1M1D

TETRAHYMENA GCN5 WITH BOUND BISUBSTRATE ANALOG INHIBITOR


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structure of the GCN5 histone acetyltransferase bound to a bisubstrate inhibitor.

Poux, A.N.Cebrat, M.Kim, C.M.Cole, P.A.Marmorstein, R.

(2002) Proc.Natl.Acad.Sci.USA 99: 14065-14070

  • DOI: 10.1073/pnas.222373899

  • PubMed Abstract: 
  • Histone acetyltransferases (HATs) use acetyl CoA to acetylate target lysine residues within histones and other transcription factors, such as the p53 tumor suppressor, to promote gene activation. HAT enzymes fall into subfamilies with divergence in s ...

    Histone acetyltransferases (HATs) use acetyl CoA to acetylate target lysine residues within histones and other transcription factors, such as the p53 tumor suppressor, to promote gene activation. HAT enzymes fall into subfamilies with divergence in sequence and substrate preference. Several HAT proteins have been implicated in human cancer. We have previously reported on the preparation of peptide-CoA conjugate inhibitors with distinct specificities for the p300/CBP [cAMP response element binding protein (CREB)-binding protein] or GCN5 HAT subfamilies. Here we report on the crystal structure of the GCN5 HAT bound to a peptide-CoA conjugate containing CoA covalently attached through an isopropionyl linker to Lys-14 of a 20-aa N-terminal fragment of histone H3. Surprisingly, the structure reveals that the H3 portion of the inhibitor is bound outside of the binding site for the histone substrate and that only five of the 20 aa residues of the inhibitor are ordered. Rearrangements within the C-terminal region of the GCN5 protein appear to mediate this peptide displacement. Mutational and enzymatic data support the hypothesis that the observed structure corresponds to a late catalytic intermediate. The structure also provides a structural scaffold for the design of HAT-specific inhibitors that may have therapeutic applications for the treatment of HAT-mediated cancers.


    Organizational Affiliation

    The Wistar Institute, and Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
TGCN5 HISTONE ACETYL TRANSFERASE
A, C
163Tetrahymena thermophilaMutation(s): 0 
Find proteins for Q27198 (Tetrahymena thermophila)
Go to UniProtKB:  Q27198
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
HISTONE H3
B, D
20Saccharomyces cerevisiae (strain ATCC 204508 / S288c)Mutation(s): 0 
Gene Names: HHT1, HHT2 (SIN2)
Find proteins for P61830 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c))
Go to UniProtKB:  P61830
Small Molecules
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
LYX
Query on LYX
B, D
L-PEPTIDE LINKINGC30 H52 N9 O19 P3 SLYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.2 Å
  • R-Value Free: 0.265 
  • R-Value Work: 0.213 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 67.420α = 90.00
b = 67.830β = 90.00
c = 74.500γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data reduction
HKL-2000data collection
AMoREphasing
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-30
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance