Crystal Structure of the S. cerevisiae Sir3 AAA+ domain

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 

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Structural basis for the role of the Sir3 AAA+ domain in silencing: interaction with Sir4 and unmethylated histone H3K79.

Ehrentraut, S.Hassler, M.Oppikofer, M.Kueng, S.Weber, J.M.Mueller, J.W.Gasser, S.M.Ladurner, A.G.Ehrenhofer-Murray, A.E.

(2011) Genes Dev 25: 1835-1846

  • DOI: https://doi.org/10.1101/gad.17175111
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The silent information regulator 2/3/4 (Sir2/3/4) complex is required for gene silencing at the silent mating-type loci and at telomeres in Saccharomyces cerevisiae. Sir3 is closely related to the origin recognition complex 1 subunit and consists of an N-terminal bromo-adjacent homology (BAH) domain and a C-terminal AAA(+) ATPase-like domain. Here, through a combination of structure biology and exhaustive mutagenesis, we identified unusual, silencing-specific features of the AAA(+) domain of Sir3. Structural analysis of the putative nucleotide-binding pocket in this domain reveals a shallow groove that would preclude nucleotide binding. Mutation of this site has little effect on Sir3 function in vivo. In contrast, several surface regions are shown to be necessary for the Sir3 silencing function. Interestingly, the Sir3 AAA(+) domain is shown here to bind chromatin in vitro in a manner sensitive to histone H3K79 methylation. Moreover, an exposed loop on the surface of this Sir3 domain is found to interact with Sir4. In summary, the unique folding of this conserved Sir3 AAA(+) domain generates novel surface regions that mediate Sir3-Sir4 and Sir3-nucleosome interactions, both being required for the proper assembly of heterochromatin in living cells.

  • Organizational Affiliation

    Abteilung für Genetik, Zentrum für Medizinische Biotechnologie (ZMB), Universität Duisburg-Essen, D-45141 Essen, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Regulatory protein SIR3
A, B
318Saccharomyces cerevisiae S288CMutation(s): 0 
Gene Names: SIR3CMT1MAR2STE8YLR442CL9753.10
Find proteins for P06701 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P06701 
Go to UniProtKB:  P06701
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP06701
Sequence Annotations
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
Query on MSE
A, B
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.276 
  • R-Value Work: 0.219 
  • R-Value Observed: 0.222 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 89.59α = 90
b = 47.019β = 95.38
c = 127.852γ = 90
Software Package:
Software NamePurpose
MxCuBEdata collection
XDSdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-08-31
    Type: Initial release
  • Version 1.1: 2011-09-14
    Changes: Database references