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Protein

NAD-dependent protein deacylase 2

Gene

cobB2

Organism
Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
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 proteins which are inactive in their acetylated form. Deacetylates the N-terminal lysine residue of Alba, the major archaeal chromatin protein and that, in turn, increases Alba's DNA binding affinity, thereby repressing transcription.UniRule annotation1 Publication

Catalytic activityi

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

Cofactori

Zn2+UniRule annotation3 PublicationsNote: Binds 1 zinc ion per subunit.UniRule annotation3 Publications

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Active sitei118 – 1181Proton acceptor
Metal bindingi126 – 1261ZincUniRule annotation2 Publications
Metal bindingi129 – 1291ZincUniRule annotation2 Publications
Metal bindingi150 – 1501ZincUniRule annotation2 Publications
Metal bindingi153 – 1531ZincUniRule annotation2 Publications
Binding sitei235 – 2351NAD; via amide nitrogenUniRule annotation2 Publications

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Nucleotide bindingi23 – 4220NADUniRule annotation2 PublicationsAdd
BLAST
Nucleotide bindingi100 – 1034NADUniRule annotation2 Publications
Nucleotide bindingi191 – 1933NADUniRule annotation2 Publications
Nucleotide bindingi217 – 2193NADUniRule annotation2 Publications

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Hydrolase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

Metal-binding, NAD, Zinc

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-116-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
NAD-dependent protein deacylase 2UniRule annotation (EC:3.5.1.-UniRule annotation)
Alternative name(s):
Regulatory protein SIR2 homolog 2UniRule annotation
SIR2-Af2
Gene namesi
Name:cobB2UniRule annotation
Synonyms:Sir2Af2
Ordered Locus Names:AF_0112
OrganismiArchaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)
Taxonomic identifieri224325 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaArchaeoglobiArchaeoglobalesArchaeoglobaceaeArchaeoglobus
Proteomesi
  • UP000002199 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 253253NAD-dependent protein deacylase 2PRO_0000110378Add
BLAST

Interactioni

Protein-protein interaction databases

STRINGi224325.AF0112.

Structurei

Secondary structure

1
253
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi2 – 1413Combined sources
Beta strandi16 – 227Combined sources
Helixi24 – 263Combined sources
Helixi41 – 444Combined sources
Helixi48 – 514Combined sources
Helixi53 – 586Combined sources
Helixi60 – 7314Combined sources
Helixi80 – 9011Combined sources
Beta strandi94 – 996Combined sources
Helixi105 – 1084Combined sources
Beta strandi113 – 1164Combined sources
Beta strandi119 – 1268Combined sources
Turni127 – 1293Combined sources
Beta strandi132 – 1343Combined sources
Helixi135 – 1373Combined sources
Helixi139 – 1435Combined sources
Turni151 – 1533Combined sources
Beta strandi158 – 1625Combined sources
Helixi171 – 18212Combined sources
Beta strandi185 – 1917Combined sources
Turni197 – 2004Combined sources
Helixi201 – 2088Combined sources
Beta strandi212 – 2198Combined sources
Helixi224 – 2263Combined sources
Beta strandi228 – 2336Combined sources
Helixi235 – 24915Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MA3X-ray2.00A1-253[»]
1S7GX-ray2.30A/B/C/D/E1-253[»]
1YC2X-ray2.40A/B/C/D/E1-253[»]
4TWJX-ray1.65A1-253[»]
ProteinModelPortaliO30124.
SMRiO30124. Positions 1-252.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiO30124.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini6 – 251246Deacetylase sirtuin-typeUniRule annotationAdd
BLAST

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiarCOG04248. Archaea.
COG0846. LUCA.
KOiK12410.
OMAiVDGFHQE.

Family and domain databases

Gene3Di3.30.1600.10. 2 hits.
3.40.50.1220. 3 hits.
HAMAPiMF_01121. Sirtuin_ClassIII.
MF_01968. Sirtuin_ClassU.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR003000. Sirtuin.
IPR026591. Sirtuin_cat_small_dom.
IPR027546. Sirtuin_class_III.
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.

O30124-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEDEIRKAAE ILAKSKHAVV FTGAGISAES GIPTFRGEDG LWRKYDPEEV
60 70 80 90 100
ASISGFKRNP RAFWEFSMEM KDKLFAEPNP AHYAIAELER MGIVKAVITQ
110 120 130 140 150
NIDMLHQRAG SRRVLELHGS MDKLDCLDCH ETYDWSEFVE DFNKGEIPRC
160 170 180 190 200
RKCGSYYVKP RVVLFGEPLP QRTLFEAIEE AKHCDAFMVV GSSLVVYPAA
210 220 230 240 250
ELPYIAKKAG AKMIIVNAEP TMADPIFDVK IIGKAGEVLP KIVEEVKRLR

SEK
Length:253
Mass (Da):28,495
Last modified:January 1, 1998 - v1
Checksum:i71A243C9012CBBFE
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB91115.1.
PIRiH69263.
RefSeqiWP_010877626.1. NC_000917.1.

Genome annotation databases

EnsemblBacteriaiAAB91115; AAB91115; AF_0112.
GeneIDi24793666.
KEGGiafu:AF_0112.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AE000782 Genomic DNA. Translation: AAB91115.1.
PIRiH69263.
RefSeqiWP_010877626.1. NC_000917.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1MA3X-ray2.00A1-253[»]
1S7GX-ray2.30A/B/C/D/E1-253[»]
1YC2X-ray2.40A/B/C/D/E1-253[»]
4TWJX-ray1.65A1-253[»]
ProteinModelPortaliO30124.
SMRiO30124. Positions 1-252.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi224325.AF0112.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB91115; AAB91115; AF_0112.
GeneIDi24793666.
KEGGiafu:AF_0112.

Phylogenomic databases

eggNOGiarCOG04248. Archaea.
COG0846. LUCA.
KOiK12410.
OMAiVDGFHQE.

Enzyme and pathway databases

BioCyciAFUL224325:GJBC-116-MONOMER.

Miscellaneous databases

EvolutionaryTraceiO30124.

Family and domain databases

Gene3Di3.30.1600.10. 2 hits.
3.40.50.1220. 3 hits.
HAMAPiMF_01121. Sirtuin_ClassIII.
MF_01968. Sirtuin_ClassU.
InterProiIPR029035. DHS-like_NAD/FAD-binding_dom.
IPR003000. Sirtuin.
IPR026591. Sirtuin_cat_small_dom.
IPR027546. Sirtuin_class_III.
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. "The complete genome sequence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus."
    Klenk H.-P., Clayton R.A., Tomb J.-F., White O., Nelson K.E., Ketchum K.A., Dodson R.J., Gwinn M.L., Hickey E.K., Peterson J.D., Richardson D.L., Kerlavage A.R., Graham D.E., Kyrpides N.C., Fleischmann R.D., Quackenbush J., Lee N.H., Sutton G.G.
    , Gill S.R., Kirkness E.F., Dougherty B.A., McKenney K., Adams M.D., Loftus B.J., Peterson S.N., Reich C.I., McNeil L.K., Badger J.H., Glodek A., Zhou L., Overbeek R., Gocayne J.D., Weidman J.F., McDonald L.A., Utterback T.R., Cotton M.D., Spriggs T., Artiach P., Kaine B.P., Sykes S.M., Sadow P.W., D'Andrea K.P., Bowman C., Fujii C., Garland S.A., Mason T.M., Olsen G.J., Fraser C.M., Smith H.O., Woese C.R., Venter J.C.
    Nature 390:364-370(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126.
  2. Cited for: FUNCTION AS A NAD-DEPENDENT DEACETYLASE.
  3. "Deciphering NAD-dependent deacetylases."
    Dutnall R.N., Pillus L.
    Cell 105:161-164(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: REVIEW.
  4. "Structure of a Sir2 enzyme bound to an acetylated p53 peptide."
    Avalos J.L., Celic I., Muhammad S., Cosgrove M.S., Boeke J.D., Wolberger C.
    Mol. Cell 10:523-535(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF COMPLEX WITH AN ACETYLATED P53 PEPTIDE AND ZINC, COFACTOR.
  5. "Structural basis for the mechanism and regulation of Sir2 enzymes."
    Avalos J.L., Boeke J.D., Wolberger C.
    Mol. Cell 13:639-648(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS) IN COMPLEX WITH ZINC AND NAD, COFACTOR.
  6. "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 (2.4 ANGSTROMS) IN COMPLEX WITH NAD; ZINC AND NICOTINAMIDE, COFACTOR.

Entry informationi

Entry nameiNPD2_ARCFU
AccessioniPrimary (citable) accession number: O30124
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2003
Last sequence update: January 1, 1998
Last modified: July 6, 2016
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Miscellaneous

The two SIR2 homologs in this organism, Af1 and Af2, display different substrate specificities in vitro. Af2 can deacetylate histones and peptides corresponding to the C-terminal part of p53 in a NAD-dependent manner (PubMed:12408821).1 Publication

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

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.