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TitleThe Saccharomyces cerevisiae Yta7 ATPase hexamer contains a unique bromodomain tier that functions in nucleosome disassembly.
Journal, issue, pagesJ Biol Chem, Vol. 299, Issue 2, Page 102852, Year 2023
Publish dateDec 30, 2022
AuthorsFeng Wang / Xiang Feng / Qing He / Hua Li / Huilin Li /
PubMed AbstractThe Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to ...The Saccharomyces cerevisiae Yta7 is a chromatin remodeler harboring a histone-interacting bromodomain (BRD) and two AAA+ modules. It is not well understood how Yta7 recognizes the histone H3 tail to promote nucleosome disassembly for DNA replication or RNA transcription. By cryo-EM analysis, here we show that Yta7 assembles a three-tiered hexamer with a top BRD tier, 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. The BIM motif is unique to the baker's yeast, and we show both BRD and BIM contribute to nucleosome recognition. We found that Yta7 binds both acetylated and nonacetylated H3 peptides but with a higher affinity for the unmodified peptide. This property is consistent with the absence of key residues of canonical BRDs involved in acetylated peptide recognition and the role of Yta7 in general nucleosome remodeling. Interestingly, the BRD tier exists in a spiral and a flat-ring form on top of the Yta7 AAA+ hexamer. The spiral is likely in a nucleosome-searching mode because the bottom BRD blocks the entry to the AAA+ chamber. The flat ring may be in a nucleosome disassembly state because the entry is unblocked and the H3 peptide has entered the AAA+ chamber and is stabilized by the AAA1 pore loops 1 and 2. Indeed, we show that the BRD tier is a flat ring when bound to the nucleosome. Overall, our study sheds light on the nucleosome disassembly by Yta7.
External linksJ Biol Chem / PubMed:36592926 / PubMed Central
MethodsEM (single particle)
Resolution3.0 - 10.0 Å
Structure data

EMDB-26682: Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS in state I
Method: EM (single particle) / Resolution: 5.6 Å

26695

7uqi

EMDB-26695, PDB-7uqi:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ADP
Method: EM (single particle) / Resolution: 3.8 Å

26696

7uqj

EMDB-26696, PDB-7uqj:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ATPgS and histone H3 tail in state II
Method: EM (single particle) / Resolution: 3.0 Å

26697

7uqk

EMDB-26697, PDB-7uqk:
Cryo-EM structure of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to ADP
Method: EM (single particle) / Resolution: 3.1 Å

EMDB-28815: Cryo-EM of the S. cerevisiae chromatin remodeler Yta7 hexamer bound to nucleosome
Method: EM (single particle) / Resolution: 10.0 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

ChemComp-AGS:
PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER / ATP-gamma-S, energy-carrying molecule analogue*YM

ChemComp-MG:
Unknown entry

Source
  • saccharomyces cerevisiae (brewer's yeast)
KeywordsTRANSFERASE / AAA+ ATPase / chromatin remodeler

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