Recognition of Histone H3 Methylation States by the PHD1 Domain of Histone Demethylase KDM5A

Abstract

PHD reader domains are chromatin binding modules often responsible for the recruitment of large protein complexes that contain histone modifying enzymes, chromatin remodelers, and DNA repair machinery. A majority of PHD domains recognize Nterminal residues of histone H3 and are sensitive to the methylation state of Lys4 in histone H3 (H3K4). Histone demethylase KDM5A, an epigenetic eraser enzyme that contains three PHD domains, is often overexpressed in various cancers, and its demethylation activity is allosterically enhanced when its PHD1 domain is bound to the H3 tail. The allosteric regulatory function of PHD1 expands roles of reader domains, suggesting unique features of this chromatin interacting module. Our previous studies determined the H3 binding site of PHD1, although it remains unclear how the H3 tail interacts with the N-terminal residues of PHD1 and how PHD1 discriminates against H3 tails with varying degrees of H3K4 methylation. Here, we have determined the solution structure of apo and H3 bound PHD1. We observe conformational changes occurring in PHD1 in order to accommodate H3, which interestingly binds in a helical conformation. We also observe differential interactions of binding residues with differently methylated H3K4 peptides (me0, me1, me2, or me3), providing a rationale for PHD1's preference for lower methylation states of H3K4. We further assessed the contributions of various H3 interacting residues in the PHD1 domain to the binding of H3 peptides. The structural details of the H3 binding site could provide useful information to aid the development of allosteric small molecule modulators of KDM5A.

Diverse Functions of KDM5 in Cancer: Transcriptional Repressor or Activator?

“…PHD1 recognizes the unmethylated H3K4 histone tail, thereby enhancing the demethylase activity of KDM5 [20][21][22]. Mechanistically, the binding of PHD1 to the H3 tail allosterically sustains substrate binding to the catalytic domain, thus increasing enzymatic efficiency [23,24]. PHD1 has also been shown to recognize H3K9me3 in KDM5C [9].…”

Chromatin sensing by the auxiliary domains of KDM5C regulates its demethylase activity and is disrupted by X-linked intellectual disability mutations

“…We observe a dependence of binding on recognition of the H3R2 residue (Figure S2D). In addition, one of the largest chemical shift perturbations that occurs in PHD1 upon H3 tail binding is at the D343 residue, a homologous residue to D312 in KDM5A PHD1 that is part of the acidic pocket involved in H3R2 recognition (Figure S2E) (47). When mutated, it disrupts binding to H3 by KDM5A PHD1 (24).…”

Joining the PARty: PARP Regulation of KDM5A during DNA Repair (and Transcription?)

“…[51] Interestingly, these PHD domains are also involved in KDM5A DNA damage functions where the PHD1 domain is required to localize KDM5A to DSBs, while the PHD3 domain, which is dispensable for break recruitment, is necessary for KDM5A DSB repair functions downstream of break recruitment (Figure 1A). [34,52] KDM5A can promote DNA repair and transcriptional silencing through the recruitment of additional effector complexes, including ZMYND8 and the NuRD complex. [34] At DSBs, ZMYND8 requires the histone acetyltransferase (HAT) TIP60 and its bromodomain (BRD) to localize to breaks, suggesting an important, yet poorly understood, requirement for acetylation in this pathway.…”