Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 34.52 kDa 
• Atom Count: 2698 
• Residue Count: 295 
• Unique protein chains: 2

1Q1A

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

• DOI: 10.2210/pdb1Q1A/pdb

• Classification: GENE REGULATION
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2003-07-18 Released: 2003-11-18 
• Deposition Author(s): Zhao, K., Chai, X., Marmorstein, R.

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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 

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

• PubMed: 14604530 
• DOI: 10.1016/j.str.2003.09.016
• Primary Citation of Related Structures:  
  1Q1A, 1Q17


• 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. 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.

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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

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HST2 protein	A	289	Saccharomyces cerevisiae	Mutation(s): 0  EC: 2.3.1.286
Find proteins for P53686 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53686  Go to UniProtKB:  P53686

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Histone H4	B	10	N/A	Mutation(s): 1
Find proteins for P02309 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P02309  Go to UniProtKB:  P02309

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
OAD	A	2'-O-ACETYL ADENOSINE-5-DIPHOSPHORIBOSE C17 H25 N5 O15 P2 BFNOPXRXIQJDHO-DLFWLGJNSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	B	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

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 = 98.421	α = 90
b = 98.421	β = 90
c = 77.254	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-07-18 
• Released Date: 2003-11-18 
Deposition Author(s): Zhao, K., Chai, X., Marmorstein, R.

Revision History 

• 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