+Search query
-Structure paper
Title | Class I histone deacetylase complex: Structure and functional correlates. |
---|---|
Journal, issue, pages | Proc Natl Acad Sci U S A, Vol. 120, Issue 30, Page e2307598120, Year 2023 |
Publish date | Jul 25, 2023 |
![]() | Xiao Wang / Yannan Wang / Simiao Liu / Yi Zhang / Ke Xu / Liting Ji / Roger D Kornberg / Heqiao Zhang / ![]() ![]() |
PubMed Abstract | The Clr6S complex, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structure of ...The Clr6S complex, a class I histone deacetylase complex, functions as a zinc-dependent enzyme to remove acetyl groups from lysine residues in histone tails. We report here the cryo-EM structure of Clr6S alone and a cryo-EM map of Clr6S in complex with a nucleosome. The active center, revealed at near-atomic resolution, includes features important for catalysis-A water molecule coordinated by zinc, the likely nucleophile for attack on the acetyl-lysine bond, and a loop that may position the substrate for catalysis. The cryo-EM map in the presence of a nucleosome reveals multiple Clr6S-nucleosome contacts and a high degree of relative motion of Clr6S and the nucleosome. Such flexibility may be attributed to interaction at a site in the flexible histone tail and is likely important for the function of the deacetylase, which acts at multiple sites in other histone tails. |
![]() | ![]() ![]() ![]() |
Methods | EM (single particle) |
Resolution | 3.2 - 4.6 Å |
Structure data | EMDB-35416, PDB-8ifg: ![]() EMDB-35417: Clr6 HDAC (Clr6S)-nucleosome complex ![]() EMDB-36278: Rpd3S-nucleosome (H3K36me3 modified) |
Chemicals | ![]() ChemComp-ZN: ![]() ChemComp-HOH: |
Source |
|
![]() | ![]() ![]() ![]() |