4C78

Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structures of Sirt3 Complexes with 4'-Bromo-Resveratrol Reveal Binding Sites and Inhibition Mechanism.

Nguyen, G.T.T.Gertz, M.Steegborn, C.

(2013) Chem.Biol. 20: 1375

  • DOI: 10.1016/j.chembiol.2013.09.019
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Sirtuins are protein deacetylases regulating aging processes and various physiological functions. Resveratrol, a polyphenol found in red wine, activates human Sirt1 and inhibits Sirt3, and it can mimic calorie restriction effects, such as lifespan ex ...

    Sirtuins are protein deacetylases regulating aging processes and various physiological functions. Resveratrol, a polyphenol found in red wine, activates human Sirt1 and inhibits Sirt3, and it can mimic calorie restriction effects, such as lifespan extension in lower organisms. The mechanism of Sirtuin modulation by resveratrol is not well understood. We used 4'-bromo-resveratrol (5-(2-(4-hydroxyphenyl)vinyl)-1,3-benzenediol) to study Sirt1 and Sirt3 modulation. Despite its similarity to the Sirt1 activator resveratrol, the compound potently inhibited both, Sirt1 and Sirt3. Crystal structures of Sirt3 in complex with a fluorophore-labeled and with a native substrate peptide, respectively, in presence of 4'-bromo-resveratrol reveal two compound binding sites. Biochemical studies identify the internal site and substrate competition as the mechanism for inhibition, providing a drug target site, and homology modeling suggests that the second, allosteric site might indicate the site for Sirt1 activation.


    Organizational Affiliation

    Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
A
284Homo 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
C
10Homo 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 2 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
BVB
Query on BVB

Download SDF File 
Download CCD File 
A
5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol
C14 H11 Br O2
NCJVLKFAQIWASE-OWOJBTEDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
C
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • Space Group: P 2 21 21
Unit Cell:
Length (Å)Angle (°)
a = 34.700α = 90.00
b = 52.600β = 90.00
c = 159.700γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-11-20
    Type: Initial release
  • Version 1.1: 2013-11-27
    Type: Database references
  • Version 1.2: 2013-12-11
    Type: Database references