Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	A Tail-Based Mechanism Drives Nucleosome Demethylation by the LSD2/NPAC Multimeric Complex.
Journal, issue, pages	Cell Rep, Vol. 27, Issue 2, Page 387-399.e7, Year 2019
Publish date	Apr 9, 2019
Authors	Chiara 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 Abstract	LSD1 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 links	Cell Rep / PubMed:30970244
Methods	SAS (X-ray synchrotron) / EM (single particle)
Resolution	4.02 - 7.95 Å
Structure data	SASDFU3: Lysine-specific Demethylase (LSD2) (Lysyne-specific Demethylase LSD2, LSD2) Method: SAXS/SANS SASDFV3: Cytokine-like nuclear factor dehydrogenase domain, NPAC DH (NPAC delta-261) Method: SAXS/SANS SASDFW3: Cytokine-like nuclear factor dehydrogenase domain, NPAC DH, plus native linker (NPAC delta-205) Method: SAXS/SANS 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 / FADYM ChemComp-ZN: Unknown entry ChemComp-HOH*: WATER
Source	homo sapiens (human) xenopus laevis (African clawed frog) synthetic construct (others)
Keywords	GENE REGULATION / Histone demethylation / chromatin reader / flavoenzyme / epigenetics / evolution of protein function / molecular recognition.