5BTR

Crystal structure of SIRT1 in complex with resveratrol and an AMC-containing peptide

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

  • Deposited: 2015-06-03 Released: 2015-07-08 
  • Deposition Author(s): Cao, D., Wang, M., Qiu, X., Liu, D., Jiang, H., Yang, N., Xu, R.M.
  • Funding Organization(s): Ministry of Science and Technology (China); National Natural Science Foundation of China; Strategic Priority Research Program of Chinese Academy of Sciences; Key Research Program of Chinese Academy of Sciences; National Key New Drug Creation and Manufacturing Program of China 

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis for allosteric, substrate-dependent stimulation of SIRT1 activity by resveratrol

Cao, D.Wang, M.Qiu, X.Liu, D.Jiang, H.Yang, N.Xu, R.M.

(2015) Genes Dev. 29: 1316-1325

  • DOI: 10.1101/gad.265462.115

  • PubMed Abstract: 
  • Sirtuins with an extended N-terminal domain (NTD), represented by yeast Sir2 and human SIRT1, harbor intrinsic mechanisms for regulation of their NAD-dependent deacetylase activities. Elucidation of the regulatory mechanisms is crucial for understand ...

    Sirtuins with an extended N-terminal domain (NTD), represented by yeast Sir2 and human SIRT1, harbor intrinsic mechanisms for regulation of their NAD-dependent deacetylase activities. Elucidation of the regulatory mechanisms is crucial for understanding the biological functions of sirtuins and development of potential therapeutics. In particular, SIRT1 has emerged as an attractive therapeutic target, and the search for SIRT1-activating compounds (STACs) has been actively pursued. However, the effectiveness of a class of reported STACs (represented by resveratrol) as direct SIRT1 activators is under debate due to the complication involving the use of fluorogenic substrates in in vitro assays. Future efforts of SIRT1-based therapeutics necessitate the dissection of the molecular mechanism of SIRT1 stimulation. We solved the structure of SIRT1 in complex with resveratrol and a 7-amino-4-methylcoumarin (AMC)-containing peptide. The structure reveals the presence of three resveratrol molecules, two of which mediate the interaction between the AMC peptide and the NTD of SIRT1. The two NTD-bound resveratrol molecules are principally responsible for promoting tighter binding between SIRT1 and the peptide and the stimulation of SIRT1 activity. The structural information provides valuable insights into regulation of SIRT1 activity and should benefit the development of authentic SIRT1 activators.


    Organizational Affiliation

    National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China;




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-1
A, B, C
397Homo sapiensGene Names: SIRT1 (SIR2L1)
EC: 3.5.1.-
Find proteins for Q96EB6 (Homo sapiens)
Go to Gene View: SIRT1
Go to UniProtKB:  Q96EB6
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
AMC-containing peptide
D, E, F
5N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
A, B, C
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
STL
Query on STL

Download SDF File 
Download CCD File 
A, B, C, D, E, F
RESVERATROL
C14 H12 O3
LUKBXSAWLPMMSZ-OWOJBTEDSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
FDL
Query on FDL
D, E, F
L-PEPTIDE LINKINGC18 H23 N3 O4LYS
ACE
Query on ACE
D, E, F
NON-POLYMERC2 H4 O

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External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
STLEC50: 23600 - 46200 nM (98) BINDINGDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.207 
  • Space Group: P 41
Unit Cell:
Length (Å)Angle (°)
a = 133.890α = 90.00
b = 133.890β = 90.00
c = 106.707γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
PDB_EXTRACTdata extraction
PHASERphasing
HKL-2000data collection
HKL-2000data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationCountryGrant Number
Ministry of Science and Technology (China)China2012CB910702
National Natural Science Foundation of ChinaChina31430018
National Natural Science Foundation of ChinaChina31210103914
Strategic Priority Research Program of Chinese Academy of SciencesChinaXDB08010100
Key Research Program of Chinese Academy of SciencesChinaKJZD-EW-L05
National Key New Drug Creation and Manufacturing Program of ChinaChina2014ZX09507002

Revision History 

  • Version 1.0: 2015-07-08
    Type: Initial release
  • Version 1.1: 2016-12-28
    Type: Other
  • Version 1.2: 2017-10-18
    Type: Author supporting evidence