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TitleA Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
Journal, issue, pagesCell Rep, Vol. 27, Issue 2, Page 387-399.e7, Year 2019
Publish dateApr 9, 2019
AuthorsChiara Marabelli / Biagina Marrocco / Simona Pilotto / Sagar Chittori / Sarah Picaud / Sara Marchese / Giuseppe Ciossani / Federico Forneris / Panagis Filippakopoulos / Guy Schoehn / Daniela Rhodes / Sriram Subramaniam / Andrea Mattevi /
PubMed AbstractLSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase ...LSD1 and LSD2 are homologous histone demethylases with opposite biological outcomes related to chromatin silencing and transcription elongation, respectively. Unlike LSD1, LSD2 nucleosome-demethylase activity relies on a specific linker peptide from the multidomain protein NPAC. We used single-particle cryoelectron microscopy (cryo-EM), in combination with kinetic and mutational analysis, to analyze the mechanisms underlying the function of the human LSD2/NPAC-linker/nucleosome complex. Weak interactions between LSD2 and DNA enable multiple binding modes for the association of the demethylase to the nucleosome. The demethylase thereby captures mono- and dimethyl Lys4 of the H3 tail to afford histone demethylation. Our studies also establish that the dehydrogenase domain of NPAC serves as a catalytically inert oligomerization module. While LSD1/CoREST forms a nucleosome docking platform at silenced gene promoters, LSD2/NPAC is a multifunctional enzyme complex with flexible linkers, tailored for rapid chromatin modification, in conjunction with the advance of the RNA polymerase on actively transcribed genes.
External linksCell Rep / PubMed:30970244
MethodsEM (single particle)
Resolution4.02 - 7.95 Å
Structure data

4704

6r1t

EMDB-4704, PDB-6r1t:
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 1, free nuclesome
Method: EM (single particle) / Resolution: 4.02 Å

4705

6r1u

EMDB-4705, PDB-6r1u:
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 2
Method: EM (single particle) / Resolution: 4.36 Å

4710

6r25

EMDB-4710, PDB-6r25:
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 3
Method: EM (single particle) / Resolution: 4.61 Å

EMDB-4711:
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 4
Method: EM (single particle) / Resolution: 6.23 Å

EMDB-4712:
Structure of LSD2/NPAC-linker/nucleosome core particle complex: Class 5
Method: EM (single particle) / Resolution: 7.95 Å

Chemicals

ChemComp-FAD:
FLAVIN-ADENINE DINUCLEOTIDE / FAD*YM / Flavin adenine dinucleotide

ChemComp-ZN:
Unknown entry

ChemComp-HOH:
WATER / Water

Source
  • xenopus laevis (African clawed frog)
  • synthetic construct (others)
  • homo sapiens (human)
KeywordsGENE REGULATION / Histone demethylation / chromatin reader / flavoenzyme / epigenetics / evolution of protein function / molecular recognition.

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