Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33910.07 
• Atom Count: 2241 
• Residue Count: 297 
• Unique protein chains: 2

3GLT

Crystal Structure of Human SIRT3 with ADPR bound to the AceCS2 peptide containing a thioacetyl lysine

• DOI: 10.2210/pdb3GLT/pdb

• Classification: HYDROLASE/HYDROLASE REGULATOR
• Organism(s): Homo sapiens
• Expression System: Escherichia coli


• Deposited: 2009-03-12 Released: 2009-06-16 
• Deposition Author(s): Jin, L., Wei, W., Jiang, Y., Peng, H., Cai, J., Mao, C., Dai, H., Bemis, J.E., Jirousek, M.R., Milne, J.C., Westphal, C.H., Perni, R.B.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 

Literature

Crystal Structures of Human SIRT3 Displaying Substrate-induced Conformational Changes.

Jin, L., Wei, W., Jiang, Y., Peng, H., Cai, J., Mao, C., Dai, H., Choy, W., Bemis, J.E., Jirousek, M.R., Milne, J.C., Westphal, C.H., Perni, R.B.

(2009) J.Biol.Chem. 284: 24394-24405

• PubMed: 19535340 
• DOI: 10.1074/jbc.M109.014928
• Primary Citation of Related Structures:  
  3GLR, 3GLU, 3GLS


• PubMed Abstract: 
  

SIRT3 is a major mitochondrial NAD(+)-dependent protein deacetylase playing important roles in regulating mitochondrial metabolism and energy production and has been linked to the beneficial effects of exercise and caloric restriction. SIRT3 is emerging as a potential therapeutic target to treat metabolic and neurological diseases. We report the first sets of crystal structures of human SIRT3, an apo-structure with no substrate, a structure with a peptide containing acetyl lysine of its natural substrate acetyl-CoA synthetase 2, a reaction intermediate structure trapped by a thioacetyl peptide, and a structure with the dethioacetylated peptide bound. These structures provide insights into the conformational changes induced by the two substrates required for the reaction, the acetylated substrate peptide and NAD(+). In addition, the binding study by isothermal titration calorimetry suggests that the acetylated peptide is the first substrate to bind to SIRT3, before NAD(+). These structures and biophysical studies provide key insight into the structural and functional relationship of the SIRT3 deacetylation activity.

---

Organizational Affiliation: 

Sirtris, a GSK Company, Cambridge, Massachusetts 02139, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD-dependent deacetylase sirtuin-3, mitochondrial	A	285	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3 (SIR2L3) EC: 2.3.1.286
Find proteins for Q9NTG7 (Homo sapiens) Go to Gene View: SIRT3 Go to UniProtKB:  Q9NTG7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Acetyl-coenzyme A synthetase 2-like, mitochondrial	B	12	Homo sapiens	Mutation(s): 0  Gene Names: ACSS1 (ACAS2L, KIAA1846) EC: 6.2.1.1
Find proteins for Q9NUB1 (Homo sapiens) Go to Gene View: ACSS1 Go to UniProtKB:  Q9NUB1

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CO3	A	CARBONATE ION C O3 BVKZGUZCCUSVTD-UHFFFAOYSA-L

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
FZN	B	L-peptide linking	C23 H37 N7 O15 P2 S		LYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.1 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 80.718	α = 90.00
b = 127.281	β = 90.00
c = 76.831	γ = 90.00

Software Package:

Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
SCALA	data scaling
MOSFLM	data reduction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2009-03-12 
• Released Date: 2009-06-16 
• Deposition Author(s): Jin, L., Wei, W., Jiang, Y., Peng, H., Cai, J., Mao, C., Dai, H., Bemis, J.E., Jirousek, M.R., Milne, J.C., Westphal, C.H., Perni, R.B.

Revision History 

• Version 1.0: 2009-06-16
  Type: Initial release
• Version 1.1: 2011-07-13
  Type: Version format compliance