4ZZJ

SIRT1/Activator/Substrate Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Crystallographic structure of a small molecule SIRT1 activator-enzyme complex.

Dai, H.Case, A.W.Riera, T.V.Considine, T.Lee, J.E.Hamuro, Y.Zhao, H.Jiang, Y.Sweitzer, S.M.Pietrak, B.Schwartz, B.Blum, C.A.Disch, J.S.Caldwell, R.Szczepankiewicz, B.Oalmann, C.Yee Ng, P.White, B.H.Casaubon, R.Narayan, R.Koppetsch, K.Bourbonais, F.Wu, B.Wang, J.Qian, D.Jiang, F.Mao, C.Wang, M.Hu, E.Wu, J.C.Perni, R.B.Vlasuk, G.P.Ellis, J.L.

(2015) Nat Commun 6: 7645-7645

  • DOI: 10.1038/ncomms8645
  • Primary Citation of Related Structures:  
    4ZZI, 4ZZH, 4ZZJ

  • PubMed Abstract: 
  • SIRT1, the founding member of the mammalian family of seven NAD(+)-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human SIRT1 construct (mini-hSIRT1) containing the minimal structural elements required for lysine deacetylation and catalytic activation by small molecule sirtuin-activating compounds (STACs) ...

    SIRT1, the founding member of the mammalian family of seven NAD(+)-dependent sirtuins, is composed of 747 amino acids forming a catalytic domain and extended N- and C-terminal regions. We report the design and characterization of an engineered human SIRT1 construct (mini-hSIRT1) containing the minimal structural elements required for lysine deacetylation and catalytic activation by small molecule sirtuin-activating compounds (STACs). Using this construct, we solved the crystal structure of a mini-hSIRT1-STAC complex, which revealed the STAC-binding site within the N-terminal domain of hSIRT1. Together with hydrogen-deuterium exchange mass spectrometry (HDX-MS) and site-directed mutagenesis using full-length hSIRT1, these data establish a specific STAC-binding site and identify key intermolecular interactions with hSIRT1. The determination of the interface governing the binding of STACs with human SIRT1 facilitates greater understanding of STAC activation of this enzyme, which holds significant promise as a therapeutic target for multiple human diseases.


    Organizational Affiliation

    1] Sirtris, a GlaxoSmithKline Company, 200 Technology Square, Suite 300, Cambridge, Massachusetts 02139, USA [2] GlaxoSmithKline, 1250S. Collegeville Road, Collegeville, Pennsylvania 19426, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-1A356Homo sapiensMutation(s): 0 
Gene Names: SIRT1SIR2L1
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt), 2.3.1 (UniProt)
Find proteins for Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
NIH Common Fund Data Resources
PHAROS:  Q96EB6
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ac-p53B7Homo sapiensMutation(s): 0 
Gene Names: TP53P53
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
NIH Common Fund Data Resources
PHAROS:  P04637
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CNA
Query on CNA

Download Ideal Coordinates CCD File 
D [auth A]CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C22 H30 N7 O13 P2
DGPLSUKWXXSBCU-VGXGLJSLSA-O
 Ligand Interaction
4TQ
Query on 4TQ

Download Ideal Coordinates CCD File 
E [auth A](3S)-1,3-dimethyl-N-[3-(1,3-oxazol-5-yl)phenyl]-6-[3-(trifluoromethyl)phenyl]-2,3-dihydropyrido[2,3-b]pyrazine-4(1H)-carboxamide
C26 H22 F3 N5 O2
NWNBKQCPAUNKSG-INIZCTEOSA-N
 Ligand Interaction
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A], G [auth A]GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download Ideal Coordinates CCD File 
C [auth A]ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
BL-PEPTIDE LINKINGC8 H16 N2 O3LYS
NLE
Query on NLE
BL-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.74 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • R-Value Observed: 0.184 
  • Space Group: I 41 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.51α = 90
b = 94.51β = 90
c = 356.84γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHASERphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2015-05-22 
  • Released Date: 2015-07-15 
  • Deposition Author(s): Dai, H.

Revision History  (Full details and data files)

  • Version 1.0: 2015-07-15
    Type: Initial release
  • Version 1.1: 2015-09-23
    Changes: Data collection