2dy8
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Solution structure of the second chromodomain of yeast Chd1
OverviewOverview
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.
About this StructureAbout this Structure
2DY8 is a Single protein structure of sequence from Saccharomyces cerevisiae. Full crystallographic information is available from OCA.
ReferenceReference
Structural polymorphism of chromodomains in Chd1., Okuda M, Horikoshi M, Nishimura Y, J Mol Biol. 2007 Jan 26;365(4):1047-62. Epub 2006 Oct 14. PMID:17098252
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