4IAO

Crystal structure of Sir2 C543S mutant in complex with SID domain of Sir4


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 

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This is version 1.1 of the entry. See complete history


Literature

Structural basis for allosteric stimulation of Sir2 activity by Sir4 binding

Hsu, H.C.Wang, C.L.Wang, M.Yang, N.Chen, Z.Sternglanz, R.Xu, R.M.

(2013) Genes Dev 27: 64-73

  • DOI: 10.1101/gad.208140.112
  • Primary Citation of Related Structures:  
    4IAO

  • PubMed Abstract: 
  • The budding yeast Sir2 (silent information regulator 2) protein is the founding member of the sirtuin family of NAD-dependent histone/protein deacetylases. Its function in transcriptional silencing requires both the highly conserved catalytic domain and a poorly understood N-terminal regulatory domain (Sir2N) ...

    The budding yeast Sir2 (silent information regulator 2) protein is the founding member of the sirtuin family of NAD-dependent histone/protein deacetylases. Its function in transcriptional silencing requires both the highly conserved catalytic domain and a poorly understood N-terminal regulatory domain (Sir2N). We determined the structure of Sir2 in complex with a fragment of Sir4, a component of the transcriptional silencing complex in Saccharomyces cerevisiae. The structure shows that Sir4 is anchored to Sir2N and contacts the interface between the Sir2N and the catalytic domains through a long loop. We discovered that the interaction between the Sir4 loop and the interdomain interface in Sir2 is critical for allosteric stimulation of the deacetylase activity of Sir2. These results bring to light the structure and function of the regulatory domain of Sir2, and the knowledge should be useful for understanding allosteric regulation of sirtuins in general.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, China.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent histone deacetylase SIR2A, B492Saccharomyces cerevisiae S288CMutation(s): 1 
Gene Names: SIR2MAR1YDL042CD2714
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt
Find proteins for P06700 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06700 
Go to UniProtKB:  P06700
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06700
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Regulatory protein SIR4C, D159Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SIR4ASD1STE9UTH2YDR227WYD9934.12
UniProt
Find proteins for P11978 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P11978 
Go to UniProtKB:  P11978
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11978
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
APR
Query on APR

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
ADENOSINE-5-DIPHOSPHORIBOSE
C15 H23 N5 O14 P2
SRNWOUGRCWSEMX-KEOHHSTQSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A],
G [auth B]
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.90 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.227 
  • R-Value Observed: 0.229 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 166.406α = 90
b = 178.752β = 90
c = 121.564γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
SHARPphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-12-26
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references