Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 33.09 kDa 
• Atom Count: 2261 
• Residue Count: 268 
• Unique protein chains: 2

4C78

Complex of human Sirt3 with Bromo-Resveratrol and ACS2 peptide

• DOI: 10.2210/pdb4C78/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2013-09-19 Released: 2013-11-20 
• Deposition Author(s): Nguyen, G.T.T., Gertz, M., Weyand, M., Steegborn, C.

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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 

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

• PubMed: 24211137 
• DOI: 10.1016/j.chembiol.2013.09.019
• Primary Citation of Related Structures:  
  4C7B, 4C78


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL	A	284	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3, SIR2L3 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	C	10	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BVB	A	5-[(E)-2-(4-bromophenyl)ethenyl]benzene-1,3-diol C14 H11 Br O2 NCJVLKFAQIWASE-OWOJBTEDSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
ALY	C	L-PEPTIDE LINKING	C8 H16 N2 O3		LYS

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 = 34.7	α = 90
b = 52.6	β = 90
c = 159.7	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-09-19 
• Released Date: 2013-11-20 
Deposition Author(s): Nguyen, G.T.T., Gertz, M., Weyand, M., Steegborn, C.

Revision History 

• 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