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| 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 |
 Authors | 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. |
 External links | Proc Natl Acad Sci U S A / PubMed:37459529 / PubMed Central |
| 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 |
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 Keywords |  TRANSCRIPTION / Rpd3S / Histone deacetylase / HDAC / Clr6 / Rpd3 / Clr6S / Clr6 HDAC |
