1M2N | pdb_00001m2n

Sir2 homologues (D102G/F159A/R170A) mutant-2'-O-acetyl ADP ribose complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 
    0.308 (Depositor) 
  • R-Value Work: 
    0.228 (Depositor) 
  • R-Value Observed: 
    0.228 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 1M2N

This is version 1.4 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.

(2003) J Biological Chem 277: 34489-34498

  • DOI: https://doi.org/10.1074/jbc.M205460200
  • Primary Citation Related Structures: 
    1M2G, 1M2H, 1M2J, 1M2K, 1M2N

  • 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 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.

Macromolecule Content 

  • Total Structure Weight: 56.2 kDa 
  • Atom Count: 4,088 
  • Modeled Residue Count: 498 
  • Deposited Residue Count: 498 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Silent Information Regulator 2
A, B
249Archaeoglobus fulgidusMutation(s): 3 
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: 2.60 Å
  • R-Value Free:  0.308 (Depositor) 
  • R-Value Work:  0.228 (Depositor) 
  • R-Value Observed: 0.228 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 84.72α = 90
b = 84.72β = 90
c = 193.087γ = 120
Software Package:
Software NamePurpose
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-04-08
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2021-11-10
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-05-29
    Changes: Data collection