3ZGV

Structure of human SIRT2 in complex with ADP-ribose

• PDB DOI: https://doi.org/10.2210/pdb3ZGV/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-12-19 Released: 2013-03-13 
• Deposition Author(s): Moniot, S., Steegborn, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.188 
• R-Value Work: 0.149 
• R-Value Observed: 0.154 

Starting Model: experimental

Literature

Crystal Structure Analysis of Human Sirt2 and its Adp-Ribose Complex

Moniot, S., Schutkowski, M., Steegborn, C.

(2013) J Struct Biol 182: 136

• PubMed: 23454361 
• DOI: https://doi.org/10.1016/j.jsb.2013.02.012
• Primary Citation of Related Structures:  
  3ZGO, 3ZGV


• PubMed Abstract: 
  

  Sirtuins are NAD(+)-dependent protein deacetylases that regulate metabolism and aging-related processes. Sirt2 is the only cytoplasmic isoform among the seven mamalian Sirtuins (Sirt1-7) and structural information concerning this isoform is limited. We crystallized Sirt2 in complex with a product analog, ADP-ribose, and solved this first crystal structure of a Sirt2 ligand complex at 2.3Å resolution. Additionally, we re-refined the structure of the Sirt2 apoform and analyzed the conformational changes associated with ligand binding to derive insights into the dynamics of the enzyme. Our analyses also provide information on Sirt2 peptide substrate binding and structural states of a Sirt2-specific protein region, and our insights and the novel Sirt2 crystal form provide helpful tools for the development of Sirt2 specific inhibitors.

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Organizational Affiliation: 

Department of Biochemistry, University of Bayreuth, 95440 Bayreuth, Germany.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 75.2 kDa 
• Atom Count: 5,115 
• Modelled Residue Count: 596 
• Deposited Residue Count: 650 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-2	A, B	325	Homo sapiens	Mutation(s): 0  EC: 3.5.1 (PDB Primary Data), 2.3.1 (UniProt), 2.3.1.286 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q8IXJ6 (Homo sapiens) Explore Q8IXJ6  Go to UniProtKB:  Q8IXJ6
PHAROS:  Q8IXJ6 GTEx:  ENSG00000068903

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AR6	E [auth A], K [auth B]	[(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL [HYDROXY-[[(2R,3S,4R,5S)-3,4,5-TRIHYDROXYOXOLAN-2-YL]METHOXY]PHOSPHORYL] HYDROGEN PHOSPHATE C15 H23 N5 O14 P2 SRNWOUGRCWSEMX-ZQSHOCFMSA-N
PGE	N [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	M [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	C [auth A], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	D [auth A], F [auth A], G [auth A], H [auth A], J [auth B], L [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.27 Å
• R-Value Free: 0.188 
• R-Value Work: 0.149 
• R-Value Observed: 0.154 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.86	α = 90
b = 77.98	β = 90
c = 114.33	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Moniot, S., Steegborn, C.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2013-04-03
  Changes: Database references
• Version 1.2: 2013-05-08
  Changes: Database references
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description, Structure summary