5FYQ

Sirt2 in complex with a 13-mer trifluoroacetylated Ran peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Insights Into Lysine-Deacetylation of Natively Folded Substrate Proteins by Sirtuins.

Knyphausen, P.De Boor, S.Kuhlmann, N.Scislowski, L.Extra, A.Baldus, L.Schacherl, M.Baumann, U.Neundorf, I.Lammers, M.

(2016) J.Biol.Chem. 291: 14677

  • DOI: 10.1074/jbc.M116.726307

  • PubMed Abstract: 
  • Sirtuins are NAD(+)-dependent lysine deacylases, regulating a variety of cellular processes. The nuclear Sirt1, the cytosolic Sirt2, and the mitochondrial Sirt3 are robust deacetylases, whereas the other sirtuins have preferences for longer acyl chai ...

    Sirtuins are NAD(+)-dependent lysine deacylases, regulating a variety of cellular processes. The nuclear Sirt1, the cytosolic Sirt2, and the mitochondrial Sirt3 are robust deacetylases, whereas the other sirtuins have preferences for longer acyl chains. Most previous studies investigated sirtuin-catalyzed deacylation on peptide substrates only. We used the genetic code expansion concept to produce natively folded, site-specific, and lysine-acetylated Sirt1-3 substrate proteins, namely Ras-related nuclear, p53, PEPCK1, superoxide dismutase, cyclophilin D, and Hsp10, and analyzed the deacetylation reaction. Some acetylated proteins such as Ras-related nuclear, p53, and Hsp10 were robustly deacetylated by Sirt1-3. However, other reported sirtuin substrate proteins such as cyclophilin D, superoxide dismutase, and PEPCK1 were not deacetylated. Using a structural and functional approach, we describe the ability of Sirt1-3 to deacetylate two adjacent acetylated lysine residues. The dynamics of this process have implications for the lifetime of acetyl modifications on di-lysine acetylation sites and thus constitute a new mechanism for the regulation of proteins by acetylation. Our studies support that, besides the primary sequence context, the protein structure is a major determinant of sirtuin substrate specificity.


    Organizational Affiliation

    the Institute for Biochemistry, Z├╝lpicher Strasse 47b, University of Cologne, 50674 Cologne, Germany.,From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and.,From the Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-associated Diseases (CECAD), Joseph-Stelzmann-Strasse 26, University of Cologne, 50931 Cologne and michael.lammers@uni-koeln.de.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2
A, B
360Homo sapiensMutation(s): 0 
Gene Names: SIRT2 (SIR2L, SIR2L2)
EC: 3.5.1.-
Find proteins for Q8IXJ6 (Homo sapiens)
Go to Gene View: SIRT2
Go to UniProtKB:  Q8IXJ6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
RAN AA 31-43
C, D
13Homo sapiensMutation(s): 0 
Gene Names: RAN (ARA24)
Find proteins for P62826 (Homo sapiens)
Go to Gene View: RAN
Go to UniProtKB:  P62826
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
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
FAK
Query on FAK
C, D
L-PEPTIDE LINKINGC8 H13 F3 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.232 
  • Space Group: P 61 2 2
Unit Cell:
Length (Å)Angle (°)
a = 114.948α = 90.00
b = 114.948β = 90.00
c = 206.476γ = 120.00
Software Package:
Software NamePurpose
MOSFLMdata reduction
PHASERphasing
REFMACrefinement
Aimlessdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2016-05-25
    Type: Initial release
  • Version 1.1: 2016-06-08
    Type: Database references
  • Version 1.2: 2016-07-27
    Type: Database references
  • Version 1.3: 2017-08-23
    Type: Data collection