Structural basis of Yta7 ATPase-mediated nucleosome disassembly

Abstract

Yta7 is a novel chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes and unfolds histone H3 to promote nucleosome disassembly for DNA replication. By cryo-EM analysis, we here show that Yta7 assembles a three-tiered hexamer ring with a top spiral, a middle AAA1-tier, and a bottom AAA2-tier. Unexpectedly, the Yta7 BRD stabilizes a four-stranded β-helix termed BRD- interacting motif (BIM) of the largely disordered N-terminal region, and they together assemble the spiral structure on top of the hexamer to engage the nucleosome. We found that the Yta7 BRD lacks key residues involved in acetylated peptide recognition, and as such, it is a noncanonical BRD that does not distinguish the H3 acetylation state, consistent with its role in general DNA replication. Upon nucleosome binding, the BRD/BIM spiral transitions into a flat ring to allow threading of the histone H3 tail into the AAA+ chamber. The H3 peptide is stabilized by the AAA1 pore loops 1 and 2 that spiral around the peptide. Therefore, Yta7 unfolds the nucleosome by pulling on the H3 peptide in a rotary staircase mechanism. Our study sheds light on the nucleosome recognition and unfolding mechanism of Yta7.

Structure of the Human ATAD2 AAA+ Histone Chaperone Reveals Mechanism of Regulation and Inter-subunit Communication

“…By rigid body docking, two copies of the human ATAD2 bromodomain (PDB ID: 3DAI) fit into the extra density in a head-to-tail arrangement, which is consistent with the orientation of the bromodomains observed in Yta7 (Fig. 6c) 41 .…”

“…6d). The resolution of the extra density is insufficient to unambiguously determine the identity of the substrate, but based on the volume of the extra density and previous structures of ATAD2 homologs 19,41 the most probable candidate would be a histone H3/H4 dimer.…”

“…Interestingly, the N-terminal LD was also proposed as a gate loop in recent structures of the ATAD2 yeast homolog, Yta7 based on its nucleotide-dependent conformational change near the nucleotide entry pocket 41 . Although the gate loop in Yta7 is not docked to seam subunits as in ATAD2 (discussed in more detail below), the idea of the N-terminal LD as a gating element that regulates nucleotide hydrolysis and exchange might be conserved between species.…”