PDBsum entry: 2h1e

Hydrolase

PDB id: 2h1e

Contents

Protein chains

166 a.a. *

Waters ×194

* Residue conservation analysis

PDB id:

2h1e

Name:

Hydrolase

Title:

Tandem chromodomains of budding yeast chd1

Structure:

Chromo domain protein 1. Chain: a, b. Fragment: chromodomain, residues 174-339. Synonym: atp-dependent helicase chd1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: chd1. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.20Å R-factor: 0.192 R-free: 0.246

Authors:

J.F.Flanagan Iv,S.Khorasanizadeh

Key ref:

J.F.Flanagan et al. (2007). Molecular Implications of Evolutionary Differences in CHD Double Chromodomains. J Mol Biol, 369, 334-342. PubMed id: 17433364 DOI: 10.1016/j.jmb.2007.03.024

Date:

16-May-06 Release date: 27-Mar-07

Protein chains

P32657  (CHD1_YEAST) -  Chromo domain-containing protein 1

Seq: 1468 a.a.

Struc: 166 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (1 term)

DOI no: 10.1016/j.jmb.2007.03.024

J Mol Biol 369:334-342 (2007)

PubMed id: 17433364

Molecular Implications of Evolutionary Differences in CHD Double Chromodomains.

J.F.Flanagan, B.J.Blus, D.Kim, K.L.Clines, F.Rastinejad, S.Khorasanizadeh.

ABSTRACT

Double chromodomains occur in CHD proteins, which are ATP-dependent chromatin remodeling factors implicated in RNA polymerase II transcription regulation. Biochemical studies suggest important differences in the histone H3 tail binding of different CHD chromodomains. In human and Drosophila, CHD1 double chromodomains bind lysine 4-methylated histone H3 tail, which is a hallmark of transcriptionally active chromatin in all eukaryotes. Here, we present the crystal structure of the yeast CHD1 double chromodomains, and pinpoint their differences with that of the human CHD1 double chromodomains. The most conserved residues in these double chromodomains are the two chromoboxes that orient adjacently. Only a subset of CHD chromoboxes can form an aromatic cage for methyllysine binding, and methyllysine binding requires correctly oriented inserts. These factors preclude yeast CHD1 double chromodomains from interacting with the histone H3 tail. Despite great sequence similarity between the human CHD1 and CHD2 chromodomains, variation within an insert likely prevents CHD2 double chromodomains from binding lysine 4-methylated histone H3 tail as efficiently as in CHD1. By using the available structural and biochemical data we highlight the evolutionary specialization of CHD double chromodomains, and provide insights about their targeting capacities.

Selected figure(s)

Figure 3.

Figure 4.
Figure 4. A phylogenetic tree constructed using the double chromodomain regions of non-redundant CHD sequences. Four major divisions are highlighted to suggest unique double chromodomain branches. Not highlighted are the four CHD proteins that exhibit significant divergence in their sequences.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 369, 334-342) copyright 2007.

Figures were selected by an automated process.