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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)DescriptionActionsGraphical viewLength
    Binding sitei92SubstrateUniRule annotation1 Publication1
    Binding sitei95SubstrateUniRule annotation1 Publication1
    Active sitei147Proton acceptorUniRule annotation1
    Metal bindingi155ZincUniRule annotation1 Publication1
    Metal bindingi174ZincUniRule annotation1 Publication1
    Binding sitei258NAD; via amide nitrogenUniRule annotation1

    Regions

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Nucleotide bindingi48 – 67NADUniRule annotationAdd BLAST20
    Nucleotide bindingi129 – 132NADUniRule annotation4
    Nucleotide bindingi214 – 216NADUniRule annotation3
    Nucleotide bindingi240 – 242NADUniRule annotation3

    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 lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacteralesEnterobacteriaceaeEscherichia
    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)DescriptionActionsGraphical viewLength
    Mutagenesisi92Y → F: 42-fold decrease in desuccinylase activity. 3-fold decrease in deacetylase activity. 1 Publication1
    Mutagenesisi95R → M: 100-fold decrease in desuccinylase activity. 3-fold decrease in deacetylase activity. 1 Publication1

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    ChainiPRO_00001103121 – 279NAD-dependent protein deacylaseAdd BLAST279

    Proteomic databases

    PaxDbiP75960.
    PRIDEiP75960.

    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 interactors.
    DIPiDIP-9301N.
    IntActiP75960. 18 interactors.
    MINTiMINT-1290133.
    STRINGi511145.b1120.

    Structurei

    Secondary structure

    1279
    Legend: HelixTurnBeta strandPDB Structure known for this area
    Show more details
    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Beta strandi43 – 47Combined sources5
    Helixi49 – 55Combined sources7
    Beta strandi62 – 64Combined sources3
    Helixi72 – 75Combined sources4
    Helixi78 – 83Combined sources6
    Helixi85 – 99Combined sources15
    Helixi108 – 120Combined sources13
    Helixi121 – 123Combined sources3
    Beta strandi124 – 129Combined sources6
    Helixi134 – 138Combined sources5
    Beta strandi148 – 155Combined sources8
    Turni156 – 158Combined sources3
    Beta strandi161 – 163Combined sources3
    Beta strandi183 – 187Combined sources5
    Helixi197 – 206Combined sources10
    Beta strandi208 – 214Combined sources7
    Helixi222 – 224Combined sources3
    Helixi225 – 231Combined sources7
    Beta strandi235 – 243Combined sources9
    Beta strandi251 – 256Combined sources6
    Helixi258 – 272Combined sources15

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1S5PX-ray1.96A40-274[»]
    ProteinModelPortaliP75960.
    SMRiP75960.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiP75960.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Domaini1 – 274Deacetylase sirtuin-typeUniRule annotationAdd BLAST274

    Domaini

    2 residues (Tyr-92 and Arg-95) 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

    CDDicd01412. SIRT5_Af1_CobB. 1 hit.
    Gene3Di3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    HAMAPiMF_01121. Sirtuin_ClassIII. 1 hit.
    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]

    Sequences (2)i

    Sequence statusi: Complete.

    This entry describes 2 isoformsi produced by alternative promoter usage. AlignAdd to basket

    Isoform CobB-LongBy similarity (identifier: P75960-1) [UniParc]FASTAAdd to basket

    This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

    « Hide

            10         20         30         40         50
    MLSRRGHRLS RFRKNKRRLR ERLRQRIFFR DKVVPEAMEK PRVLVLTGAG
    60 70 80 90 100
    ISAESGIRTF RAADGLWEEH RVEDVATPEG FDRDPELVQA FYNARRRQLQ
    110 120 130 140 150
    QPEIQPNAAH LALAKLQDAL GDRFLLVTQN IDNLHERAGN TNVIHMHGEL
    160 170 180 190 200
    LKVRCSQSGQ VLDWTGDVTP EDKCHCCQFP APLRPHVVWF GEMPLGMDEI
    210 220 230 240 250
    YMALSMADIF IAIGTSGHVY PAAGFVHEAK LHGAHTVELN LEPSQVGNEF
    260 270
    AEKYYGPASQ VVPEFVEKLL KGLKAGSIA
    Length:279
    Mass (Da):31,464
    Last modified:September 7, 2016 - v3
    Checksum:i779CF84961325CB9
    GO
    Isoform CobB-ShortBy similarity (identifier: P75960-2) [UniParc]FASTAAdd to basket

    The sequence of this isoform differs from the canonical sequence as follows:
         1-37: Missing.

    Show »
    Length:242
    Mass (Da):26,716
    Checksum:iD4EEEBF856898698
    GO

    Sequence cautioni

    The sequence AAC74204 differs from that shown. Reason: Erroneous initiation. Translation N-terminally extended.Curated

    Alternative sequence

    Feature keyPosition(s)DescriptionActionsGraphical viewLength
    Alternative sequenceiVSP_0584581 – 37Missing in isoform CobB-Short. By similarityAdd BLAST37

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74204.2. Different initiation.
    AP009048 Genomic DNA. Translation: BAA35940.1.
    PIRiE64856.
    RefSeqiNP_415638.2. NC_000913.3.
    WP_000952737.1. NZ_LN832404.1.

    Genome annotation databases

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

    Keywords - Coding sequence diversityi

    Alternative promoter usage

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBLi
    GenBanki
    DDBJi
    Links Updated
    U00096 Genomic DNA. Translation: AAC74204.2. Different initiation.
    AP009048 Genomic DNA. Translation: BAA35940.1.
    PIRiE64856.
    RefSeqiNP_415638.2. NC_000913.3.
    WP_000952737.1. NZ_LN832404.1.

    3D structure databases

    Select the link destinations:
    PDBei
    RCSB PDBi
    PDBji
    Links Updated
    PDB entryMethodResolution (Å)ChainPositionsPDBsum
    1S5PX-ray1.96A40-274[»]
    ProteinModelPortaliP75960.
    SMRiP75960.
    ModBaseiSearch...
    MobiDBiSearch...

    Protein-protein interaction databases

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

    Proteomic databases

    PaxDbiP75960.
    PRIDEiP75960.

    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

    CDDicd01412. SIRT5_Af1_CobB. 1 hit.
    Gene3Di3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    HAMAPiMF_01121. Sirtuin_ClassIII. 1 hit.
    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...

    Entry informationi

    Entry nameiNPD_ECOLI
    AccessioniPrimary (citable) accession number: P75960
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 18, 2001
    Last sequence update: September 7, 2016
    Last modified: November 30, 2016
    This is version 140 of the entry and version 3 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.