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Molecular architecture of the Jumonji C family histone demethylase KDM5B

Jerzy Dorosz, Line Hyltoft Kristensen, Nanda G. Aduri, Osman Mirza, Rikke Lousen, Saskia Bucciarelli, Ved Mehta, Selene Sellés-Baiget, Sara Marie Øie Solbak, Anders Bach, Pablo Mesa, Pablo Alcon Hernandez, Guillermo Montoya, Tam T. T. N. Nguyen, Kasper D. Rand, Thomas Boesen & Michael Gajhede

By 8 April 2019 April 16th, 2019 No Comments

Scientific Reports, 2019, vol 9, Article number: 4019

DOI:

Abstract

The full length human histone 3 lysine 4 demethylase KDM5B (PLU-1/Jarid1B) has been studied using Hydrogen/Deuterium exchange mass spectrometry, homology modelling, sequence analysis, small angle X-ray scattering and electron microscopy. This first structure on an intact multi-domain Jumonji histone demethylase reveal that the so-called PLU region, in the central region of KDM5B, has a curved α-helical three-dimensional structure, that acts as a rigid linker between the catalytic core and a region comprising four α-helices, a loop comprising the PHD2 domain, two large intrinsically disordered loops and the PHD3 domain in close proximity. The dumbbell shaped and curved KDM5B architecture observed by electron microscopy is complementary to the nucleosome surface and has a striking overall similarity to that of the functionally related KDM1A/CoREST complex. This could suggest that there are similarities between the demethylation mechanisms employed by the two histone 3 lysine 4 demethylases at the molecular level.

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