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Q9WYW0

- NPD_THEMA

UniProt

Q9WYW0 - NPD_THEMA

Protein

NAD-dependent protein deacetylase

Gene

cobB

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed - Annotation score: 5 out of 5- Experimental evidence at protein leveli
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    • History
      Entry version 95 (01 Oct 2014)
      Sequence version 1 (01 Nov 1999)
      Previous versions | rss
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    Functioni

    NAD-dependent protein deacetylase which modulates the activities of several enzymes which are inactive in their acetylated form. Has also depropionylation activity in vitro. Also able to ADP-ribosylate peptide substrates with Arg or Lys in the +2 position. The role of this function in vivo is not clear.3 PublicationsUniRule annotation

    Catalytic activityi

    NAD+ + an acetylprotein = nicotinamide + O-acetyl-ADP-ribose + a protein.1 PublicationUniRule annotation

    Cofactori

    Binds 1 zinc ion per subunit.3 PublicationsUniRule annotation

    Enzyme regulationi

    Non-competitively inhibited by nicotinamide but not by nicotinic acid.1 Publication

    Sites

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Active sitei116 – 1161Proton acceptorCurated
    Metal bindingi124 – 1241Zinc
    Metal bindingi127 – 1271Zinc
    Metal bindingi148 – 1481Zinc
    Metal bindingi151 – 1511Zinc

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Nucleotide bindingi21 – 4020NADAdd
    BLAST
    Nucleotide bindingi98 – 1014NAD
    Nucleotide bindingi188 – 1903NAD
    Nucleotide bindingi214 – 2163NAD
    Nucleotide bindingi231 – 2322NAD

    GO - Molecular functioni

    1. NAD+ binding Source: UniProtKB-HAMAP
    2. NAD-dependent protein deacetylase activity Source: UniProtKB-HAMAP
    3. zinc ion binding Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Hydrolase

    Keywords - Ligandi

    Metal-binding, NAD, Zinc

    Enzyme and pathway databases

    BioCyciTMAR243274:GC6P-514-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    NAD-dependent protein deacetylaseUniRule annotation (EC:3.5.1.-UniRule annotation)
    Alternative name(s):
    Regulatory protein SIR2 homologUniRule annotation
    Short name:
    Sir2Tm
    Gene namesi
    Name:cobBUniRule annotation
    Synonyms:sir2
    Ordered Locus Names:TM_0490
    OrganismiThermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
    Taxonomic identifieri243274 [NCBI]
    Taxonomic lineageiBacteriaThermotogaeThermotogalesThermotogaceaeThermotoga
    ProteomesiUP000008183: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    Pathology & Biotechi

    Mutagenesis

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Mutagenesisi33 – 331F → A: Reduces kcat for NAD(+), greatly increases sensitivity to nicotinamide inhibition. 1 Publication
    Mutagenesisi101 – 1011D → N: Alters cosubstrate specificity, decreases Km for NAD(+), enzyme unable to discriminate between NAD(+) and nicotinic acid adenine dinucleotide (NAAD). 1 Publication
    Mutagenesisi116 – 1161H → A: 2-fold decrease in turnover and peptide affinity. 1 Publication
    Mutagenesisi116 – 1161H → Y: 10-fold decrease in turnover and peptide affinity. 1 Publication
    Mutagenesisi165 – 1651N → D: Increased affinity for substrate peptides with a lysine or arginine at position -1. 1 Publication

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 246246NAD-dependent protein deacetylasePRO_0000110362Add
    BLAST

    Interactioni

    Protein-protein interaction databases

    DIPiDIP-29141N.
    STRINGi243274.TM0490.

    Structurei

    Secondary structure

    1
    246
    Legend: HelixTurnBeta strand
    Show more details
    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Helixi4 – 129
    Beta strandi14 – 207
    Helixi22 – 243
    Helixi26 – 283
    Beta strandi33 – 353
    Helixi38 – 425
    Turni45 – 484
    Helixi50 – 556
    Helixi57 – 6711
    Helixi69 – 735
    Helixi78 – 8811
    Beta strandi93 – 975
    Helixi103 – 1064
    Beta strandi112 – 1143
    Beta strandi117 – 1248
    Turni125 – 1273
    Beta strandi130 – 1323
    Helixi133 – 1397
    Turni140 – 1423
    Beta strandi143 – 1453
    Turni149 – 1513
    Beta strandi154 – 1596
    Helixi168 – 18013
    Beta strandi182 – 1887
    Helixi196 – 1983
    Helixi199 – 2068
    Beta strandi209 – 2135
    Helixi221 – 2233
    Beta strandi225 – 2284
    Helixi232 – 24312

