5BWN

Crystal Structure of SIRT3 with a H3K9 Peptide Containing a Myristoyl Lysine


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Crystal structures of SIRT3 reveal that the alpha 2-alpha 3 loop and alpha 3-helix affect the interaction with long-chain acyl lysine.

Gai, W.Li, H.Jiang, H.Long, Y.Liu, D.

(2016) Febs Lett. 590: 3019-3028

  • DOI: 10.1002/1873-3468.12345
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • SIRT1-7 play important roles in many biological processes and age-related diseases. In addition to a NAD(+) -dependent deacetylase activity, they can catalyze several other reactions, including the hydrolysis of long-chain fatty acyl lysine. To study ...

    SIRT1-7 play important roles in many biological processes and age-related diseases. In addition to a NAD(+) -dependent deacetylase activity, they can catalyze several other reactions, including the hydrolysis of long-chain fatty acyl lysine. To study the binding modes of sirtuins to long-chain acyl lysines, we solved the crystal structures of SIRT3 bound to either a H3K9-myristoylated- or a H3K9-palmitoylated peptide. Interaction of SIRT3 with the palmitoyl group led to unfolding of the α3-helix. The myristoyl and palmitoyl groups bind to the C-pocket and an allosteric site near the α3-helix, respectively. We found that the residues preceding the α3-helix determine the size of the C-pocket. The flexibility of the α2-α3 loop and the plasticity of the α3-helix affect the interaction with long-chain acyl lysine.


    Organizational Affiliation

    Drug Design and Development Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China.,University of Chinese Academy of Sciences, Beijing, China.,Department of Medicinal Chemistry, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China.,Department of Pharmacology III, Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, China.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
myristoyl H3K9 peptide
B
10Homo sapiensMutation(s): 0 
Gene Names: H3F3C
Find proteins for Q6NXT2 (Homo sapiens)
Go to Gene View: H3F3C
Go to UniProtKB:  Q6NXT2
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-3, mitochondrial
A
309Homo 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
Small Molecules
Ligands 1 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MYK
Query on MYK
B
L-peptide linkingC20 H40 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.942 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.102α = 90.00
b = 54.691β = 90.00
c = 117.257γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-06-08 
  • Released Date: 2016-07-13 
  • Deposition Author(s): Gai, W., Liu, D.

Revision History 

  • Version 1.0: 2016-07-13
    Type: Initial release
  • Version 1.1: 2016-12-07
    Type: Database references