4HDA

Crystal structure of human Sirt5 in complex with Fluor-de-Lys peptide and resveratrol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

A molecular mechanism for direct sirtuin activation by resveratrol.

Gertz, M.Nguyen, G.T.Fischer, F.Suenkel, B.Schlicker, C.Franzel, B.Tomaschewski, J.Aladini, F.Becker, C.Wolters, D.Steegborn, C.

(2012) Plos One 7: e49761-e49761

  • DOI: 10.1371/journal.pone.0049761
  • Primary Citation of Related Structures:  4HD8

  • PubMed Abstract: 
  • Sirtuins are protein deacetylases regulating metabolism, stress responses, and aging processes, and they were suggested to mediate the lifespan extending effect of a low calorie diet. Sirtuin activation by the polyphenol resveratrol can mimic such li ...

    Sirtuins are protein deacetylases regulating metabolism, stress responses, and aging processes, and they were suggested to mediate the lifespan extending effect of a low calorie diet. Sirtuin activation by the polyphenol resveratrol can mimic such lifespan extending effects and alleviate metabolic diseases. The mechanism of Sirtuin stimulation is unknown, hindering the development of improved activators. Here we show that resveratrol inhibits human Sirt3 and stimulates Sirt5, in addition to Sirt1, against fluorophore-labeled peptide substrates but also against peptides and proteins lacking the non-physiological fluorophore modification. We further present crystal structures of Sirt3 and Sirt5 in complex with fluorogenic substrate peptide and modulator. The compound acts as a top cover, closing the Sirtuin's polypeptide binding pocket and influencing details of peptide binding by directly interacting with this substrate. Our results provide a mechanism for the direct activation of Sirtuins by small molecules and suggest that activators have to be tailored to a specific Sirtuin/substrate pair.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacylase sirtuin-5, mitochondrial
A, B
275Homo sapiensGene Names: SIRT5 (SIR2L5)
EC: 3.5.1.-
Find proteins for Q9NXA8 (Homo sapiens)
Go to Gene View: SIRT5
Go to UniProtKB:  Q9NXA8
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fluor-de-Lys peptide
F
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

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

Download SDF File 
Download CCD File 
B
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FDL
Query on FDL
F
L-PEPTIDE LINKINGC18 H23 N3 O4LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.601 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.199 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 41.300α = 90.00
b = 112.690β = 90.05
c = 55.890γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
MOLREPphasing
XDSdata reduction
XDSdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-12-05
    Type: Initial release
  • Version 1.1: 2013-02-20
    Type: Database references