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

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 

wwPDB Validation   3D Report Full Report



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

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

  • 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 inhibiti ...

    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.

    Organizational Affiliation: 

    Department of Biochemistry and Research Center for Bio-Macromolecules, University of Bayreuth, 95440 Bayreuth, Germany.



Macromolecules
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(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL A284Homo sapiensMutation(s): 0 
Gene Names: SIRT3, SIR2L3
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
GTEx:  ENSG00000142082
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
ACETYL-COENZYME A SYNTHETASE 2-LIKE, MITOCHONDRIAL B10Homo sapiensMutation(s): 0 
Gene Names: ACSS1, ACAS2L, KIAA1846
EC: 6.2.1.1 (PDB Primary Data), 6.2.1.17 (UniProt)
Find proteins for Q9NUB1 (Homo sapiens)
Explore Q9NUB1 
Go to UniProtKB:  Q9NUB1
NIH Common Fund Data Resources
PHAROS:  Q9NUB1
GTEx:  ENSG00000154930
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
XYQ
Query on XYQ
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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
C17 H25 N5 O15 P2
IJOUKWCBVUMMCR-DLFWLGJNSA-N		 Ligand Interaction
PEG
Query on PEG
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A
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N		 Ligand Interaction
SO4
Query on SO4
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A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L		 Ligand Interaction
GOL
Query on GOL
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A
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N		 Ligand Interaction
ZN
Query on ZN
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A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
EDO
Query on EDO
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A
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N		 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.248 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.186 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.023α = 90
b = 131.329β = 90
c = 76.508γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

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