Structural Insights into Ternary Complex Formation of Human CARM1

Nov 9, 2015 - Here, the crystal structures of human CARM1 with the S-adenosylmethione (SAM) mimic sinefungin and three different peptide sequences fro...
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Structural Insights into Ternary Complex Formation of Human CARM1 with Various Substrates P. Ann Boriack-Sjodin,* Lei Jin,† Suzanne L. Jacques, Allison Drew, Chris Sneeringer,‡ Margaret Porter Scott,‡ Mikel P. Moyer,§ Scott Ribich, Oscar Moradei, and Robert A. Copeland Epizyme, Inc. 400 Technology Square, Cambridge, Massachusetts 02139, United States ABSTRACT: Coactivator-associated arginine methyltransferase 1 (CARM1) is a protein arginine N-methyltransferase (PRMT) enzyme that has been implicated in a variety of cancers. CARM1 is known to methylate histone H3 and nonhistone substrates. To date, several crystal structures of CARM1 have been solved, including structures with small molecule inhibitors, but no ternary structures with nucleoside and peptide substrates have been reported. Here, the crystal structures of human CARM1 with the S-adenosylmethione (SAM) mimic sinefungin and three different peptide sequences from histone H3 and PABP1 are presented, with both nonmethylated and singly methylated arginine residues exemplified. This is the first example of multiple substrate sequences solved in a single PRMT enzyme and demonstrates how the CARM1 binding site is capable of accommodating a variety of peptide sequences while maintaining a core binding mode for the unmethylated and monomethylated substrates. Comparison of these with other PRMT enzyme-peptide structures shows hydrogen bonding patterns that may be thematic of these binding sites.

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mechanisms.10 Consistent with its role as a transcriptional coactivator, its nonhistone substrates include nuclear receptors and nuclear receptor-associated coactivators such as SRC-3,11 NCOA2,2 and EP300.12 CARM1 also plays a multifaceted role in the regulation of post-transcriptional processing and turnover through the methylation of proteins such as PABP1 and SmB.8,13,14 CARM1 may therefore impact gene expression at multiple levels, both as a direct regulator of transcription as well as through modification of post-transcriptional RNA processing. Overexpression of CARM1 in multiple cancer types suggests that its dysregulation can contribute to oncogenesis; however the mechanism by which this occurs is currently not well understood. The PRMT family of enzymes has been well characterized by X-ray crystallography. To date, structures of the methyltransferase domains of mammalian proteins are publically available for PRMT1, -3, -5, -6, and CARM1. Crystal structures of the catalytic domains of CARM1 were first solved in 2007,15,16 revealing the catalytic core common to the type I PRMTs that includes a methyltransferase (MTase) domain that is similar to the Rossman fold and includes the residues needed for SAM binding, a β-barrel domain, and a dimerization domain. CARM1 also contains domains at its N- and C-termini that are unique in the type I enzymes and are important for its function.17 The structure of the N-terminal domain alone revealed this domain to have a PH-like fold; however, a larger

ore than half of the known chromatin-remodeling enzymes add or remove methyl groups from protein or DNA substrates; thus protein methylation is a key driver of biological processes. Dysregulation of methylation has been linked to a variety of diseases including cancer. The type I protein arginine methyltransferase (PRMT) CARM1 (coactivator-associated arginine methyltransferase 1, also known as PRMT4) has been implicated in multiple cancers including AML1 and breast,2 prostate,3 lung,4 and colorectal5 carcinomas, making it a potential target for drug discovery efforts. Ten mammalian PRMTs have been identified to date and are classified into three subclasses,6 distinguished by their ability to transfer one or two methyl groups to the nitrogen atoms of the guanidinium side chains of arginine residues using Sadenosylmethionine (SAM) as the methyl donor. The addition of methyl groups by type I PRMTs (PRMT1, PRMT2, PRMT3, PRMT6, PRMT8, and CARM1) can result in both ωNG-monomethyl (Rme1) and asymmetrical ω-NG-dimethylarginine (aDMA). In contrast, type II enzymes, including PRMT5, perform symmetric dimethylation (sDMA). CARM1 catalyzes the transfer of up to two methyl groups to arginine residues on protein substrates.7 CARM1 methylates multiple histone and nonhistone substrates through which it can mediate effects on many cellular processes including transcriptional coactivation, RNA splicing and processing, control of the cell cycle, and cellular differentiation. The substrate motifs preferred by CARM1 are distinct from those preferred by other type I RMTs including PRMT1.8 CARM1’s histone substrates include arginine 17 of histone H3 (H3R17) and H3R26.9 H3R17 methylation is primarily thought to promote active transcription through the recruitment of transcriptional elongation complexes and other © XXXX American Chemical Society

Special Issue: Epigenetics Received: September 24, 2015 Accepted: November 9, 2015

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DOI: 10.1021/acschembio.5b00773 ACS Chem. Biol. XXXX, XXX, XXX−XXX

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sequence-specific interactions. Additionally, understanding protein dynamics within the peptide binding site could be beneficial for any drug discovery efforts that may occur for CARM1. Therefore, crystallization experiments were initiated using a truncated, catalytically active form of CARM1 (amino acids 134−479). Two peptide sequences from known substrates of CARM1, histone H3 and PABP1, were chosen for the crystallization experiments (Figure 1). The first publication identifying

construct including both the N-terminal domain and methyltransferase domain showed this domain to be flexible with respect to the catalytic domain.15 In 2011, crystal structures of two CARM1-inhibitor complexes were the first to document inhibitors bound to a PRMT enzyme and showed two different chemical scaffolds bound in the arginine pocket.18 Although researchers have had marked success in solving crystal structures of several lysine methyltransferases in the presence of peptides, structures of complexes with the PRMT family and their protein substrates have been more elusive. The first published structure of a ternary complex with an arginine methyltransferase was of rat PRMT1 with an RGG repeat sequence and the product S-adenosyl homocysteine (SAH).19 Although density for the substrate arginine residue was seen in the binding pocket, the remaining density for the peptides could not be resolved fully, potentially due to a mixture of binding states. More recently, the structure of the human PRMT5:MEP50 complex was solved with a peptide from histone H4 and a SAM analog.20 With clear density for eight residues of the peptide, this provided the first elucidation of the interactions involved in the extended binding site and revealed the critical role of two glutamic acids (Glu435 and Glu444 in PRMT5) in enzyme catalysis. A structure of PRMT7 from the parasitic protozoan Trypanosoma brucei with an unmethylated histone H4 peptide has also been solved with three visible peptide residues.21 Nature often seeks to achieve maximal parsimony in cell biology, by utilizing a single protein for multiple biochemical functions. This principle is well-exemplified by CARM1, a protein that participates in a cornucopia of protein−protein and protein−DNA interactions, as well as catalyzing mono- and dimethylation of arginine residues within a spectrum of protein substrates. Understanding how CARM1 achieves this catalytic promiscuity and what the common recognition determinants are for its various substrates is a critical unanswered question for this enzyme, and for the PRMT family in general. In this report, we address this question by presenting the crystal structures of human CARM1 with the SAM mimic sinefungin and three different peptide sequences from histone H3 and PAPB1, exemplifying both nonmethylated and monomethylated arginine-containing substrates. This is the first PRMT for which structures of multiple substrate sequences have been solved by crystallographic methods, and the first example of defined density for a type I PRMT substrate for amino acids beyond the substrate arginine. This wealth of structural information provides an opportunity to compare these structures to determine the key binding interactions that are conserved between substrates. Additionally, it provides insight into changes made by the enzyme to accommodate different primary sequences adjacent to the arginine substrate. This information may be useful for targeting CARM1 with small molecule inhibitors, and comparisons of these structures with known inhibitors are discussed within.

Figure 1. Peptide sequences used for crystallization. Labels refer to the substrate from which the sequence was based, the arginine residue number seen in the arginine channel of CARM1, and the methylation state of the arginine in the substrate channel. Sequences have been aligned around the arginine residue that occupies the catalytic site, shown in bold text. Arginine residues are denoted with zero, one, or two marks indicting un-, mono-, or dimethylated residues. Residues visible in all monomers of the asymmetric unit are in green; residues seen in at least 1 monomer are in blue. Numbers in parentheses indicate the number of peptides in the asymmetric unit. Btn = Biotin. Ahx = aminohexanoic acid.

CARM1 as a methyltransferase also identified histone H3 as a CARM1 substrate.7 Extensive characterization of the biochemical activity against histone H3 has been performed (S. Jacques, unpublished data); therefore, histone H3 peptides were chosen for structural analysis to complement the kinetic studies. CARM1 is also known to methylate nonhistone substrates. PABP1 was the first nonhistone substrate for CARM1 to be identified, and methylation of PABP1 is known to occur at arginine residues at positions 455 and 460.8 Notably, PABP1 and histone H3 sequences contain proline residues at different locations relative to the arginine substrate. Selection of these sequences provides an opportunity to understand how the CARM1 binding site accommodates this conformationally restrictive amino acid in various sites within the peptide sequence. For PABP1, peptides containing arginine residues in various methylation states at positions 455 and 460 were synthesized. For H3, unmethylated peptides containing lysine mutations for arginine residues at positions 17 or 26 were synthesized along with wild type sequences, while a methylated peptide at Arg17 with a lysine point mutation at residue 26 was made. Peptide sequences and methylation states exemplified in this study are shown in Figure 1. Crystallization and Structure Determination of CARM1−Peptide Complexes. Co-crystallization and soaking experiments were attempted with all peptide substrates with nucleoside cofactors SAM and sinefungin. Crystals grown in the presence of SAM and peptide resulted in structures with the product of the methyl transfer reaction, SAH, bound to the enzyme in the SAM pocket and no evidence of peptide in the binding site. Structures of crystals grown in the presence of SAM without peptides unambiguously showed electron density for SAH and no evidence of the methyl group (data not shown), indicating hydrolysis of SAM can occur during the crystallization experiment. In contrast, crystals with the

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RESULTS AND DISCUSSION Selection of Substrate Peptide Sequences. CARM1, like other PRMT enzymes, is able to methylate multiple substrates with diverse sequences. However, how these varied sequences are recognized remains enigmatic. X-ray crystallography is able to provide a snapshot of the ternary complex between the methyltransferase enzyme and the nucleoside and peptide substrates, but structures of multiple sequences are needed to differentiate common, conserved interactions from B

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proximity to the C-terminus of the CARM1 construct used for crystallization. For both H3 and PABP1 peptides, clear density for flanking residues allowed for the sequences to be modeled consistent with R17 (H3) and R455 (PABP1) in the arginine channel (Figure 3A,B). The quality of the electron density also allowed unambiguous determination of the methylation state of the arginine residue, and both nonmethylated and singly methylated structures were able to be determined for both substrates. A PABP1 peptide containing an asymmetrically dimethylated Arg455 residue was included in the crystallization experiments in an attempt to obtain a structure of the final product state. However, upon investigation of the initial difference maps, it was clear that the arginine binding site contained a singly methylated arginine residue and the surrounding residues were consistent with the sequence around Arg460 rather than Arg455 (Figure 3C). Therefore, this structure represents a third distinct sequence bound to the CARM1 binding site that can be used in the structural analysis. Structure of the CARM1−Sinefungin Complex. The structure of CARM1 complexed with sinefungin alone was solved in order to obtain an uncomplexed structure of the human enzyme with the same SAM analog bound as in the peptide structures. The structure with sinefungin is very similar to other human CARM1 structures solved18 (Dombrovski et al., Structural Genomic Consortium, PDB ID: 4IKP). Root mean square deviation (RMSD) of Cα residues ranges between 0.27 and 0.84 Å2 for equivalent monomers in the asymmetric unit. This is similar to an RMSD range of 0.23−0.73 Å2 for monomers within the asymmetric unit of the CARM1− sinefungin complex, indicating global differences between the human crystal structures are negligible. Differences between the Dombrovski et al. structure, which utilized a SAM analog containing a methyl amine moiety in place of the SAM methyl group, and the CARM1−sinefungin complex in this study are seen in the nucleoside binding portion of the molecule and appear to be caused by the increased bulk resulting from the additional methylene group of the nucleoside. Comparison of the sinefungin complex with the CARM1-inhibitor complexes18 shows most differences in side chain conformation are isolated to the regions external to the arginine channel, with the uncomplexed structure being most similar to the indole scaffold containing a methylethanamine moiety in the arginine pocket that was also solved with sinefungin. Similarly, comparison of the peptide bound structures with the sinefingin structure also shows no conformational differences in the arginine pocket and variations in side chain orientations only external to the substrate channel. CARM1−Peptide Interactions Are Conserved Across Peptide Sequences and Methylation States. The arginine residue bound in the substrate pocket makes several hydrogen bond interactions with residues conserved between Type 1 PRMT enzymes (Figure 4A). A bidentate interaction with Glu257 and single hydrogen bonds with His414 and Glu266 anchors the substrate side chain in the binding site. These interactions and the position of the arginine in the binding site are unchanged after a single methylation event, as seen in the overlays of the different methylated arginine residues. The remaining interactions between the protein and peptide are largely sequence independent, as they are made with backbone residues of the peptide. Due to the differences in sequences of the peptides studied, the nomenclature in Figure 4B will be used to describe the interactions. Glu266 and Asn265 make

