4C78

Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 

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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:  
    4C78, 4C7B

  • 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 extension in lower organisms ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIALA284Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NTG7
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIALB [auth C]10Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NUB1
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BVB
Query on BVB

Download Ideal Coordinates CCD File 
C [auth A]5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol
C14 H11 Br O2
NCJVLKFAQIWASE-OWOJBTEDSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
D [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B [auth C]L-PEPTIDE LINKINGC8 H16 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.00 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.196 
  • Space Group: P 2 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 34.7α = 90
b = 52.6β = 90
c = 159.7γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

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