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.