3GLT

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


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

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

  • DOI: 10.1074/jbc.M109.014928
  • Primary Citation of Related Structures:  

  • 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 emerg ...

    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. leijin05@yahoo.com




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent deacetylase sirtuin-3, mitochondrial
A
285Homo sapiensMutation(s): 0 
Gene Names: SIRT3 (SIR2L3)
EC: 3.5.1.-
Find proteins for Q9NTG7 (Homo sapiens)
Go to Gene View: SIRT3
Go to UniProtKB:  Q9NTG7
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Acetyl-coenzyme A synthetase 2-like, mitochondrial
B
12Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CO3
Query on CO3

Download SDF File 
Download CCD File 
A
CARBONATE ION
C O3
BVKZGUZCCUSVTD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FZN
Query on FZN
B
L-peptide linkingC23 H37 N7 O15 P2 SLYS
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 = 80.718α = 90.00
b = 127.281β = 90.00
c = 76.831γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
MOLREPphasing
SCALAdata scaling
MOSFLMdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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