Crystal structure of the chromodomain helicase DNA-binding protein 1 (Chd1) DNA-binding domain in complex with DNA.
Chromatin remodelers are ATP-dependent machines that dynamically alter the chromatin packaging of eukaryotic genomes by assembling, sliding, and displacing nucleosomes. The Chd1 chromatin remodeler possesses a C-terminal DNA-binding domain that is required for efficient nucleosome sliding and believed to be essential for sensing the length of DNA flanking the nucleosome core. The structure of the Chd1 DNA-binding domain was recently shown to consist of a SANT and SLIDE domain, analogous to the DNA-binding domain of the ISWI family, yet the details of how Chd1 recognized DNA were not known. Here we present the crystal structure of the Saccharomyces cerevisiae Chd1 DNA-binding domain in complex with a DNA duplex. The bound DNA duplex is straight, consistent with the preference exhibited by the Chd1 DNA-binding domain for extranucleosomal DNA. Comparison of this structure with the recently solved ISW1a DNA-binding domain bound to DNA reveals that DNA lays across each protein at a distinct angle, yet contacts similar surfaces on the SANT and SLIDE domains. In contrast to the minor groove binding seen for Isw1 and predicted for Chd1, the SLIDE domain of the Chd1 DNA-binding domain contacts the DNA major groove. The majority of direct contacts with the phosphate backbone occur only on one DNA strand, suggesting that Chd1 may not strongly discriminate between major and minor grooves.
Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218.
Amit
A
Sharma
Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218.
Katherine R
KR
Jenkins
Biology Department, Brookhaven National Laboratory, Upton, New York 11973.
Annie
A
Héroux
Thomas C. Jenkins Department of Biophysics, Johns Hopkins University, Baltimore, Maryland 21218. Electronic address: gdbowman@jhu.edu.
Gregory D
GD
Bowman
D002843:Chromatin / Q000737:chemistry; D042002:Chromatin Assembly and Disassembly; D018360:Crystallography, X-Ray / Q000379:methods; D004247:DNA / Q000737:chemistry; D004271:DNA, Fungal / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D008958:Models, Molecular; D008968:Molecular Conformation; D009696:Nucleic Acids / Q000737:chemistry; D009707:Nucleosomes / Q000378:metabolism; D011485:Protein Binding; D017433:Protein Structure, Secondary; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000378:metabolism*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics* / Q000378:metabolism
C489847:CHD1 protein, S cerevisiae; D002843:Chromatin; D004271:DNA, Fungal; D004268:DNA-Binding Proteins; D009696:Nucleic Acids; D009707:Nucleosomes; D029701:Saccharomyces cerevisiae Proteins; D004247:DNA