1Q1A

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-acetyl ADP ribose and histone peptide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 

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Literature

Structure of the yeast Hst2 protein deacetylase in ternary complex with 2'-O-Acetyl ADP ribose and histone peptide.

Zhao, K., Chai, X., Marmorstein, R.

(2003) Structure 11: 1403-1411

  • DOI: 10.1016/j.str.2003.09.016
  • Primary Citation of Related Structures:  
    1Q17, 1Q1A

  • PubMed Abstract: 

    • Sir2 proteins are NAD(+)-dependant protein deactylases that have been implicated in playing roles in gene silencing, DNA repair, genome stability, longevity, metabolism, and cell physiology. To define the mechanism of Sir2 activity, we report the 1.5 A crystal structure of the yeast Hst2 (yHst2) Sir2 protein in ternary complex with 2'-O-acetyl ADP ribose and an acetylated histone H4 peptide ...

    Sir2 proteins are NAD(+)-dependant protein deactylases that have been implicated in playing roles in gene silencing, DNA repair, genome stability, longevity, metabolism, and cell physiology. To define the mechanism of Sir2 activity, we report the 1.5 A crystal structure of the yeast Hst2 (yHst2) Sir2 protein in ternary complex with 2'-O-acetyl ADP ribose and an acetylated histone H4 peptide. The structure captures both ligands meeting within an enclosed tunnel between the small and large domains of the catalytic protein core and permits the assignment of a detailed catalytic mechanism for the Sir2 proteins that is consistent with solution and enzymatic studies. Comparison of the ternary complex with the yHst2/NAD(+) complex, also reported here, and nascent yHst2 structure also reveals that NAD(+) binding accompanies intramolecular loop rearrangement for more stable NAD(+) and acetyl-lysine binding, and that acetyl-lysine peptide binding induces a trimer-monomer protein transition involving nonconserved Sir2 residues.

    Related Citations: 
    • Structure and autoregulation of the yeast Hst2 homolog of Sir2
      Zhao, K., Chai, X., Clements, A., Marmorstein, R.
      (2003) Nat Struct Biol 10: 864
    Organizational Affiliation: 

    The Wistar Institute, University of Pennsylvania, Philadelphia, PA 19104, USA.



Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HST2 proteinA289Saccharomyces cerevisiaeMutation(s): 0 
EC: 2.3.1.286
UniProt
Find proteins for P53686 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P53686 
Go to UniProtKB:  P53686
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP53686
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Histone H4B10N/AMutation(s): 1 
UniProt
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Explore P02309 
Go to UniProtKB:  P02309
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP02309
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OAD
Query on OAD
Download Ideal Coordinates CCD File 
D [auth A]2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE
C17 H25 N5 O15 P2
BFNOPXRXIQJDHO-DLFWLGJNSA-N		 Ligand Interaction
ZN
Query on ZN
Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY		B L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.50 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.183 
  • R-Value Observed: 0.183 
  • Space Group: H 3
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 98.421α = 90
b = 98.421β = 90
c = 77.254γ = 120
Software Package:
Software NamePurpose
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-11-18
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance