1M2G

Sir2 homologue-ADP ribose complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Structural basis for the NAD-dependent deacetylase mechanism of Sir2

Chang, J.H., Kim, H.C., Hwang, K.Y., Lee, J.W., Jackson, S.P., Bell, S.D., Cho, Y.

(2002) J.BIOL.CHEM. 277: 34489-34498

  • DOI: 10.1074/jbc.M205460200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    • The NAD-dependent histone/protein deacetylase activity of Sir2 (silent information regulator 2) accounts for its diverse biological roles including gene silencing, DNA damage repair, cell cycle regulation, and life span extension. We provide crystall ...

    The NAD-dependent histone/protein deacetylase activity of Sir2 (silent information regulator 2) accounts for its diverse biological roles including gene silencing, DNA damage repair, cell cycle regulation, and life span extension. We provide crystallographic evidence that 2'-O-acetyl ADP-ribose is the reaction product that is formed at the active site of Sir2 from the 2.6-A co-crystal structure of 2'-O-acetyl-ADP-ribose and Sir2 from Archaeoglobus fulgidus. In addition, we show that His-116 and Phe-159 play critical roles in the catalysis and substrate recognition. The conserved Ser-24 and Asp-101 contribute to the stability for NAD binding rather than being directly involved in the catalysis. The crystal structures of wild type and mutant derivatives of Sir2, in conjunction with biochemical analyses of the mutants, provide novel insights into the reaction mechanism of Sir2-mediated deacetylation.

    Organizational Affiliation: 

    National Creative Research Initiative Center for Structural Biology and Department of Life Science, Pohang University of Science and Technology, Hyo-ja dong, San31, Pohang, KyungBook 790-784, South Korea.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Silent Information Regulator 2
A
249Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126)Mutation(s): 0 
Gene Names: cobB1
EC: 2.3.1.286
Find proteins for O28597 (Archaeoglobus fulgidus (strain ATCC 49558 / VC-16 / DSM 4304 / JCM 9628 / NBRC 100126))
Go to UniProtKB:  O28597
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR
Download SDF File 
Download CCD File 
A
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.7 Å
  • R-Value Free: 0.220 
  • R-Value Work: 0.189 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 35.917α = 90.00
b = 85.512β = 112.34
c = 44.854γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

  • Deposited Date: 2002-06-24 
  • Released Date: 2003-04-08 
  • Deposition Author(s): Chang, J., Cho, Y.

Revision History 

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance