Structural basis for lower lysine methylation state-specific readout by MBT repeats of L3MBTL1 and an engineered PHD finger

Abstract

Human L3MBTL1, which contains three malignant brain tumor (MBT) repeats, binds monomethylated and dimethylated lysines, but not trimethylated lysines, in several histone sequence contexts. In crystal structures of L3MBTL1 complexes, the monomethyl- and dimethyllysines insert into a narrow and deep cavity of aromatic residue-lined pocket 2, while a proline ring inserts into shallower pocket 1. We have also engineered a single Y to E substitution within the aromatic cage of the BPTF PHD finger, resulting in a reversal of binding preference from trimethyl- to dimethyllysine in an H3K4 sequence context. In both the "cavity insertion" (L3MBTL1) and "surface groove" (PHD finger) modes of methyllysine recognition, a carboxylate group both hydrogen bonds and ion pairs to the methylammonium proton. Our structural and binding studies of these two modules provide insights into the molecular principles governing the decoding of lysine methylation states, thereby highlighting a methylation state-specific layer of histone mark readout impacting on epigenetic regulation.

Figure 1. Structural and Functional Characterization of L3MBTL1 as a Lower Lysine Methylation State-Specific Effector Module

(A) Domain architecture of the L3MBTL_1197–526 used for structural and functional study in this figure. (B) (Left panel) Fluorescence polarization titration curves for wild-type L3MBTL1_197–526 with H3_1–15 peptides containing either unmodified (blue) or mono- (red), di- (green), and tri- (purple) methyllysine at position 9. (Right panel) Fluorescence polarization titration curves for H3_1–15K9me1 peptide binding to L3MBTL119_7–526 proteins containing Asp to Asn mutants in each of the three binding pockets. The binding curves are black for wild-type L3MBTL1, orange for pocket 1 D248N mutant, red for pocket 2 D355N mutant, and cyan for pocket 3 D459N mutant. The apparent dissociation constants (K_D) are listed in each panel. In each case, parameters are reported as the mean (±average deviation from the mean) obtained from three independent titration experiments. (C) Surface representation of crystal structure of L3MBTL1_197–526-H1.5_23–27K27me2 complex with “PS”-containing C-terminal tail of a symmetry-related L3MBTL1 molecule in pocket 1, K27me2 in pocket 2, and PEG ligand in pocket 3. The red to blue coloring encodes an electrostatic potential distribution ranging from −20 to 20 kT/e on the protein surface. (D to F) Structural details of Pro insertion of PS peptide into pocket 1 (D), K27me2 insertion into pocket 2 (E), and PEG ligand insertion into one of the entrances to pocket 3 (F).The aromatic residues of each pocket are highlighted in the “dotted” van der Waals radius representation. The hydrogen bonds involving the Asp residue lining the aromatic cage are shown as red dashes, with bond length listed nearby.

Figure 2. Pro-Ser Step-Containing Peptide Binding by L3MBTL1 Pocket 1

(A) Domain architecture of the L3MBTL1 constructs used for structural and functional study in this figure. For the L3MBTL1-H3.3 construct, a Gly-Gly-Gly linker was used to separate L3MBTL1 and the covalently attached histone 3.3_28–34 segment. (B) Insertion of proline into a shallow cavity of symmetry-related L3MBTL1 pocket 1 in the Kme2-L3MBTL1 complex is shown. The Pro ring is sandwiched within the narrow walls at the base of the pocket. The interior parts of the surface are colored in gray, and exterior parts are colored by their electrostatic potential as described for Figure 1C. The Pro ligand is shown in the dotted van der Waals radius representation. The “EPS” peptide segment is shown, with part of the Ser omitted from the drawing for clarity. (C) Relative positioning of PS step containing C-terminal L3MBTL1 segment in pocket 1 and Kme2 in pocket 2 on the same L3MBTL1 surface in the Kme2-L3MBTL1 complex. (D) Stereo view of the PS step containing H3.3 SAPSTGG segment with its Pro ring inserted into pocket 1 of the Kme2-L3MBTL1-H3.3_28–34 complex. Key residues participating in pocket formation are shown in stick representation (cyan) with main-chain atoms omitted for clarity. Water molecules are shown as small red spheres and hydrogen bonds indicated by dashed red lines. (E) Stereo view of the relative positioning of PS step containing H3.3 SAPSTGG segment in pocket 1 and Kme2 in pocket 2 on the same L3MBTL1 surface in the Kme2- L3MBTL1-H3.3_28–34 complex. Note that the type II β-turn formed at the “APST” motif in pocket 1 helps to direct the C-terminal GG segment of H3.3 toward the Kme2-bound pocket 2. Water molecules are shown as small red spheres and hydrogen bonds indicated by dashed red lines.

Figure 3. Structural Details for Specific Readout of Kme1 and Kme2 by L3MBTL1 Pocket 2

(A and C) Stereo view of Kme2 (A) and Kme1 (C) bound to L3MBTL1 pocket 2. Four strands of the β subunit core are numbered 1,2,3, and 4 and colored in gray. The gating (Lg), caging (Lc), and extra (Le) loops are highlighted in orange. Key residues participating in pocket formation are shown in stick representation (cyan) with main-chain atoms omitted for clarity. Water molecules that mediate hydrogen bonding between L3MBTL1 and Kme2/Kme1 are shown as small red spheres (C). The F_o − F_c omit electron densities (green) are contoured at 4.5 σ level. (Band D) Protein surface cut-away views of Kme2(B) and Kme1 (D). The color code is as described for Figure 2B. Kme2(B)and Kme1 (D) are inserted into a deep, narrow, and negatively charged cavity in L3MBTL1 pocket 2. (E) Superpositioned views of Kme2 (beige) and Kme1 (cyan) inserted into pocket 2, based on the least-squares fitting of Cα atoms within the second MBT module (349–416) of L3MBTL1. (F) Cartoon representation of the three-leaved propeller architecture of L3MBTL1. The MBT repeats 1, 2, and 3 are colored green, cyan, and red, respectively. The bound Kme1 ligand within pocket 2 is represented in CPK mode. Two α helices in each of the three MBT modules are labeled α′_N and α_C and shown as cylinders. (G) Sequence comparison among different MBT modules and other related methyllysine reader modules within the Royal family. Key residues participating or predicted to participate in pocket formation are shaded in yellow, and those that are directly involved in methyllysine recognition are boxed in red. Accession numbers are as follows: hL3MBTL1, AAH39820.1; hSCML2, AAH64617; dsfMBT, NP_723786.1; hCGI72, NP_057102; 53BP1, PDB_id: 2IG0; and HP1, PDB_id:1KNA. All listed modules (MBT, tudor, and chromo) generate their reader pockets at one end of a common “SH3-like” β-barrel. β_H denotes the histone H3(5–10)K9me peptide.

Figure 4. Stereo Views of Pocket 2 Comparing Superpositioned Kme2-Bound Wild-Type and Mutant L3MBTL1 Complexes

(A–D) The wild-type L3MBTL1 complex with bound Kme2 is shown in beige (A–D). The D355N mutant complex is shown in light blue (A), the D355A mutant is shown in dark blue (B), the N358Q mutant is shown in light green (C), and the N358A mutant is shown in dark green (D). Kme2 was not detected in pocket 2 for complexes with D355N (A), D355A (B), N358Q (C), and N358A (D). Superpositioning is based on least-squares fitting of Cα atoms within the second MBT module (349–416) of L3MBTL1.

Figure 5. Structural and Functional Analysis of State-Specific Readout of Kme2 Marks by an Engineered Y17E BPTF PHD Finger

(A) Surface plasmon resonance curves monitoring the methylation state-dependent binding and release of H3K4 peptides by the BPTF PHD finger (left panel, previously reported in Li et al., 2006 and included for comparison purposes) and its Y17E mutant (right panel). Color representations are K4me1 (red), K4me2 (green), and K4me3 (blue). (B) Fluorescence polarization curves monitoring the methylation state-dependent binding of H3K4 peptides by the BPTF PHD finger and its Y17E mutant (right panel). Color representations are unmodified K4 (black), K4me1 (red), K4me2 (green), and K4me3 (blue). (C) Electrostatic potential surface representation of BPTF Y17E PHD finger in complex with H3_1–9K4me2 peptide. Red to blue coloring represents a surface charge distribution from −20 to 20 kT/e. This view emphasizes the surface groove recognition mode of complex formation. (D) Position of Kme2 side chain of H3_1–9K4me2 peptide inserted into an engineered Glu-containing aromatic-lined cage of the Y17E mutant BPTF PHD finger. The aromatic residues are shown in the dotted van der Waals radius representation. The proper positioning and orientation of Y17E side chain results in a direct hydrogen bond (≈2.7 Å) between the dimethylammonium group of K4me2 and the carboxylate of E17. (E) Summary of fluorescence polarization-based binding constants. Fluorescence anisotropy of the fluorescein-labeled peptide was used to determine the apparent dissociation constant K_D (based on an assumption of a 1:1 binding stoichiometry). In each case, parameters are reported as the mean (±average deviation from the mean) obtained from two independent titration experiments.