PDBsum entry: 2dy8

Hydrolase

PDB id: 2dy8

Contents

Protein chain

69 a.a. *

* Residue conservation analysis

PDB id:

2dy8

Name:

Hydrolase

Title:

Solution structure of the second chromodomain of yeast chd1

Structure:

Chromo domain protein 1. Chain: a. Fragment: chromodomain 2. Synonym: atp-dependent helicase chd1. Engineered: yes

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: chd1/yer164w. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

NMR struc:

20 models

Authors:

M.Okuda,Y.Nishimura

Key ref:

M.Okuda et al. (2007). Structural polymorphism of chromodomains in Chd1. J Mol Biol, 365, 1047-1062. PubMed id: 17098252 DOI: 10.1016/j.jmb.2006.10.039

Date:

07-Sep-06 Release date: 28-Nov-06

Protein chain

P32657  (CHD1_YEAST) -  Chromo domain-containing protein 1

Seq: 1468 a.a.

Struc: 69 a.a.

 Gene Ontology (GO) functional annotation 

• Cellular component: nucleus (2 terms)
• Biological process: chromatin assembly or disassembly (1 term)
• Biochemical function: chromatin binding (1 term)

DOI no: 10.1016/j.jmb.2006.10.039

J Mol Biol 365:1047-1062 (2007)

PubMed id: 17098252

Structural polymorphism of chromodomains in Chd1.

M.Okuda, M.Horikoshi, Y.Nishimura.

ABSTRACT

Chromodomain from heterochromatin protein 1 and polycomb protein is known to be a lysine-methylated histone H3 tail-binding module. Chromo-helicase/ATPase DNA-binding protein 1 (CHD1) is an ATP-dependent chromatin remodeling factor, containing two tandem chromodomains. In human CHD1, both chromodomains are essential for specific binding to a K4 methylated histone H3 (H3 MeK4) peptide and are found to bind cooperatively in the crystal structure. For the budding yeast homologue, Chd1, the second but not the first chromodomain was once reported to bind to an H3 MeK4 peptide. Here, we reveal that neither the second chromodomain nor a region containing tandem chromodomains from yeast Chd1 bind to any lysine-methylated or arginine-methylated histone peptides that we examined. In addition, we examined the structures of the chromodomains from Chd1 by NMR. Although the tertiary structure of the region containing tandem chromodomains could not be obtained, the secondary structure deduced from NMR is well conserved in the tertiary structures of the corresponding first and second chromodomains determined individually by NMR. Both chromodomains of Chd1 demonstrate a structure similar to that of the corresponding part of CHD1, consisting of a three-stranded beta-sheet followed by a C-terminal alpha-helix. However, an additional helix between the first and second beta-strands, which is found in both of the first chromodomains of Chd1 and CHD1, is positioned in an entirely different manner in Chd1 and CHD1. In human CHD1 this helix forms the peptide-binding site. The amino acid sequences of the chromodomains could be well aligned on the basis of these structures. The alignment showed that yeast Chd1 lacks several key functional residues, which are responsible for specific binding to a methylated lysine residue in other chromodomains. Chd1 is likely to have no binding affinity for any H3 MeK peptide, as found in other chromodomain proteins.

Selected figure(s)

Figure 4.
Figure 4. Solution structures of yeast Chd1 chromodomains, Cd1 and Cd2. (a) Best-fit superposition of the ensemble of the final 20 NMR structures of Cd1 (left) and schematic ribbon diagram of the average structure (right). The side-chains of Cys207 and Cys246 are shown in yellow. (b) Best-fit superposition of the ensemble of the final 20 NMR structures of Cd2 (left) and schematic ribbon diagram of the average structure (right). Figure 4. Solution structures of yeast Chd1 chromodomains, Cd1 and Cd2. (a) Best-fit superposition of the ensemble of the final 20 NMR structures of Cd1 (left) and schematic ribbon diagram of the average structure (right). The side-chains of Cys207 and Cys246 are shown in yellow. (b) Best-fit superposition of the ensemble of the final 20 NMR structures of Cd2 (left) and schematic ribbon diagram of the average structure (right).

