4ZZJ

SIRT1/Activator/Substrate Complex

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7403 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 

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:  

  • 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, 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NAD-dependent protein deacetylase sirtuin-1
A
356Homo sapiensMutation(s): 0 
Gene 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
Ac-p53
B
7Homo sapiensMutation(s): 0 
Gene Names: TP53 (P53)
Find proteins for P04637 (Homo sapiens)
Go to Gene View: TP53
Go to UniProtKB:  P04637
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN
Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
CNA
Query on CNA
Download SDF File 
Download CCD File 
A
CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE
C22 H30 N7 O13 P2
DGPLSUKWXXSBCU-VGXGLJSLSA-O
 Ligand Interaction
GOL
Query on GOL
Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
4TQ
Query on 4TQ
Download SDF File 
Download CCD File 
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
Modified Residues  2 Unique
IDChainsTypeFormula2D DiagramParent
ALY
Query on ALY
B
L-PEPTIDE LINKINGC8 H16 N2 O3LYS
NLE
Query on NLE
B
L-PEPTIDE LINKINGC6 H13 N O2LEU
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7403 Å
  • R-Value Free: 0.221 
  • R-Value Work: 0.182 
  • Space Group: I 41 2 2
Unit Cell:
Length (Å)Angle (°)
a = 94.510α = 90.00
b = 94.510β = 90.00
c = 356.840γ = 90.00
Software Package:
Software NamePurpose
xia2data reduction
PHENIXrefinement
PHASERphasing
xia2data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

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

Revision History 

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