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-Structure paper
Title | Class I histone deacetylase complex: Structure and functional correlates. |
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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 |