Histone Peptide Recognition by KDM5B-PHD1: A Case Study

Abstract

A detailed understanding of the energetic contributions to histone peptide recognition would be valuable for a better understanding of chromatin anchoring mechanisms and histone diagnostic design. Here, we probed the energetic contributions to recognize the same unmodified histone H3 by three different plant homeodomain (PHD) H3K4me0 readers: hKDM5B-PHD1 (first PHD finger of hKDM5B), hBAZ2A-PHD, and hAIRE-PHD1. The energetic contributions of residues differ significantly from one complex to the next. For example, H3K4A substitution completely aborts the formation of the hAIRE-histone peptide complex, while it has only a small destabilizing effect on binding of the other readers, even though H3K4 methylation disrupts all three complexes. Packing density suggests that methylation of more tightly packed Lys/Arg residues can disrupt binding, even if the energetic contribution is small. The binding behavior of hKDM5B-PHD1 and hBAZ2A-PHD is similar, and like PHD H3R2 readers, both possess a pair of Asp residues in the treble clef for interaction with H3R2. PHD subtype sequences, especially the tandem PHD-PHD fingers, show enrichment in the treble clef Asp residues, suggesting that it is a subtype-specific property. These Asp residues make significant energetic contributions to the formation of the hKDM5B-histone peptide complex, suggesting that there are interactions in addition to those reported in the recent NMR structure. However, the presence of the treble clef Asp in PHD sequences may not always be sufficient for histone peptide binding. This study showcases reader-histone peptide interactions in the context of residue conservation, energetic contributions, interfacial packing, and sequence-based reader subtype predictability.

Structural basis of molecular recognition of helical histone H3 tail by PHD finger domains

“…Our data show that K4-T6 residues are not critical for binding to the PHD fingers of BAZ2A and BAZ2B, while R2-T3 are crucial. These results are consistent with those recently reported by Chakravarty et al [37] for BAZ2A PHD and the first PHD domain of KDM5B but are distinct from the results of the first PHD of AIRE, which is known to bind H3 in an extended conformation. In that case, the T3A mutation was tolerated, whereas the K4A mutation abolished binding [37].…”

“…Among these are all the PHD fingers of the BAZ family, CREBBP [33] and the homologous EP300 [34], all members of the DPF family of proteins: DPF1, DPF2 and DPF3, as well as members of the KDM5/JARID1 histone lysine demethylase family: KDM5A, KDM5B, KDM5C and KDM5D [35,36]. Interestingly, we noted that, in all four KDM5 members, only the first PHD domain, which like BAZ2A/B recognizes unmodified K4, but not the second or third, has an acidic residue at this position, and this is mutually exclusive with the presence of the conserved tryptophan residue characteristic of the aromatic cage for methyl-K4 recognition (Figure 2C) [37]. Indeed, only 5 of the 36 sequences containing the acidic wall residue also contain this tryptophan (Supplementary Figure S5).…”

FRETting about the affinity of bimolecular protein–protein interactions

“…For our interests in histone‐mediated PPIs, we have also utilized the FRET assay for rapid interpretation of interactions between N‐terminal unmodified histone H3 and histone readers such as the PHD finger module [Fig. (b)].…”

“…The K D values of the listed interactions were obtained from the following references: ePDZ (molecular clamp), MDM2, SAP SH2, AIRE PHD, cpSPRP43, YAP WW, hRPA, ubiquitin, and Nck2 SH3.…”

Targeting Ligandable Pockets on Plant Homeodomain (PHD) Zinc Finger Domains by a Fragment-Based Approach

“… 10 , 11 It was also shown that the mutation to alanine of the second and third residues of the H3 histone tail abolishes binding. 11 , 20 Therefore, we hypothesized that the H3 N-terminal 3-mer motif “ART” might be essential to anchor the histone tail to the surface of BAZ2 PHDs. To test this hypothesis, we synthesized and biophysically characterized the binding of ART against both PHD domains.…”