1ICI

CRYSTAL STRUCTURE OF A SIR2 HOMOLOG-NAD COMPLEX

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free: 
    0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work: 
    0.199 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.203 (Depositor) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

This is version 1.4 of the entry. See complete history. 


Literature

Crystal structure of a SIR2 homolog-NAD complex.

Min, J., Landry, J., Sternglanz, R., Xu, R.M.

(2001) Cell 105: 269-279

  • DOI: https://doi.org/10.1016/s0092-8674(01)00317-8
  • Primary Citation of Related Structures:  
    1ICI

  • PubMed Abstract: 

    The SIR2 protein family comprises a novel class of nicotinamide-adenine dinucleotide (NAD)-dependent protein deacetylases that function in transcriptional silencing, DNA repair, and life-span extension in Saccharomyces cerevisiae. Two crystal structures of a SIR2 homolog from Archaeoglobus fulgidus complexed with NAD have been determined at 2.1 A and 2.4 A resolutions. The structures reveal that the protein consists of a large domain having a Rossmann fold and a small domain containing a three-stranded zinc ribbon motif. NAD is bound in a pocket between the two domains. A distinct mode of NAD binding and an unusual configuration of the zinc ribbon motif are observed. The structures also provide important insights into the catalytic mechanism of NAD-dependent protein deacetylation by this family of enzymes.

    • Organizational Affiliation: 

    W. M. Keck Structural Biology Laboratory, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY 11724, USA.


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
TRANSCRIPTIONAL REGULATORY PROTEIN, SIR2 FAMILY
A, B
256Archaeoglobus fulgidusMutation(s): 0 
Gene Names: AF1676
EC: 2.3.1.286
UniProt
Find proteins for O28597 (Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16))
Explore O28597 
Go to UniProtKB:  O28597
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO28597
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.10 Å
  • R-Value Free:  0.249 (Depositor), 0.240 (DCC) 
  • R-Value Work:  0.199 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.203 (Depositor) 
Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.41α = 90
b = 94.54β = 95.29
c = 93.78γ = 90
Software Package:
Software NamePurpose
PHASESphasing
CNSrefinement
MADNESSdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted NADClick on this verticalbar to view details

View more in-depth experimental data
Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-05-02
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-04
    Changes: Refinement description
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations