Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.91 kDa 
• Atom Count: 2383 
• Residue Count: 280 
• 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
• Mutation(s): No 


• 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.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

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, 3GLS, 3GLT, 3GLU


• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent deacetylase sirtuin-3, mitochondrial	A	285	Homo sapiens	Mutation(s): 0  Gene Names: SIR2L3, SIRT3 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7  Go to UniProtKB:  Q9NTG7
NIH Common Fund Data Resources
PHAROS:  Q9NTG7 GTEx:  ENSG00000142082

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Acetyl-coenzyme A synthetase 2-like, mitochondrial	B	12	Homo sapiens	Mutation(s): 0  Gene Names: ACSS1, ACAS2L, KIAA1846 EC: 6.2.1.1 (PDB Primary Data), 6.2.1.17 (UniProt)
Find proteins for Q9NUB1 (Homo sapiens) Explore Q9NUB1  Go to UniProtKB:  Q9NUB1
NIH Common Fund Data Resources
PHAROS:  Q9NUB1 GTEx:  ENSG00000154930

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
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: 2.10 Å
• R-Value Free: 0.228 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 80.718	α = 90
b = 127.281	β = 90
c = 76.831	γ = 90

Software Package:

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

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
  Changes: Version format compliance