Figure 6.
Figure 6. Inter-domain interactions of chromodomains of yeast Chd1 and human CHD1. (a) Superposition of the ^1H, ^15N-TROSY-HSQC^41 spectra of yeast Chd1 Cd1, Cd2 and Cd12. All samples were dissolved in 20 mM potassium phosphate (pH 6.4), 50 mM NaCl, 10% ^2H[2]O. The spectra were measured at 20 °C on a Bruker Avance 800 spectrometer equipped with a cryo-probe. Cd1, red; Cd2, blue; Cd12, black. (b) Chemical shift differences of backbone ^1HN and ^15N between the isolated yeast Cd1, Cd2 and each domain of Cd12. Those of the side-chain ^1HN and ^15N of tryptophan residue are shown on the right. Chemical shift difference was calculated as Δδ = [(ΔHN)^2+(ΔN/5)^2]^1/2. A broken line indicates an average Δδ of 0.18. Residues with Δδ >0.30 are labeled with the name. (c, d) Superposition of yeast Chd1 Cd1 and Cd2 on the structure of human CHD1. Yeast Chd1 Cd1,orange; polymorphic region 1 of Cd1, brown; Cd2, blue; human CD12, light gray. (c) Interaction with linker helix. Residues with Δδ of average and over are shown and residues facing the H4 linker helix of CD12 are labeled by name and relevant Δδ. (d) Chemical shift changes around the C terminus of yeast Cd1. The C-terminal and nearby residues of yeast Cd1 are shown and labeled by name and relevant Δδ. (e) and (f) Inter-domain interaction. The inter-domain junction of human CHD1 chromodomains is shown. CD1, green and deep green; linker, light gray; CD2, cyan. Interacting residues are labeled by name together with corresponding residue names of yeast Chd1 and relevant Δδ colored green for human CD1, orange for yeast Cd1, light gray for human and yeast linker, cyan for human CD2 and blue for yeast Cd2. Figure 6. Inter-domain interactions of chromodomains of yeast Chd1 and human CHD1. (a) Superposition of the ^1H, ^15N-TROSY-HSQC[3]^41 spectra of yeast Chd1 Cd1, Cd2 and Cd12. All samples were dissolved in 20 mM potassium phosphate (pH 6.4), 50 mM NaCl, 10% ^2H[2]O. The spectra were measured at 20 °C on a Bruker Avance 800 spectrometer equipped with a cryo-probe. Cd1, red; Cd2, blue; Cd12, black. (b) Chemical shift differences of backbone ^1HN and ^15N between the isolated yeast Cd1, Cd2 and each domain of Cd12. Those of the side-chain ^1HN and ^15N of tryptophan residue are shown on the right. Chemical shift difference was calculated as Δδ = [(ΔHN)^2+(ΔN/5)^2]^1/2. A broken line indicates an average Δδ of 0.18. Residues with Δδ >0.30 are labeled with the name. (c, d) Superposition of yeast Chd1 Cd1 and Cd2 on the structure of human CHD1. Yeast Chd1 Cd1,orange; polymorphic region 1 of Cd1, brown; Cd2, blue; human CD12, light gray. (c) Interaction with linker helix. Residues with Δδ of average and over are shown and residues facing the H4 linker helix of CD12 are labeled by name and relevant Δδ. (d) Chemical shift changes around the C terminus of yeast Cd1. The C-terminal and nearby residues of yeast Cd1 are shown and labeled by name and relevant Δδ. (e) and (f) Inter-domain interaction. The inter-domain junction of human CHD1 chromodomains is shown. CD1, green and deep green; linker, light gray; CD2, cyan. Interacting residues are labeled by name together with corresponding residue names of yeast Chd1 and relevant Δδ colored green for human CD1, orange for yeast Cd1, light gray for human and yeast linker, cyan for human CD2 and blue for yeast Cd2.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2007, 365, 1047-1062) copyright 2007.

Figures were selected by an automated process.