphate isomerase B (rpiB)
    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 sitei12 – 121Substrate
    Active sitei75 – 751Proton acceptorSequence analysis
    Active sitei102 – 1021Proton donorCurated
    Binding sitei113 – 1131Substrate
    Binding sitei137 – 1371Substrate
    Binding sitei141 – 1411Substrate

    GO - Molecular functioni

    • ribose-5-phosphate isomerase activity Source: MTBBASE

    GO - Biological processi

    Complete GO annotation...

    Keywords - Molecular functioni

    Isomerase

    Keywords - Biological processi

    Carbohydrate metabolism

    Enzyme and pathway databases

    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
    Ordered Locus Names:Rv2465c
    ORF Names:MTV008.21c
    OrganismiMycobacterium tuberculosis (strain ATCC 25618 / H37Rv)
    Taxonomic identifieri83332 [NCBI]
    Taxonomic lineageiBacteriaActinobacteriaCorynebacterialesMycobacteriaceaeMycobacteriumMycobacterium tuberculosis complex
    Proteomesi
    • UP000001584 Componenti: Chromosome

    Organism-specific databases

    TubercuListiRv2465c.

    Subcellular locationi

    GO - Cellular componenti

    • extracellular region Source: MTBBASE
    Complete GO annotation...

    Pathology & Biotechi

    Chemistry

    ChEMBLiCHEMBL1770044.

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 162162Ribose-5-phosphate isomerase BPRO_0000251148Add
    BLAST

    Proteomic databases

    PaxDbiP9WKD7.

    Interactioni

    Subunit structurei

    Homodimer.2 Publications

    Protein-protein interaction databases

    STRINGi83332.Rv2465c.

    Chemistry

    BindingDBiP9WKD7.

    Structurei

    Secondary structure

    1
    162
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi5 – 106Combined sources
    Helixi12 – 2716Combined sources
    Beta strandi31 – 344Combined sources
    Helixi47 – 5913Combined sources
    Beta strandi64 – 729Combined sources
    Helixi73 – 808Combined sources
    Beta strandi87 – 893Combined sources
    Helixi93 – 1019Combined sources
    Beta strandi106 – 1116Combined sources
    Helixi112 – 1143Combined sources
    Helixi117 – 12913Combined sources
    Helixi136 – 15116Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1USLX-ray1.88A/B/C/D/E1-162[»]
    2BESX-ray2.10A/B/C/D/E1-162[»]
    2BETX-ray2.20A/B/C/D/E1-162[»]
    2VVOX-ray1.85A/B/C/D/E1-162[»]
    2VVPX-ray1.65A/B/C/D/E1-162[»]
    2VVQX-ray2.00A/B/C/D/E1-162[»]
    ProteinModelPortaliP9WKD7.
    SMRiP9WKD7. Positions 3-160.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni70 – 756Substrate binding

    Sequence similaritiesi

    Belongs to the LacAB/RpiB family.Curated

    Phylogenomic databases

    eggNOGiENOG4108YZG. Bacteria.
    COG0698. LUCA.
    KOiK01808.
    OMAiDYPDFVH.
    PhylomeDBiP9WKD7.

    Family and domain databases

    Gene3Di3.40.1400.10. 1 hit.
    InterProiIPR011860. Rib-5-P_Isoase.
    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.
    TIGRFAMsiTIGR02133. RPI_actino. 1 hit.
    TIGR00689. rpiB_lacA_lacB. 1 hit.

    Sequencei

    Sequence statusi: Complete.

    P9WKD7-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MSGMRVYLGA DHAGYELKQR IIEHLKQTGH EPIDCGALRY DADDDYPAFC
    60 70 80 90 100
    IAAATRTVAD PGSLGIVLGG SGNGEQIAAN KVPGARCALA WSVQTAALAR
    110 120 130 140 150
    EHNNAQLIGI GGRMHTVAEA LAIVDAFVTT PWSKAQRHQR RIDILAEYER
    160
    THEAPPVPGA PA
    Length:162
    Mass (Da):17,278
    Last modified:April 16, 2014 - v1
    Checksum:i31EF834F28783E00
    GO

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL123456 Genomic DNA. Translation: CCP45258.1.
    RefSeqiWP_003899332.1. NC_000962.3.
    YP_177884.1. NC_000962.3.

    Genome annotation databases

    EnsemblBacteriaiCCP45258; CCP45258; Rv2465c.
    GeneIDi887225.
    KEGGimtu:Rv2465c.
    mtv:RVBD_2465c.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    AL123456 Genomic DNA. Translation: CCP45258.1.
    RefSeqiWP_003899332.1. NC_000962.3.
    YP_177884.1. NC_000962.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1USLX-ray1.88A/B/C/D/E1-162[»]
    2BESX-ray2.10A/B/C/D/E1-162[»]
    2BETX-ray2.20A/B/C/D/E1-162[»]
    2VVOX-ray1.85A/B/C/D/E1-162[»]
    2VVPX-ray1.65A/B/C/D/E1-162[»]
    2VVQX-ray2.00A/B/C/D/E1-162[»]
    ProteinModelPortaliP9WKD7.
    SMRiP9WKD7. Positions 3-160.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    STRINGi83332.Rv2465c.

    Chemistry

    BindingDBiP9WKD7.
    ChEMBLiCHEMBL1770044.

    Proteomic databases

    PaxDbiP9WKD7.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiCCP45258; CCP45258; Rv2465c.
    GeneIDi887225.
    KEGGimtu:Rv2465c.
    mtv:RVBD_2465c.

    Organism-specific databases

    TubercuListiRv2465c.

    Phylogenomic databases

    eggNOGiENOG4108YZG. Bacteria.
    COG0698. LUCA.
    KOiK01808.
    OMAiDYPDFVH.
    PhylomeDBiP9WKD7.

    Enzyme and pathway databases

    UniPathwayiUPA00115; UER00412.

    Family and domain databases

    Gene3Di3.40.1400.10. 1 hit.
    InterProiIPR011860. Rib-5-P_Isoase.
    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.
    TIGRFAMsiTIGR02133. RPI_actino. 1 hit.
    TIGR00689. rpiB_lacA_lacB. 1 hit.
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 25618 / H37Rv.
    2. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
      Strain: ATCC 25618 / H37Rv.
    3. "Competitive inhibitors of Mycobacterium tuberculosis ribose-5-phosphate isomerase B reveal new information about the reaction mechanism."
      Roos A.K., Burgos E., Ericsson D.J., Salmon L., Mowbray S.L.
      J. Biol. Chem. 280:6416-6422(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS) IN COMPLEX WITH SUBSTRATE ANALOGS.
    4. "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 (1.65 ANGSTROMS) IN COMPLEX WITH RIBULOSE-5-PHOSPHATE AND SUBSTRATE ANALOGS, FUNCTION, SUBUNIT, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES.

    Entry informationi

    Entry nameiRPIB_MYCTU
    AccessioniPrimary (citable) accession number: P9WKD7
    Secondary accession number(s): L0TCF4, Q79FD7, Q7D737
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: April 16, 2014
    Last sequence update: April 16, 2014
    Last modified: December 9, 2015
    This is version 18 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, Reference proteome

    Documents

    1. Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh
      Mycobacterium tuberculosis strains ATCC 25618 / H37Rv and CDC 1551 / Oshkosh: entries and gene names
    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.