Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A 

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

Macromolecule Content

• Total Structure Weight: 32428.25 
• Atom Count: 2293 
• Residue Count: 284 
• Unique protein chains: 1

4BN4

Structure of human SIRT3 in complex with ADP-ribose

• DOI: 10.2210/pdb4BN4/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2013-05-13 Released: 2013-06-26 
• Deposition Author(s): Nguyen, G.T.T., Schaefer, S., Gertz, M., Weyand, M., Steegborn, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.179 
• R-Value Work: 0.138 

Literature

Structures of Human Sirtuin 3 Complexes with Adp-Ribose and with Carba-Nad+ and Srt1720: Binding Details and Inhibition Mechanism

Nguyen, G.T.T., Schaefer, S., Gertz, M., Weyand, M., Steegborn, C.

(2013) Acta Crystallogr.,Sect.D 69: 1423

• PubMed: 23897466 
• DOI: 10.1107/S0907444913015448
• Primary Citation of Related Structures:  
  4BN5


• PubMed Abstract: 
  

Sirtuins are NAD(+)-dependent protein deacetylases that regulate metabolism and aging processes and are considered to be attractive therapeutic targets. Most available sirtuin modulators are little understood mechanistically, hindering their improvement. SRT1720 was initially described as an activator of human Sirt1, but it also potently inhibits human Sirt3. Here, the molecular mechanism of the inhibition of Sirt3 by SRT1720 is described. A crystal structure of Sirt3 in complex with SRT1720 and an NAD(+) analogue reveals that the compound partially occupies the acetyl-Lys binding site, thus explaining the reported competition with the peptide substrate. The compound packs against a hydrophobic protein patch and binds with its opposite surface to the NAD(+)  nicotinamide, resulting in an exceptionally tight sandwich-like interaction. The observed arrangement rationalizes the uncompetitive inhibition with NAD(+), and binding measurements confirm that the nicotinamide moiety of NAD(+) supports inhibitor binding. Consistently, no inhibitor is bound in a second crystal structure of Sirt3 that was solved complexed with ADP-ribose and crystallized in the presence of SRT1720. These results reveal a novel sirtuin inhibitor binding site and mechanism, and provide a structural basis for compound improvement.

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Organizational Affiliation: 

Department of Biochemistry, University of Bayreuth, Universitätsstrasse 30, 95445 Bayreuth, Germany.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL	A	284	Homo sapiens	Mutation(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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
OP2	A	2-[2-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]ethanoic acid C12 H24 O8 SXGGZTBEWZFLBZ-UHFFFAOYSA-N
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
NA	A	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N
AR6	A	[(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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.3 Å
• R-Value Free: 0.179 
• R-Value Work: 0.138 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 63.900	α = 90.00
b = 66.670	β = 90.00
c = 66.850	γ = 90.00

Software Package:

Software Name	Purpose
XDS	data reduction
PHASER	phasing
REFMAC	refinement
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-05-13 
• Released Date: 2013-06-26 
• Deposition Author(s): Nguyen, G.T.T., Schaefer, S., Gertz, M., Weyand, M., Steegborn, C.

Revision History 

• Version 1.0: 2013-06-26
  Type: Initial release
• Version 1.1: 2013-07-24
  Type: Atomic model, Other
• Version 1.2: 2013-07-31
  Type: Database references
• Version 1.3: 2013-08-07
  Type: Atomic model, Other
• Version 1.4: 2013-08-14
  Type: Atomic model, Other
• Version 1.5: 2013-08-28
  Type: Atomic model, Other