Histone H3 binding to the PHD1 domain of histone demethylase KDM5A enables active site remodeling

James E Longbotham,Devrishi Goswami,Karen Ruiz,Cynthia M Chio,Danica Galonić Fujimori,Patrick R Griffin,Idelisse Ortiz Torres,Alma L Burlingame,Venkatasubramanian Dharmarajan,Michael J Trnka

doi:10.1038/s41467-018-07829-z

Abstract

Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. The in vitro demethylase activity of KDM5A is allosterically enhanced by binding of its product, unmodified H3 peptides, to its PHD1 reader domain. However, the molecular basis of this allosteric enhancement is unclear. Here we show that saturation of the PHD1 domain by the H3 N-terminal tail peptides stabilizes binding of the substrate to the catalytic domain and improves the catalytic efficiency of demethylation. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation. However, they vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. Furthermore, hydrogen/deuterium exchange coupled with mass spectrometry (HDX-MS) experiments reveal conformational changes in the allosterically enhanced state. Our findings may enable future development of anti-cancer therapies targeting regions involved in allosteric regulation.

Highlights

Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer
PHD1KDM5A binds the N-terminal tail of histone H3 with a preference for unmodified H3, and binding affinity decreases with an increase in H3K4 methylation[40]
Here we show that the allosteric stimulation of KDM5A activity, caused by binding of H3 N-terminal tail effector peptides to the

Summary

Introduction

Histone demethylase KDM5A removes methyl marks from lysine 4 of histone H3 and is often overexpressed in cancer. When present in saturating concentrations, differently modified H3 N-terminal tail peptides have a similar effect on demethylation They vary greatly in their affinity towards the PHD1 domain, suggesting that H3 modifications can tune KDM5A activity. A broader range of demethylation is possible by the jumonji C (JmjC) domain-containing family of KDMs (KDM2-9) that utilize a Fe(II)- and αketoglutarate (α-KG)-dependent mechanism as they are able to demethylate mono-, di- and tri- methylated lysines[7]. They predominantly act on histone proteins, but in some instances catalyze demethylation of non-histone substrates[8,9]. There is evidence for overexpression of KDM5A in cancer drug resistance in lung cancer models[26] as well as osteoporosis[27]

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