Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.

Walport, LJ; Hopkinson, RJ; Chowdhury, R; Zhang, Y; Bonnici, J; Schiller, R; Kawamura, A; Schofield, CJ

Mechanistic and structural studies of KDM-catalysed demethylation of histone 1 isotype 4 at lysine 26.

journal contribution

posted on 2019-09-24, 12:56 authored by LJ Walport, RJ Hopkinson, R Chowdhury, Y Zhang, J Bonnici, R Schiller, A Kawamura, CJ Schofield

N-Methylation of lysyl residues is widely observed on histone proteins. Using isolated enzymes, we report mechanistic and structural studies on histone lysine demethylase (KDM)-catalysed demethylation of Nε -methylated lysine 26 on histone 1 isotype 4 (H1.4). The results reveal that methylated H1.4K26 is a substrate for all members of the KDM4 subfamily and that KDM4A-catalysed demethylation of H1.4K26me3 peptide is similarly efficient to that of H3K9me3. Crystallographic studies of an H1.4K26me3:KDM4A complex reveal a conserved binding geometry to that of H3K9me3. In the light of the high activity of the KDM4s on this mark, our results suggest JmjC KDM-catalysed demethylation of H1.4K26 may be as prevalent as demethylation on the H3 tail and warrants further investigation in cells.

Funding

This work was supported by grants from Cancer Research UK (C8717/A18245), the Wellcome Trust (091857/7/10/7) and the Biotechnology and Biological Sciences Research Council. This project has received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Skłodowska‐Curie grant agreement No 657292 to LJW. RJH acknowledges a William R. Miller Junior Research Fellowship, St. Edmund Hall. AK acknowledges a Royal Society Dorothy Hodgkin Fellowship (DH120028), ERC Starting Grant (679479) and the Engineering and Physical Science Research Council (EP/L003376/1). JB acknowledges a studentship from the Engineering and Physical Science Research Council (EP/M508111/1). We thank Tristan Smart for purification of KDM2A, the Structural Genomics Consortium for providing KDM5C protein, Sarah Madden for KDM4A protein and Eidarus Salah for KDM4B and KDM4D protein.

History

Citation

FEBS Letters, 2018, 592 (19), pp. 3264-3273

Author affiliation

/Organisation/COLLEGE OF SCIENCE AND ENGINEERING/Department of Chemistry

Version

VoR (Version of Record)

Published in

FEBS Letters

Publisher

Wiley, Federation of European Biochemical Societies

eissn

1873-3468

Acceptance date

2018-08-24

Copyright date

2018

Available date

2019-09-24

Publisher DOI

https://doi.org/10.1002/1873-3468.13231

Publisher version

https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.13231

Notes

Additional supporting information may be found online in the Supporting Information section at the end of the article. Fig. S1. Stereoview from a KDM4A.Ni.NOG.H1.4(18- 32)K26me3 crystal structure. Fig. S2. KDM4E catalyses lysine demethylation at H1.4K26. Fig. S3. KDM2A does not catalyse lysine demethylation at H1.4K26 under the tested conditions. Fig. S4. KDM3A does not catalyse lysine demethylation at H1.4K26 under the tested conditions. Fig. S5. KDM5C does not catalyse lysine demethylation at H1.4K26 under the tested conditions. Fig. S6. KDM6B does not catalyse lysine demethylation at H1.4K26 under the tested conditions. Fig. S7. KDM7A catalyses lysine demethylation at H1.4K26. Fig. S8. KDM4A catalyses lysine demethylation at H1.4K26. Fig. S9. KDM4B catalyses lysine demethylation at H1.4K26. Fig. S10. KDM4C catalyses lysine demethylation at H1.4K26. Fig. S11. KDM4D catalyses lysine demethylation at H1.4K26. Fig. S12. PHF8/KDM7B only catalyses lysine demethylation at H1.4K26 at high concentration. Fig. S13. Analysis of KDM4A demethylation by 1 H NMR. Fig. S14. Specific activity determination for KDM4 enzymes. Table S1. Peptide sequences used in this study. Table S2. Crystallographic data processing and refinement statistics.