Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 34367.48 
• Atom Count: 2309 
• Residue Count: 294 
• Unique protein chains: 2

4BVG

CRYSTAL STRUCTURE OF HUMAN SIRT3 IN COMPLEX WITH NATIVE ALKYLIMIDATE FORMED FROM ACETYL-LYSINE ACS2-PEPTIDE CRYSTALLIZED IN PRESENCE OF THE INHIBITOR EX-527

• DOI: 10.2210/pdb4BVG/pdb

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


• Deposited: 2013-06-25 Released: 2013-07-17 
• Deposition Author(s): Nguyen, G.T.T., Gertz, M., Weyand, M., Steegborn, C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.248 
• R-Value Work: 0.182 

Literature

Ex-527 inhibits Sirtuins by exploiting their unique NAD+-dependent deacetylation mechanism.

Gertz, M., Fischer, F., Nguyen, G.T., Lakshminarasimhan, M., Schutkowski, M., Weyand, M., Steegborn, C.

(2013) Proc. Natl. Acad. Sci. U.S.A. 110: E2772-E2781

• PubMed: 23840057 
• DOI: 10.1073/pnas.1303628110
• Primary Citation of Related Structures:  
  4BVH, 4BVF, 4BVE, 4BVB, 4BV3, 4BV2, 4BUZ


• PubMed Abstract: 
  

Sirtuins are protein deacetylases regulating metabolism and stress responses. The seven human Sirtuins (Sirt1-7) are attractive drug targets, but Sirtuin inhibition mechanisms are mostly unidentified. We report the molecular mechanism of Sirtuin inhibition by 6-chloro-2,3,4,9-tetrahydro-1H-carbazole-1-carboxamide (Ex-527). Inhibitor binding to potently inhibited Sirt1 and Thermotoga maritima Sir2 and to moderately inhibited Sirt3 requires NAD(+), alone or together with acetylpeptide. Crystal structures of several Sirtuin inhibitor complexes show that Ex-527 occupies the nicotinamide site and a neighboring pocket and contacts the ribose of NAD(+) or of the coproduct 2'-O-acetyl-ADP ribose. Complex structures with native alkylimidate and thio-analog support its catalytic relevance and show, together with biochemical assays, that only the coproduct complex is relevant for inhibition by Ex-527, which stabilizes the closed enzyme conformation preventing product release. Ex-527 inhibition thus exploits Sirtuin catalysis, and kinetic isoform differences explain its selectivity. Our results provide insights in Sirtuin catalysis and inhibition with important implications for drug development.

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Organizational Affiliation: 

Department of Biochemistry and Research Center for Bio-Macromolecules, University of Bayreuth, 95440 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: 2.3.1.286
Find proteins for Q9NTG7 (Homo sapiens) Go to Gene View: SIRT3 Go to UniProtKB:  Q9NTG7

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL	B	10	Homo sapiens	Mutation(s): 0  Gene Names: ACSS1 (ACAS2L, KIAA1846) EC: 6.2.1.1
Find proteins for Q9NUB1 (Homo sapiens) Go to Gene View: ACSS1 Go to UniProtKB:  Q9NUB1

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
ZN	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
SO4	A	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	A	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
XYQ	B	(2R,3R,4S,5R)-5-({[(R)-{[(R)-{[(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]OXY}METHYL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL ACETATE ACETYL-RIBOSYL-ADP C17 H25 N5 O15 P2 IJOUKWCBVUMMCR-DLFWLGJNSA-N
EDO	A	1,2-ETHANEDIOL ETHYLENE GLYCOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
PEG	A	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.248 
• R-Value Work: 0.182 
• Space Group: C 2 2 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 78.023	α = 90.00
b = 131.329	β = 90.00
c = 76.508	γ = 90.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2013-06-25 
• Released Date: 2013-07-17 
• Deposition Author(s): Nguyen, G.T.T., Gertz, M., Weyand, M., Steegborn, C.

Revision History 

• Version 1.0: 2013-07-17
  Type: Initial release
• Version 1.1: 2013-08-07
  Type: Database references
• Version 2.0: 2019-01-30
  Type: Atomic model, Data collection, Database references, Derived calculations, Experimental preparation, Non-polymer description, Structure summary