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TitleClass I histone deacetylase complex: Structure and functional correlates.
Journal, issue, pagesProc Natl Acad Sci U S A, Vol. 120, Issue 30, Page e2307598120, Year 2023
Publish dateJul 25, 2023
AuthorsXiao Wang / Yannan Wang / Simiao Liu / Yi Zhang / Ke Xu / Liting Ji / Roger D Kornberg / Heqiao Zhang /
PubMed AbstractThe 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 linksProc Natl Acad Sci U S A / PubMed:37459529 / PubMed Central
MethodsEM (single particle)
Resolution3.2 - 4.6 Å
Structure data

35416

8ifg

EMDB-35416, PDB-8ifg:
Cryo-EM structure of the Clr6S (Clr6-HDAC) complex from S. pombe
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-35417: Clr6 HDAC (Clr6S)-nucleosome complex
Method: EM (single particle) / Resolution: 3.9 Å

EMDB-36278: Rpd3S-nucleosome (H3K36me3 modified)
Method: EM (single particle) / Resolution: 4.6 Å

Chemicals

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER

Source
  • Schizosaccharomyces pombe (fission yeast)
  • schizosaccharomyces pombe (strain 972 / atcc 24843) (yeast)
KeywordsTRANSCRIPTION / Rpd3S / Histone deacetylase / HDAC / Clr6 / Rpd3 / Clr6S / Clr6 HDAC

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