3GLU

Crystal Structure of Human SIRT3 with AceCS2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 

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:  
    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 ...

    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:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent deacetylase sirtuin-3, mitochondrialA285Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens)
Explore Q9NTG7 
Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Acetyl-coenzyme A synthetase 2-like, mitochondrialB12Homo sapiensMutation(s): 0 
Gene Names: ACSS1ACAS2LKIAA1846
EC: 6.2.1.1 (PDB Primary Data), 6.2.1.17 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NUB1 (Homo sapiens)
Explore Q9NUB1 
Go to UniProtKB:  Q9NUB1
PHAROS:  Q9NUB1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download Ideal Coordinates CCD File 
C [auth A], D [auth A]SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
E [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.205 
  • R-Value Observed: 0.208 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 77.497α = 90
b = 129.46β = 90
c = 78.6γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

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