3KWQ

Structural characterization of H3K56Q nucleosomes and nucleosomal arrays

Summary for 3KWQ

• Entry DOI: 10.2210/pdb3kwq/pdb
• Related: 1AOI
• Descriptor: Histone H3.2, Histone H4, Histone H2A, ... (6 entities in total)
• Functional Keywords: nucleosome transcription k56 mutation, acetylation, chromosomal protein, dna-binding, methylation, nucleosome core, nucleus, phosphoprotein, isopeptide bond, ubl conjugation, structural protein-dna complex, structural protein/dna
• Biological source: Xenopus laevis (clawed frog,common platanna,platanna); More
• Cellular location: Nucleus: P84233 P62799 P02281; Nucleus (By similarity): Q6AZJ8
• Total number of polymer chains: 10
• Total formula weight: 176135.75

Authors

Lilyestrom, W.G.,Clark, N. (deposition date: 2009-12-01, release date: 2010-05-12, Last modification date: 2023-09-06)

Primary citation

Watanabe, S.,Resch, M.,Lilyestrom, W.,Clark, N.,Hansen, J.C.,Peterson, C.,Luger, K.
Structural characterization of H3K56Q nucleosomes and nucleosomal arrays.
Biochim.Biophys.Acta, 1799:480-486,

PubMed Abstract: The post-translational modification of histones is a key mechanism for the modulation of DNA accessibility. Acetylated lysine 56 in histone H3 is associated with nucleosome assembly during replication and DNA repair, and is thus likely to predominate in regions of chromatin containing nucleosome-free regions. Here we show by X-ray crystallography that mutation of H3 lysine 56 to glutamine (to mimic acetylation) or glutamate (to cause a charge reversal) has no detectable effects on the structure of the nucleosome. At the level of higher order chromatin structure, the K to Q substitution has no effect on the folding of model nucleosomal arrays in cis, regardless of the degree of nucleosome density. In contrast, defects in array-array interactions in trans ('oligomerization') are selectively observed for mutant H3 lysine 56 arrays that contain nucleosome-free regions. Our data suggests that H3K56 acetylation is one of the molecular mechanisms employed to keep chromatin with nucleosome-free regions accessible to the DNA replication and repair machinery.

PubMed: 20100606
DOI: 10.1016/j.bbagrm.2010.01.009

Experimental method

X-RAY DIFFRACTION (3.5 Å)