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Q9WYW0

- NPD_THEMA

UniProt

Q9WYW0 - NPD_THEMA

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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: 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

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-HAMAP
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 – 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.
InParanoidiQ9WYW0.
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

        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:
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.
InParanoidi Q9WYW0.
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

« 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: October 29, 2014
This is version 96 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