4BN4

Structure of human SIRT3 in complex with ADP-ribose


Experimental Data Snapshot

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

wwPDB Validation 3D Report Full Report


This is version 1.5 of the entry. See complete history

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

  • DOI: 10.1107/S0907444913015448
  • Primary Citation of Related Structures:  

  • 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 improvem ...

    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.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-DEPENDENT PROTEIN DEACETYLASE SIRTUIN-3, MITOCHONDRIAL
A
284Homo sapiensMutation(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
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OP2
Query on OP2

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Download CCD File 
A
2-[2-[2-[2-[2-(2-hydroxyethyloxy)ethoxy]ethoxy]ethoxy]ethoxy]ethanoic acid
C12 H24 O8
SXGGZTBEWZFLBZ-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
AR6
Query on AR6

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Download CCD File 
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
 Ligand Interaction
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 = 63.900α = 90.00
b = 66.670β = 90.00
c = 66.850γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
PHASERphasing
REFMACrefinement
XSCALEdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

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