PDBsum entry 1s4z

Gene regulation

PDB id: 1s4z

Contents

Protein chains

75 a.a. *

30 a.a. *

* Residue conservation analysis

PDB id:

1s4z

Name:

Gene regulation

Title:

Hp1 chromo shadow domain in complex with pxvxl motif of caf-1

Structure:

Chromobox protein homolog 1. Chain: a, b. Fragment: chromo shadow domain. Synonym: heterochromatin protein 1 homolog beta, hp1 beta, modifier 1 protein, m31, heterochromatin protein p25. Engineered: yes. Chromatin assembly factor 1 subunit a. Chain: c. Fragment: chromatin assembly factor 1.

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: cbx1, cbx. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Gene: chaf1a, caip150.

NMR struc:

25 models

Authors:

A.Thiru,D.Nietlispach,H.R.Mott,M.Okuwaki,D.Lyon,P.R.Nielsen, M.Hirshberg,A.Verreault,N.V.Murzina,E.D.Laue

Key ref:

A.Thiru et al. (2004). Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin. EMBO J, 23, 489-499. PubMed id: 14765118 DOI: 10.1038/sj.emboj.7600088

Date:

19-Jan-04 Release date: 23-Mar-04

Protein chains

P83917  (CBX1_MOUSE) -  Chromobox protein homolog 1 from Mus musculus

Seq: 185 a.a.

Struc: 75 a.a.*

Protein chain

Q9QWF0  (CAF1A_MOUSE) -  Chromatin assembly factor 1 subunit A from Mus musculus

Seq: 911 a.a.

Struc: 30 a.a.*

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Enzyme reactions

• Enzyme class: Chains A, B, C: E.C.?

DOI no: 10.1038/sj.emboj.7600088

EMBO J 23:489-499 (2004)

PubMed id: 14765118

Structural basis of HP1/PXVXL motif peptide interactions and HP1 localisation to heterochromatin.

A.Thiru, D.Nietlispach, H.R.Mott, M.Okuwaki, D.Lyon, P.R.Nielsen, M.Hirshberg, A.Verreault, N.V.Murzina, E.D.Laue.

ABSTRACT

HP1 family proteins are adaptor molecules, containing two related chromo domains that are required for chromatin packaging and gene silencing. Here we present the structure of the chromo shadow domain from mouse HP1beta bound to a peptide containing a consensus PXVXL motif found in many HP1 binding partners. The shadow domain exhibits a novel mode of peptide recognition, where the peptide binds across the dimer interface, sandwiched in a beta-sheet between strands from each monomer. The structure allows us to predict which other shadow domains bind similar PXVXL motif-containing peptides and provides a framework for predicting the sequence specificity of the others. We show that targeting of HP1beta to heterochromatin requires shadow domain interactions with PXVXL-containing proteins in addition to chromo domain recognition of Lys-9-methylated histone H3. Interestingly, it also appears to require the simultaneous recognition of two Lys-9-methylated histone H3 molecules. This finding implies a further complexity to the histone code for regulation of chromatin structure and suggests how binding of HP1 family proteins may lead to its condensation.

Selected figure(s)

Figure 2.
Figure 2 Structure of the HP1 shadow domain/CAF-1 complex. (A) The backbone of residues 110 -172 of HP1 and 214 -232 of CAF-1 from the 25 lowest energy structures (out of 72 that converged from the 100 computed). The structure has good covalent geometry and nonbonded contacts (Table 1). The peptide backbone around residues Asp-214 -Glu-219 of CAF-1 is not well defined in the structure because only the Phe-217 and Ile-218 side chains interact with the shadow domain. 15N relaxation studies show that the peptide backbone in this region has increased mobility within the complex when compared to residues in the PXVXL motif (Figure 1A). (B) The structure closest to the mean, rotated by 90° about the z-axis, compared to the orientation shown in (A). This structure is compared with that of the free shadow domain (PDB code: 1DZ1; Brasher et al, 2000) and the chromo domain/histone H3 complex (PDB code: 1GUW; Nielsen et al, 2002). In the structure of the free shadow domain, the side chains of Trp-170, which stabilise the position of the C-terminal tails, are shown. (C) Stereoview of the structure closest to the mean showing side chains of residues involved in the HP1 /CAF-1 peptide interface. (D, E) Close-up views of the interactions made by (D) Val-224 (position 0) and (E) Pro-222 and Leu-226 (positions -2/+2), Phe-217/Ile-218 (-7/-6 positions) and Ile-229/Leu-230 (+5/+6 positions). In (A -D), the HP1 monomers are coloured blue and magenta and the CAF-1 peptide is coloured green. (Note: Trp-170 is not shown on monomer A because it does not interact with Leu-226 at the +2 position.)

Figure 3.
Figure 3 Shadow domain alignment in which the residues involved in complex formation are highlighted (numbering is for mouse HP1 ). Residues important for recognition of the PXVXL motif are highlighted in yellow (Val-224) and red (Pro-222/Leu-226 at the -2/+2 positions). Residues that form the hydrophobic patch that interacts with the flanking N- and C-terminal sequences (Phe-217/Ile-218 and Ile-229/Leu-230 at the -6/-7 and +5/+6 positions, respectively) are highlighted in blue. Residues that are not conserved and are predicted to alter specificity are boxed. Conserved residues that define the fold of the shadow domain are highlighted in grey, while residues important for dimerisation are indicated by blue triangles. Phe-163 (indicated by a green dot) is important for both the structure of the shadow domain and peptide binding. The positions of secondary structure elements in mouse HP1 are indicated by purple arrows ( -strands) and cylinders ( -helices)--the dots indicate the positions of the conserved bulges in the first strand. Sequences are labelled by species name (Mm--Mus musculus, Hs--Homo sapiens, Gg--Gallus gallus, Xl--Xenopus laevis, Dm--Drosophila melanogaster, Dv--Drosophila virilis, Os--Oryza sativa, Zm--Zea mays, At--Arabidopsis thaliana, Dc--Daucus carota, Sp--Schizosaccharomyces pombe, Ec--Encephalitozoon cuniculi, Ce--Caenorhabditis elegans, Le--Lycopersicon esculentum).

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 489-499) copyright 2004.

Figures were selected by the author.