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Protein

NAD-dependent protein deacylase

Gene

cobB

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

Functioni

NAD-dependent lysine deacetylase and desuccinylase that specifically removes acetyl and succinyl groups on target proteins. Modulates the activities of several proteins which are inactive in their acylated form. Activates the enzyme acetyl-CoA synthetase by deacetylating 'Lys-609' in the inactive, acetylated form of the enzyme. May also modulate the activity of other propionyl-adenosine monophosphate (AMP)-forming enzymes.UniRule annotation3 Publications

Catalytic activityi

NAD+ + an acetylprotein = nicotinamide + O-acetyl-ADP-ribose + a protein.UniRule annotation
NAD+ + a succinylprotein = nicotinamide + O-succinyl-ADP-ribose + a protein.UniRule annotation

Cofactori

Zn2+UniRule annotation1 PublicationNote: Binds 1 zinc ion per subunit.UniRule annotation1 Publication

Kineticsi

kcat is 0.135 sec(-1) for acetyllysine peptide. kcat is 0.242 sec(-1) for succinyllysine peptide.

  1. KM=15.1 µM for a synthetic histone H3K9 acetyllysine peptide1 Publication
  2. KM=86 µM for a synthetic histone H3K9 succinyllysine peptide1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Binding sitei55 – 551SubstrateUniRule annotation
    Binding sitei58 – 581SubstrateUniRule annotation
    Active sitei110 – 1101Proton acceptorUniRule annotation
    Metal bindingi118 – 1181ZincUniRule annotation1 Publication
    Metal bindingi137 – 1371ZincUniRule annotation1 Publication
    Binding sitei221 – 2211NAD; via amide nitrogenUniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi11 – 3020NADUniRule annotationAdd
    BLAST
    Nucleotide bindingi92 – 954NADUniRule annotation
    Nucleotide bindingi177 – 1793NADUniRule annotation
    Nucleotide bindingi203 – 2053NADUniRule annotation

    GO - Molecular functioni

    GO - Biological processi

    • chemotaxis Source: EcoCyc
    • peptidyl-lysine deacetylation Source: EcoCyc
    • peptidyl-lysine desuccinylation Source: EcoCyc
    Complete GO annotation...

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, NAD, Zinc

    Enzyme and pathway databases

    BioCyciEcoCyc:G6577-MONOMER.
    ECOL316407:JW1106-MONOMER.
    MetaCyc:G6577-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NAD-dependent protein deacylaseUniRule annotation (EC:3.5.1.-UniRule annotation)
    Alternative name(s):
    Regulatory protein SIR2 homologUniRule annotation
    Gene namesi
    Name:cobBUniRule annotation
    Synonyms:ycfY
    Ordered Locus Names:b1120, JW1106
    OrganismiEscherichia coli (strain K12)
    Taxonomic identifieri83333 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeEscherichia
    Proteomesi
    • UP000000318 Componenti: Chromosome
    • UP000000625 Componenti: Chromosome

    Organism-specific databases

    EcoGeneiEG13443. cobB.

    Subcellular locationi

    • Cytoplasm UniRule annotation

    GO - Cellular componenti

    Complete GO annotation...

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi55 – 551Y → F: 42-fold decrease in desuccinylase activity. 3-fold decrease in deacetylase activity. 1 Publication
    Mutagenesisi58 – 581R → M: 100-fold decrease in desuccinylase activity. 3-fold decrease in deacetylase activity. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 242242NAD-dependent protein deacylasePRO_0000110312Add
    BLAST

    Proteomic databases

    PaxDbiP75960.

    Interactioni

    Subunit structurei

    Forms a 1:1 complex with acetyl-CoA synthetase (Acs).1 Publication

    Binary interactionsi

    WithEntry#Exp.IntActNotes
    sxyP758698EBI-544459,EBI-544452

    Protein-protein interaction databases

    BioGridi4260089. 13 interactions.
    DIPiDIP-9301N.
    IntActiP75960. 18 interactions.
    MINTiMINT-1290133.
    STRINGi511145.b1120.

    Structurei

    Secondary structure

    1
    242
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Beta strandi6 – 105Combined sources
    Helixi12 – 187Combined sources
    Beta strandi25 – 273Combined sources
    Helixi35 – 384Combined sources
    Helixi41 – 466Combined sources
    Helixi48 – 6215Combined sources
    Helixi71 – 8313Combined sources
    Helixi84 – 863Combined sources
    Beta strandi87 – 926Combined sources
    Helixi97 – 1015Combined sources
    Beta strandi111 – 1188Combined sources
    Turni119 – 1213Combined sources
    Beta strandi124 – 1263Combined sources
    Beta strandi146 – 1505Combined sources
    Helixi160 – 16910Combined sources
    Beta strandi171 – 1777Combined sources
    Helixi185 – 1873Combined sources
    Helixi188 – 1947Combined sources
    Beta strandi198 – 2069Combined sources
    Beta strandi214 – 2196Combined sources
    Helixi221 – 23515Combined sources

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1S5PX-ray1.96A3-237[»]
    ProteinModelPortaliP75960.
    SMRiP75960. Positions 3-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP75960.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini1 – 237237Deacetylase sirtuin-typeUniRule annotationAdd
    BLAST

    Domaini

    2 residues (Tyr-55 and Arg-58) present in a large hydrophobic pocket are probably involved in substrate specificity. They are important for desuccinylation activity, but dispensable for deacetylation activity.UniRule annotation1 Publication

    Sequence similaritiesi

    Belongs to the sirtuin family. Class III subfamily.UniRule annotation
    Contains 1 deacetylase sirtuin-type domain.UniRule annotation

    Phylogenomic databases

    eggNOGiENOG4105NDF. Bacteria.
    COG0846. LUCA.
    HOGENOMiHOG000085950.
    InParanoidiP75960.
    KOiK12410.
    PhylomeDBiP75960.

    Family and domain databases

    Gene3Di3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    HAMAPiMF_01121. Sirtuin_ClassIII.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR003000. Sirtuin.
    IPR026591. Sirtuin_cat_small_dom.
    IPR027546. Sirtuin_class_III.
    IPR026590. Ssirtuin_cat_dom.
    [Graphical view]
    PANTHERiPTHR11085. PTHR11085. 1 hit.
    PfamiPF02146. SIR2. 1 hit.
    [Graphical view]
    SUPFAMiSSF52467. SSF52467. 1 hit.
    PROSITEiPS50305. SIRTUIN. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P75960-1 [UniParc]FASTAAdd to basket

    « Hide

            10         20         30         40         50
    MEKPRVLVLT GAGISAESGI RTFRAADGLW EEHRVEDVAT PEGFDRDPEL
    60 70 80 90 100
    VQAFYNARRR QLQQPEIQPN AAHLALAKLQ DALGDRFLLV TQNIDNLHER
    110 120 130 140 150
    AGNTNVIHMH GELLKVRCSQ SGQVLDWTGD VTPEDKCHCC QFPAPLRPHV
    160 170 180 190 200
    VWFGEMPLGM DEIYMALSMA DIFIAIGTSG HVYPAAGFVH EAKLHGAHTV
    210 220 230 240
    ELNLEPSQVG NEFAEKYYGP ASQVVPEFVE KLLKGLKAGS IA
    Length:242
    Mass (Da):26,716
    Last modified:November 30, 2010 - v2
    Checksum:iD4EEEBF856898698
    GO

    Sequence cautioni

    The sequence BAA35940.1 differs from that shown. Reason: Erroneous initiation. Translation N-terminally shortened.Curated

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74204.2.
    AP009048 Genomic DNA. Translation: BAA35940.1. Different initiation.
    PIRiE64856.
    RefSeqiNP_415638.2. NC_000913.3.

    Genome annotation databases

    EnsemblBacteriaiAAC74204; AAC74204; b1120.
    BAA35940; BAA35940; BAA35940.
    GeneIDi945687.
    KEGGiecj:JW1106.
    eco:b1120.
    PATRICi32117487. VBIEscCol129921_1166.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74204.2.
    AP009048 Genomic DNA. Translation: BAA35940.1. Different initiation.
    PIRiE64856.
    RefSeqiNP_415638.2. NC_000913.3.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1S5PX-ray1.96A3-237[»]
    ProteinModelPortaliP75960.
    SMRiP75960. Positions 3-237.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

    BioGridi4260089. 13 interactions.
    DIPiDIP-9301N.
    IntActiP75960. 18 interactions.
    MINTiMINT-1290133.
    STRINGi511145.b1120.

    Proteomic databases

    PaxDbiP75960.

    Protocols and materials databases

    Structural Biology KnowledgebaseSearch...

    Genome annotation databases

    EnsemblBacteriaiAAC74204; AAC74204; b1120.
    BAA35940; BAA35940; BAA35940.
    GeneIDi945687.
    KEGGiecj:JW1106.
    eco:b1120.
    PATRICi32117487. VBIEscCol129921_1166.

    Organism-specific databases

    EchoBASEiEB3217.
    EcoGeneiEG13443. cobB.

    Phylogenomic databases

    eggNOGiENOG4105NDF. Bacteria.
    COG0846. LUCA.
    HOGENOMiHOG000085950.
    InParanoidiP75960.
    KOiK12410.
    PhylomeDBiP75960.

    Enzyme and pathway databases

    BioCyciEcoCyc:G6577-MONOMER.
    ECOL316407:JW1106-MONOMER.
    MetaCyc:G6577-MONOMER.

    Miscellaneous databases

    EvolutionaryTraceiP75960.
    PROiP75960.

    Family and domain databases

    Gene3Di3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    HAMAPiMF_01121. Sirtuin_ClassIII.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR003000. Sirtuin.
    IPR026591. Sirtuin_cat_small_dom.
    IPR027546. Sirtuin_class_III.
    IPR026590. Ssirtuin_cat_dom.
    [Graphical view]
    PANTHERiPTHR11085. PTHR11085. 1 hit.
    PfamiPF02146. SIR2. 1 hit.
    [Graphical view]
    SUPFAMiSSF52467. SSF52467. 1 hit.
    PROSITEiPS50305. SIRTUIN. 1 hit.
    [Graphical view]
    ProtoNetiSearch...

    Publicationsi

    « Hide 'large scale' publications
    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / W3110 / ATCC 27325 / DSM 5911.
    2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: K12 / MG1655 / ATCC 47076.
    3. "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.
    4. "Characterization of five human cDNAs with homology to the yeast SIR2 gene: Sir2-like proteins (sirtuins) metabolize NAD and may have protein ADP-ribosyltransferase activity."
      Frye R.A.
      Biochem. Biophys. Res. Commun. 260:273-279(1999) [PubMed] [Europe PMC] [Abstract]
      Cited for: WEAK ADP-RIBOSYLTRANSFERASE ACTIVITY.
      Strain: K12 / MG1655 / ATCC 47076.
    5. "The silencing protein SIR2 and its homologs are NAD-dependent protein deacetylases."
      Landry J., Sutton A., Tafrov S.T., Heller R.C., Stebbins J., Pillus L., Sternglanz R.
      Proc. Natl. Acad. Sci. U.S.A. 97:5807-5811(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION, CATALYTIC ACTIVITY.
      Strain: K12 / MG1655 / ATCC 47076.
    6. "Identification of lysine succinylation substrates and the succinylation regulatory enzyme CobB in E. coli."
      Colak G., Xie Z., Zhu A.Y., Dai L., Lu Z., Zhang Y., Wan X., Chen Y., Cha Y.H., Lin H., Zhao Y., Tan M.
      Mol. Cell. Proteomics 12:3509-3520(2013) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION AS A DEACETYLASE AND A DESUCCINYLASE, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, DOMAIN, MUTAGENESIS OF TYR-55 AND ARG-58.
    7. "Structure and substrate binding properties of cobB, a Sir2 homolog protein deacetylase from Escherichia coli."
      Zhao K., Chai X., Marmorstein R.
      J. Mol. Biol. 337:731-741(2004) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.96 ANGSTROMS) OF 3-237 IN COMPLEX WITH PEPTIDE SUBSTRATE AND ZINC, CATALYTIC ACTIVITY, FUNCTION, SUBSTRATE, INTERACTION WITH ACETYL-COA SYNTHETASE, COFACTOR.

    Entry informationi

    Entry nameiNPD_ECOLI
    AccessioniPrimary (citable) accession number: P75960
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 18, 2001
    Last sequence update: November 30, 2010
    Last modified: July 6, 2016
    This is version 136 of the entry and version 2 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Caution

    Was originally thought to be involved in cobalamin biosynthesis.Curated
    In contrast to human SIRT5, which has only weak deacetylation activity, CobB shows comparable lysine deacetylation and lysine desuccinylation activities.1 Publication
    PubMed:10381378 has reported that this protein has a weak ADP-ribosyltransferase activity, but that is probably not its primary activity in vivo.Curated

    Keywords - Technical termi

    3D-structure, Complete proteome, Reference proteome

    Documents

    1. Escherichia coli
      Escherichia coli (strain K12): entries and cross-references to EcoGene
    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.