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 

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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:  
    4ZZH, 4ZZI, 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
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
NAD-dependent protein deacetylase sirtuin-1A356Homo sapiensMutation(s): 0 
Gene Names: SIRT1, SIR2L1
EC: 3.5.1 (PDB Primary Data), 2.3.1.286 (UniProt), 2.3.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for Q96EB6 (Homo sapiens)
Explore Q96EB6 
Go to UniProtKB:  Q96EB6
PHAROS:  Q96EB6
GTEx:  ENSG00000096717 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ96EB6
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Ac-p53B7Homo sapiensMutation(s): 0 
Gene Names: TP53, P53
UniProt & NIH Common Fund Data Resources
Find proteins for P04637 (Homo sapiens)
Explore P04637 
Go to UniProtKB:  P04637
PHAROS:  P04637
GTEx:  ENSG00000141510 
Entity Groups  
UniProt GroupP04637
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		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: 2.74 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

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Ligand Structure Quality Assessment 


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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