5BWN

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


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 

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:  
    5BWO, 5BWN

  • 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 the ...

    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

    University of Chinese Academy of Sciences, Beijing, China.



Macromolecules
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
myristoyl H3K9 peptide B10synthetic constructMutation(s): 0 
Find proteins for Q6NXT2 (Homo sapiens)
Explore Q6NXT2 
Go to UniProtKB:  Q6NXT2
NIH Common Fund Data Resources
PHAROS:  Q6NXT2
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-3, mitochondrial A309Homo sapiensMutation(s): 0 
Gene Names: SIRT3SIR2L3
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download Ideal Coordinates CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MYK
Query on MYK
BL-PEPTIDE LINKINGC20 H40 N2 O3LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.94 Å
  • R-Value Free: 0.275 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.231 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.102α = 90
b = 54.691β = 90
c = 117.257γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
HKL-2000data scaling
PHENIXmodel building

Structure Validation

View Full Validation Report



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
    Changes: Database references