2QIC

Crystal Structure of the ING1 PHD Finger in complex with a Histone H3K4ME3 peptide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Histone H3K4me3 binding is required for the DNA repair and apoptotic activities of ING1 tumor suppressor.

Pena, P.V.Hom, R.A.Hung, T.Lin, H.Kuo, A.J.Wong, R.P.Subach, O.M.Champagne, K.S.Zhao, R.Verkhusha, V.V.Li, G.Gozani, O.Kutateladze, T.G.

(2008) J.Mol.Biol. 380: 303-312

  • DOI: 10.1016/j.jmb.2008.04.061

  • PubMed Abstract: 
  • Inhibitor of growth 1 (ING1) is implicated in oncogenesis, DNA damage repair, and apoptosis. Mutations within the ING1 gene and altered expression levels of ING1 are found in multiple human cancers. Here, we show that both DNA repair and apoptotic ac ...

    Inhibitor of growth 1 (ING1) is implicated in oncogenesis, DNA damage repair, and apoptosis. Mutations within the ING1 gene and altered expression levels of ING1 are found in multiple human cancers. Here, we show that both DNA repair and apoptotic activities of ING1 require the interaction of the C-terminal plant homeodomain (PHD) finger with histone H3 trimethylated at Lys4 (H3K4me3). The ING1 PHD finger recognizes methylated H3K4 but not other histone modifications as revealed by the peptide microarrays. The molecular mechanism of the histone recognition is elucidated based on a 2.1 A-resolution crystal structure of the PHD-H3K4me3 complex. The K4me3 occupies a deep hydrophobic pocket formed by the conserved Y212 and W235 residues that make cation-pi contacts with the trimethylammonium group. Both aromatic residues are essential in the H3K4me3 recognition, as substitution of these residues with Ala disrupts the interaction. Unlike the wild-type ING1, the W235A mutant, overexpressed in the stable clones of melanoma cells or in HT1080 cells, was unable to stimulate DNA repair after UV irradiation or promote DNA-damage-induced apoptosis, indicating that H3K4me3 binding is necessary for these biological functions of ING1. Furthermore, N216S, V218I, and G221V mutations, found in human malignancies, impair the ability of ING1 to associate with H3K4me3 or to induce nucleotide repair and cell death, linking the tumorigenic activity of ING1 with epigenetic regulation. Together, our findings reveal the critical role of the H3K4me3 interaction in mediating cellular responses to genotoxic stresses and offer new insight into the molecular mechanism underlying the tumor suppressive activity of ING1.


    Organizational Affiliation

    Department of Pharmacology, University of Colorado Health Sciences Center, 12801 East 17th Avenue, Aurora, CO 80045-0511, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Inhibitor of growth protein 1
A
62Homo sapiensMutation(s): 0 
Gene Names: ING1
Find proteins for Q9UK53 (Homo sapiens)
Go to Gene View: ING1
Go to UniProtKB:  Q9UK53
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
H3K4ME3 PEPTIDE
B
12N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 1 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
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
M3L
Query on M3L
B
L-PEPTIDE LINKINGC9 H21 N2 O2LYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.264 
  • R-Value Work: 0.240 
  • Space Group: P 32 2 1
Unit Cell:
Length (Å)Angle (°)
a = 49.060α = 90.00
b = 49.060β = 90.00
c = 52.620γ = 120.00
Software Package:
Software NamePurpose
d*TREKdata scaling
d*TREKdata reduction
CNSphasing
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2008-05-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance