PDBsum entry: 2pnx

Gene regulation

PDB id: 2pnx

Contents

Protein chains

51 a.a. *

51 a.a. *

11 a.a. *

Ligands

ALA-ARG-THR-M3L-GLN-THR-ALA-ARG

Metals

_ZN ×4

Waters ×130

* Residue conservation analysis

PDB id:

2pnx

Name:

Gene regulation

Title:

The phd finger of ing4 in complex with an h3k4me3 histone peptide

Structure:

Inhibitor of growth protein 4. Chain: a, c. Fragment: phd domain, residues 194-246. Synonym: p29ing4. Engineered: yes. H3k4me3 peptide. Chain: b, d. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: ing4. Expressed in: escherichia coli. Expression_system_taxid: 562. Synthetic: yes. Other_details: the peptide h3k4me3 is naturally found in homo sapiens (human).

Resolution:

1.80Å R-factor: 0.199 R-free: 0.211

Authors:

K.S.Champagne,K.Johnson,T.G.Kutateladze

Key ref:

T.Hung et al. (2009). ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation. Mol Cell, 33, 248-256. PubMed id: 19187765 DOI: 10.1016/j.molcel.2008.12.016

Date:

25-Apr-07 Release date: 15-Apr-08

Protein chain

Q9UNL4  (ING4_HUMAN) -  Inhibitor of growth protein 4

Seq: 249 a.a.

Struc: 51 a.a.

Protein chain

Q9UNL4  (ING4_HUMAN) -  Inhibitor of growth protein 4

Seq: 249 a.a.

Struc: 51 a.a.

Protein chain

No UniProt id for this chain

 Gene Ontology (GO) functional annotation 

• Biochemical function: protein binding (2 terms)

DOI no: 10.1016/j.molcel.2008.12.016

Mol Cell 33:248-256 (2009)

PubMed id: 19187765

ING4 mediates crosstalk between histone H3 K4 trimethylation and H3 acetylation to attenuate cellular transformation.

T.Hung, O.Binda, K.S.Champagne, A.J.Kuo, K.Johnson, H.Y.Chang, M.D.Simon, T.G.Kutateladze, O.Gozani.

ABSTRACT

Aberrations in chromatin dynamics play a fundamental role in tumorigenesis, yet relatively little is known of the molecular mechanisms linking histone lysine methylation to neoplastic disease. ING4 (Inhibitor of Growth 4) is a native subunit of an HBO1 histone acetyltransferase (HAT) complex and a tumor suppressor protein. Here we show a critical role for specific recognition of histone H3 trimethylated at lysine 4 (H3K4me3) by the ING4 PHD finger in mediating ING4 gene expression and tumor suppressor functions. The interaction between ING4 and H3K4me3 augments HBO1 acetylation activity on H3 tails and drives H3 acetylation at ING4 target promoters. Further, ING4 facilitates apoptosis in response to genotoxic stress and inhibits anchorage-independent cell growth, and these functions depend on ING4 interactions with H3K4me3. Together, our results demonstrate a mechanism for brokering crosstalk between H3K4 methylation and H3 acetylation and reveal a molecular link between chromatin modulation and tumor suppressor mechanisms.

Selected figure(s)

Figure 1.
Figure 1. The ING4 PHD Finger Binds Specifically to H3K4me3
(A) ING4[PHD] preferentially binds H3K4me3 peptides. Microarrays spotted with the indicated histone peptides (as in Matthews et al., 2007) were probed with glutathione S-transferase (GST) fused to ING4[195–241] (ING4[PHD]). Red spots indicate positive binding. H3, histone H3; H4, histone H4; me, methylation; ac, acetylation; ph, phosphorylation; s, symmetric; a, asymmetric.
(B) Western analysis of histone peptide pulldowns with GST-ING4[PHD] and the indicated biotinylated peptides.
(C) Full-length ING4, but not ING4[ΔPHD], recognizes H3K4me3. Histone peptide pulldowns are as in (B) with the indicated protein.
(D) 1.8 Å crystal structure of the ING4[PHD]-H3K4me3 complex. The PHD finger is shown as a solid surface with the binding site residues colored and labeled. H3K4 and H3R2 binding grooves are in brown and yellow. The histone peptide is shown as ball-and-stick model with C, O, and N atoms colored green, red, and blue, respectively.
(E) Superimposition of the backbone structures of the ING4 (brown) and ING2 (gray) PHD fingers bound to H3K4me3 (green and gray stick models, respectively).
(F) ING4[PHD] binds with highest affinity to H3K4me3. Tryptophan fluorescence was used to determine disassociation constants (Kds) for the interaction between the ING4[PHD] and the indicated peptides. ^*H3K4me3 Kd was previously determined (Pena et al., 2006).

Figure 2.
Figure 2. ING4[PHD] Binding to H3K4me3 Promotes HBO1 Acetylation of Histone H3
(A) Identification of residues in the ING4 PHD finger critical for H3K4me3 binding. Western blot of histone peptide pull-down assays with the indicated GST-fusion proteins and biotinylated peptides.
(B) ING4[PHD] binding to polynucleosomes is abrogated by substitution of critical residues in the H3K4me3-binding surface. The indicated recombinant proteins were incubated with purified polynucleosomes and binding was determined by western analysis with antibodies against the four core histones and H3K4me3 and H3K9me3 antibodies.
(C) The ING4 interaction with H3K4me3 occurs at chromatin in vivo and requires an intact PHD finger. Western analysis of wild-type or mutant Flag-ING4 protein-protein ChIPs. ING2 is used as a positive control. Input represents 5% of total.
(D) Western analysis of affinity-purified Flag-ING4 and Flag-ING4[D213A] complexes with the indicated antibodies. Control, empty vector IP.
(E and F) Histone acetylation by HBO1 in wild-type, but not mutant, ING4 complexes is increased by binding to H3K4me. Autoradiograms of in vitro HAT reactions by ING4 complexes with the indicated MLA nucleosomes. Western analysis of histones is shown as a loading control.
(G) Quantitation of HAT activity of ING4 and ING4[D213A] complexes on the indicated histone peptides from three independent experiments, except for asterisks (^*), which indicate two independent experiments. Error bars indicate the SEM.

The above figures are reprinted by permission from Cell Press: Mol Cell (2009, 33, 248-256) copyright 2009.

Figures were selected by an automated process.