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Protein

NAD-dependent protein deacetylase

Gene

cobB

Organism
Thermotoga maritima (strain ATCC 43589 / MSB8 / DSM 3109 / JCM 10099)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

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

Zn2+3 PublicationsUniRule annotationNote: 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
Complete GO annotation...

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
Complete GO annotation...

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 – 129Combined sources
Beta strandi14 – 207Combined sources
Helixi22 – 243Combined sources
Helixi26 – 283Combined sources
Beta strandi33 – 353Combined sources
Helixi38 – 425Combined sources
Turni45 – 484Combined sources
Helixi50 – 556Combined sources
Helixi57 – 6711Combined sources
Helixi69 – 735Combined sources
Helixi78 – 8811Combined sources
Beta strandi93 – 975Combined sources
Helixi103 – 1064Combined sources
Beta strandi112 – 1143Combined sources
Beta strandi117 – 1248Combined sources
Turni125 – 1273Combined sources
Beta strandi130 – 1323Combined sources
Helixi133 – 1397Combined sources
Turni140 – 1423Combined sources
Beta strandi143 – 1453Combined sources
Turni149 – 1513Combined sources
Beta strandi154 – 1596Combined sources
Helixi168 – 18013Combined sources
Beta strandi182 – 1887Combined sources
Helixi196 – 1983Combined sources
Helixi199 – 2068Combined sources
Beta strandi209 – 2135Combined sources
Helixi221 – 2233Combined sources
Beta strandi225 – 2284Combined sources
Helixi232 – 24312Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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.
InParanoidiQ9WYW0.
KOiK12410.
OMAiVTEFHGN.
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

        10         20         30         40         50
MKMKEFLDLL NESRLTVTLT GAGISTPSGI PDFRGPNGIY KKYSQNVFDI
60 70 80 90 100
DFFYSHPEEF YRFAKEGIFP MLQAKPNLAH VLLAKLEEKG LIEAVITQNI
110 120 130 140 150
DRLHQRAGSK KVIELHGNVE EYYCVRCEKK YTVEDVIKKL ESSDVPLCDD
160 170 180 190 200
CNSLIRPNIV FFGENLPQDA LREAIGLSSR ASLMIVLGSS LVVYPAAELP
210 220 230 240
LITVRSGGKL VIVNLGETPF DDIATLKYNM DVVEFARRVM EEGGIS
Length:246
Mass (Da):27,538
Last modified:November 1, 1999 - v1
Checksum:i6BD2EF1B751C190D
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD35575.1.
PIRiA72370.
RefSeqiNP_228300.1. NC_000853.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000512 Genomic DNA. Translation: AAD35575.1.
PIRiA72370.
RefSeqiNP_228300.1. NC_000853.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
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...

Protein-protein interaction databases

DIPiDIP-29141N.
STRINGi243274.TM0490.

Protocols and materials databases

DNASUi897531.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0846.
InParanoidiQ9WYW0.
KOiK12410.
OMAiVTEFHGN.
OrthoDBiEOG6VQPX1.

Enzyme and pathway databases

BioCyciTMAR243274:GC6P-514-MONOMER.

Miscellaneous databases

EvolutionaryTraceiQ9WYW0.

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]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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: March 4, 2015
This is version 99 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

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.