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    EntryMethodResolution (Å)ChainPositionsPDBsum
    1YC5X-ray1.40A1-246[»]
    2H2DX-ray1.70A1-246[»]
    2H2FX-ray2.20A1-246[»]
    2H2GX-ray1.63A1-246[»]
    2H2HX-ray2.20A1-246[»]
    2H2IX-ray1.80A1-246[»]
    2H4FX-ray2.00A1-246[»]
    2H4HX-ray1.99A1-246[»]
    2H4JX-ray2.10A1-246[»]
    2H59X-ray1.90A/B1-246[»]
    3D4BX-ray1.90A1-246[»]
    3D81X-ray2.50A1-246[»]
    3JR3X-ray1.50A1-246[»]
    3PDHX-ray1.80A1-246[»]
    4BUZX-ray1.90A1-246[»]
    4BV2X-ray3.30A/B1-246[»]
    ProteinModelPortaliQ9WYW0.
    SMRiQ9WYW0. Positions 1-244.
    ModBaseiSearch...
    MobiDBiSearch...

    Miscellaneous databases

    EvolutionaryTraceiQ9WYW0.

    Family & Domainsi

    Domains and Repeats

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Domaini4 – 246243Deacetylase sirtuin-typeUniRule annotationAdd
    BLAST

    Sequence similaritiesi

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

    Phylogenomic databases

    eggNOGiCOG0846.
    KOiK12410.
    OMAiRFYCINC.
    OrthoDBiEOG6VQPX1.

    Family and domain databases

    Gene3Di3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    HAMAPiMF_01968. Sirtuin_ClassU.
    InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR003000. Sirtuin.
    IPR026591. Sirtuin_cat_small_dom.
    IPR028628. Sirtuin_class_U.
    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.

    Q9WYW0-1 [UniParc]FASTAAdd to Basket

    « Hide

    MKMKEFLDLL NESRLTVTLT GAGISTPSGI PDFRGPNGIY KKYSQNVFDI    50
    DFFYSHPEEF YRFAKEGIFP MLQAKPNLAH VLLAKLEEKG LIEAVITQNI 100
    DRLHQRAGSK KVIELHGNVE EYYCVRCEKK YTVEDVIKKL ESSDVPLCDD 150
    CNSLIRPNIV FFGENLPQDA LREAIGLSSR ASLMIVLGSS LVVYPAAELP 200
    LITVRSGGKL VIVNLGETPF DDIATLKYNM DVVEFARRVM EEGGIS 246
    Length:246
    Mass (Da):27,538
    Last modified:November 1, 1999 - v1
    Checksum:i6BD2EF1B751C190D
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000512 Genomic DNA. Translation: AAD35575.1.
    PIRiA72370.
    RefSeqiNP_228300.1. NC_000853.1.
    WP_010865133.1. NC_000853.1.

    Genome annotation databases

    EnsemblBacteriaiAAD35575; AAD35575; TM_0490.
    GeneIDi897531.
    KEGGitma:TM0490.
    PATRICi23935885. VBITheMar51294_0497.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    AE000512 Genomic DNA. Translation: AAD35575.1 .
    PIRi A72370.
    RefSeqi NP_228300.1. NC_000853.1.
    WP_010865133.1. NC_000853.1.

    3D structure databases

    Select the link destinations:
    PDBe
    RCSB PDB
    PDBj
    Links Updated
    Entry Method Resolution (Å) Chain Positions PDBsum
    1YC5 X-ray 1.40 A 1-246 [» ]
    2H2D X-ray 1.70 A 1-246 [» ]
    2H2F X-ray 2.20 A 1-246 [» ]
    2H2G X-ray 1.63 A 1-246 [» ]
    2H2H X-ray 2.20 A 1-246 [» ]
    2H2I X-ray 1.80 A 1-246 [» ]
    2H4F X-ray 2.00 A 1-246 [» ]
    2H4H X-ray 1.99 A 1-246 [» ]
    2H4J X-ray 2.10 A 1-246 [» ]
    2H59 X-ray 1.90 A/B 1-246 [» ]
    3D4B X-ray 1.90 A 1-246 [» ]
    3D81 X-ray 2.50 A 1-246 [» ]
    3JR3 X-ray 1.50 A 1-246 [» ]
    3PDH X-ray 1.80 A 1-246 [» ]
    4BUZ X-ray 1.90 A 1-246 [» ]
    4BV2 X-ray 3.30 A/B 1-246 [» ]
    ProteinModelPortali Q9WYW0.
    SMRi Q9WYW0. Positions 1-244.
    ModBasei Search...
    MobiDBi Search...

    Protein-protein interaction databases

    DIPi DIP-29141N.
    STRINGi 243274.TM0490.

    Protocols and materials databases

    DNASUi 897531.
    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai AAD35575 ; AAD35575 ; TM_0490 .
    GeneIDi 897531.
    KEGGi tma:TM0490.
    PATRICi 23935885. VBITheMar51294_0497.

    Phylogenomic databases

    eggNOGi COG0846.
    KOi K12410.
    OMAi RFYCINC.
    OrthoDBi EOG6VQPX1.

    Enzyme and pathway databases

    BioCyci TMAR243274:GC6P-514-MONOMER.

    Miscellaneous databases

    EvolutionaryTracei Q9WYW0.

    Family and domain databases

    Gene3Di 3.30.1600.10. 2 hits.
    3.40.50.1220. 3 hits.
    HAMAPi MF_01968. Sirtuin_ClassU.
    InterProi IPR029035. DHS-like_NAD/FAD-binding_dom.
    IPR003000. Sirtuin.
    IPR026591. Sirtuin_cat_small_dom.
    IPR028628. Sirtuin_class_U.
    IPR026590. Ssirtuin_cat_dom.
    [Graphical view ]
    PANTHERi PTHR11085. PTHR11085. 1 hit.
    Pfami PF02146. SIR2. 1 hit.
    [Graphical view ]
    SUPFAMi SSF52467. SSF52467. 1 hit.
    PROSITEi PS50305. SIRTUIN. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: ATCC 43589 / MSB8 / DSM 3109 / JCM 10099.
    2. "N-lysine propionylation controls the activity of propionyl-CoA synthetase."
      Garrity J., Gardner J.G., Hawse W., Wolberger C., Escalante-Semerena J.C.
      J. Biol. Chem. 282:30239-30245(2007) [PubMed] [Europe PMC] [Abstract]
      Cited for: FUNCTION.
    3. "Mechanism of sirtuin inhibition by nicotinamide: altering the NAD(+) cosubstrate specificity of a Sir2 enzyme."
      Avalos J.L., Bever K.M., Wolberger C.
      Mol. Cell 17:855-868(2005) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.4 ANGSTROMS) IN COMPLEX WITH NICOTINAMIDE, ENZYME REGULATION, COFACTOR, MUTAGENESIS OF ASP-101.
    4. Cited for: X-RAY CRYSTALLOGRAPHY (1.63 ANGSTROMS) IN COMPLEX WITH PEPTIDE SUBSTRATES, COFACTOR, MUTAGENESIS OF ASN-165.
    5. "Insights into the sirtuin mechanism from ternary complexes containing NAD+ and acetylated peptide."
      Hoff K.G., Avalos J.L., Sens K., Wolberger C.
      Structure 14:1231-1240(2006) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN TERNARY COMPLEX WITH NAD AND PEPTIDE SUBSTRATE, FUNCTION, CATALYTIC ACTIVITY, COFACTOR, MUTAGENESIS OF HIS-116.
    6. "Structural insights into intermediate steps in the Sir2 deacetylation reaction."
      Hawse W.F., Hoff K.G., Fatkins D.G., Daines A., Zubkova O.V., Schramm V.L., Zheng W., Wolberger C.
      Structure 16:1368-1377(2008) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) IN COMPLEX WITH ANALOGS, MUTAGENESIS OF PHE-33.
    7. "Structure of Sir2Tm bound to a propionylated peptide."
      Bheda P., Wang J.T., Escalante-Semerena J.C., Wolberger C.
      Protein Sci. 20:131-139(2011) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.8 ANGSTROMS).
    8. "Structure-based mechanism of ADP-ribosylation by sirtuins."
      Hawse W.F., Wolberger C.
      J. Biol. Chem. 284:33654-33661(2009) [PubMed] [Europe PMC] [Abstract]
      Cited for: X-RAY CRYSTALLOGRAPHY (1.5 ANGSTROMS) IN COMPLEX WITH PEPTIDE SUBSTRATES, FUNCTION, CHARACTERIZATION OF ADP-RIBOSYLATION ACTIVITY.

    Entry informationi

    Entry nameiNPD_THEMA
    AccessioniPrimary (citable) accession number: Q9WYW0
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: October 31, 2003
    Last sequence update: November 1, 1999
    Last modified: October 1, 2014
    This is version 95 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. PDB cross-references
      Index of Protein Data Bank (PDB) cross-references
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3