Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | 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: 35.77 kDa 
• Atom Count: 2338 
• Modelled Residue Count: 283 
• Deposited Residue Count: 319 
• Unique protein chains: 2

5BWN

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

• PDB DOI: 10.2210/pdb5BWN/pdb

• Classification: PEPTIDE/HYDROLASE
• Organism(s): synthetic construct, Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


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

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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 

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

• PubMed: 27501476 
• DOI: 10.1002/1873-3468.12345
• Primary Citation of Related Structures:  
  5BWN, 5BWO


• 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 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.

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Organizational Affiliation: 

University of Chinese Academy of Sciences, Beijing, China.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
myristoyl H3K9 peptide	A [auth B]	10	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q6NXT2 (Homo sapiens) Explore Q6NXT2  Go to UniProtKB:  Q6NXT2
PHAROS:  Q6NXT2

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-dependent protein deacetylase sirtuin-3, mitochondrial	B [auth A]	309	Homo sapiens	Mutation(s): 0  Gene Names: SIRT3, SIR2L3 EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NTG7 (Homo sapiens) Explore Q9NTG7  Go to UniProtKB:  Q9NTG7
PHAROS:  Q9NTG7

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MYK	A [auth B]	L-PEPTIDE LINKING	C20 H40 N2 O3		LYS

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 = 44.102	α = 90
b = 54.691	β = 90
c = 117.257	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data scaling
PHENIX	model building

Structure Validation

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