2HJH

Crystal Structure of the Sir2 deacetylase

• PDB DOI: https://doi.org/10.2210/pdb2HJH/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2006-06-30 Released: 2008-04-08 
• Deposition Author(s): Hall, B.E., Ellenberger, T.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.215 
• R-Value Work: 0.171 

Literature

Autoregulation of the yeast Sir2 deacetylase by reaction and trapping of a pseudosubstrate motif in the active site

Hall, B.E., Buchberger, J.R., Gerber, S.A., Ambrosio, A.L.B., Gygi, S.P., Filman, D., Moazed, D., Ellenberger, T.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 82.98 kDa 
• Atom Count: 5,747 
• Modelled Residue Count: 651 
• Deposited Residue Count: 708 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent histone deacetylase SIR2	A, B	354	Saccharomyces cerevisiae	Mutation(s): 0  Gene Names: SIR2, MAR1 EC: 3.5.1
UniProt
Find proteins for P06700 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P06700  Go to UniProtKB:  P06700

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
XYQ	D [auth A], G [auth B]	(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE C17 H25 N5 O15 P2 IJOUKWCBVUMMCR-DLFWLGJNSA-N
NCA	E [auth A], H [auth B]	NICOTINAMIDE C6 H6 N2 O DFPAKSUCGFBDDF-UHFFFAOYSA-N
ZN	C [auth A], F [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A, B	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Binding Affinity Annotations
ID	Source	Binding Affinity
NCA	BindingDB:  2HJH	IC50: 5.00e+4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.85 Å
• R-Value Free: 0.215 
• R-Value Work: 0.171 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.353	α = 90
b = 89.566	β = 104.95
c = 94.51	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-04-08 
Deposition Author(s): Hall, B.E., Ellenberger, T.E.

Revision History  

• Version 1.0: 2008-04-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description