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The ATPase motor of the Chd1 chromatin remodeler is negatively regulated by a pair of N‐terminal chromodomains

ATP‐dependent chromatin remodeling complexes play a central role in the assembly, disassembly, and repositioning of nucleosomes. While the remodeling reaction is driven by a conserved ATPase motor, it is not known how this motor is regulated by auxiliary domains. We have solved the crystal structure of the Chd1 chromodomains coupled to the ATPase motor, which suggests that the chromodomains negatively regulate the ATPase motor. In the crystal, a conserved acidic helical linker between the chromodomains contacts a DNA‐binding surface on the ATPase motor, blocking DNA access to the motor. Naked DNA is a poor substrate for the Chd1 ATPase, and we find that disruption of this chromodomain‐ATPase interface permits naked DNA to stimulate ATPase activity to the same extent as nucleosome substrates. Small‐angle X‐ray scattering (SAXS) experiments suggest that in solution the chromodomains are not rigidly fixed against the ATPase motor but instead may occupy conformations distinct from that observed in the crystal structure. We propose that the chromodomains allow Chd1 to distinguish between nucleosomes and naked DNA by physically gating access to the ATPase motor.