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Structure paper

TitleStructural basis of paralog-specific KDM2A/B nucleosome recognition.
Journal, issue, pagesNat Chem Biol, Vol. 19, Issue 5, Page 624-632, Year 2023
Publish dateFeb 16, 2023
AuthorsCathy J Spangler / Aleksandra Skrajna / Caroline A Foley / Anh Nguyen / Gabrielle R Budziszewski / Dalal N Azzam / Eyla C Arteaga / Holly C Simmons / Charlotte B Smith / Nathaniel A Wesley / Emily M Wilkerson / Jeanne-Marie E McPherson / Dmitri Kireev / Lindsey I James / Stephen V Frye / Dennis Goldfarb / Robert K McGinty /
PubMed AbstractThe nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. To define the molecular basis of acidic ...The nucleosome acidic patch is a major interaction hub for chromatin, providing a platform for enzymes to dock and orient for nucleosome-targeted activities. To define the molecular basis of acidic patch recognition proteome wide, we performed an amino acid resolution acidic patch interactome screen. We discovered that the histone H3 lysine 36 (H3K36) demethylase KDM2A, but not its closely related paralog, KDM2B, requires the acidic patch for nucleosome binding. Despite fundamental roles in transcriptional repression in health and disease, the molecular mechanisms governing nucleosome substrate specificity of KDM2A/B, or any related JumonjiC (JmjC) domain lysine demethylase, remain unclear. We used a covalent conjugate between H3K36 and a demethylase inhibitor to solve cryogenic electron microscopy structures of KDM2A and KDM2B trapped in action on a nucleosome substrate. Our structures show that KDM2-nucleosome binding is paralog specific and facilitated by dynamic nucleosomal DNA unwrapping and histone charge shielding that mobilize the H3K36 sequence for demethylation.
External linksNat Chem Biol / PubMed:36797403 / PubMed Central
MethodsEM (single particle) / X-ray diffraction
Resolution1.98 - 3.6 Å
Structure data

26809

7uv9

EMDB-26809, PDB-7uv9:
KDM2A-nucleosome structure stabilized by H3K36C-UNC8015 covalent conjugate
Method: EM (single particle) / Resolution: 3.2 Å

EMDB-26810: KDM2B-nucleosome complex stabilized by H3K36C-UNC8015 covalent conjugate
Method: EM (single particle) / Resolution: 3.6 Å

PDB-7uva:
Crystal structure of KDM2A histone demethylase catalytic domain in complex with an H3C36 peptide modified by UNC8015
Method: X-RAY DIFFRACTION / Resolution: 1.98 Å

Chemicals

ChemComp-OH0:
N-heptanoyl-N-hydroxy-beta-alanine

ChemComp-FE:
Unknown entry / Iron

ChemComp-HOH:
WATER / Water

Source
  • homo sapiens (human)
  • synthetic construct (others)
  • mus musculus (house mouse)
KeywordsGENE REGULATION/DNA / chromatin nucleosome lysine demethylase JmjC protein / GENE REGULATION-DNA complex / GENE REGULATION / demethylase / histone / inhibitor

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