nonhydrolyzable sinefungin showed clear density for the sinefungin free amine and the peptide in the binding site. Yue and colleagues noted their failed efforts to obtain a structure of CARM1 substrate in the presence of SAH;16 the results of the present study are consistent with this observation. All structures in this study were solved in the space group P21212 previously seen for human CARM1 and contained two copies of the CARM1 dimer. Unlike the structures of CARM1 complexed with small molecules, in which all four CARM1 molecules in the asymmetric unit contained a ligand,18 a subset of peptide structures in this report had fewer than four peptide molecules bound, although all had at least one peptide bound to each dimer in the asymmetric unit (Figure 1). Additionally, the length of the peptide visible in the electron density of each monomer in the asymmetric unit varied for each structure, with a range of 6−11 amino acids over all five structures presented in this study. The substrate arginine residue was flanked by 1−4 residues on the N-terminal side and 3−7 residues on the Cterminal side. The unmodeled peptide residues are presumed to occupy multiple conformational states within the crystal and therefore are not seen in the electron density maps. The active sites of the CARM1 monomers involved in the formation of each dimer face one another in the quaternary structure, and therefore binding of peptide in one CARM1 monomer could potentially influence binding in the dimer partner molecule. For those structures that have peptides bound in both monomers of a dimer, amino acids that are three or four residues N-terminal to the catalytic arginine and visible in the electron density maps are in close proximity to the peptide in the opposing dimer site (Figure 2). As detailed

Figure 2. CARM1 dimer. Monomers within the dimer (green, purple) are shown complexed with sinefungin (stick representation) and peptide (yellow, magenta). The H3 R17 structure is shown.

below, these residues are not involved in the conserved binding interactions for the peptides to CARM1, and it is not believed that dimer interactions influence the core binding mode of the peptide substrate. However, the number and sequence of peptides bound in a CARM1 dimer could influence the exact position of the N-terminal portions of these peptides. In contrast, the C-terminal residues of the peptide are in a solvent exposed region for all monomers and are located in close C

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Figure 3. Electron density maps for the three, distinct peptide sequences (yellow) solved in CARM1 (green): (A) H3 R17, (B) PABP R455(Me), (C) PABP1 R460(Me). 2Fo-Fc maps are contoured at 1.0σ; sinefingin (SFG; green) is shown in stick representation. The methylation state and sequence of the bound peptides can be unambiguously determined.

Comparison with Other PRMT Complexes. Comparison of the CARM1−peptide complexes to the only other type I PRMT molecule bound to peptide, PRMT1,19 shows distinct differences between the two structures in the orientation of the arginine side chain and in the positions of residues known to be important for catalysis, such as Glu266 (Glu153 in PRMT1; Figure 5A). Glu266 makes a single hydrogen bond to the arginine residue, rather than a bidentate interaction as was speculated in modeling of the peptide with the PRMT3 protein, and a bidentate interaction through the ε-nitrogen atoms of the guanidine is observed with Glu257 (Glu144 in PRMT1), rather than a single hydrogen bond. The pattern of CARM1 binding to these catalytically important residues is more similar to that seen in the type II enzyme, PRMT5, bound to a histonederived peptide and a SAM analog,20 where both Glu residues (Glu444 and Glu435) engage in bidentate interactions (Figure 5B). As previously noted, some of the structural differences in the binding site of PRMT1 may be due to low pH in crystallization conditions;19 in contrast, the CARM1 structures presented here were solved at pH 8.5 and the protonation state of all acidic residues match the physiological state. Additionally, the PRMT1−peptide complex was solved in the presence of SAH, whereas the CARM1 structures contain the SAM analog, sinefungin. It is currently unknown if similar differences in the

water-mediated interactions with the N1 carbonyl, and this is the only hydrogen bond interaction seen on the residues Nterminal to the substrate arginine (Figure 4A,B). In contrast, several backbone interactions are made on the C-terminal side of the bound arginine (Figure 4B,C). The amide of Asn161 engages in two hydrogen bonds to the peptide, one to the carbonyl of residue C1 and one with the backbone nitrogen of C3. The hydroxyl of Tyr416 engages the carbonyl C2. In a subset of structures, Tyr476 is within hydrogen bonding distance of the backbone NH of residue C2, but this interaction appears to be dependent on the identity of the C1 and C2 residues and the subsequent position of the side chain Phe474, which influences the orientation of the side chain of Tyr476 and can cause it to rotate (Figure 4C). The binding interactions of the peptide allow for the presence of flanking proline residues both N- and C-terminal to the substrate arginine. This is significant, as proline is conformationally constrained compared to other amino acids and lacks a backbone NH to interact with hydrogen bond acceptors. Unsurprisingly, residues that do not make interactions with CARM1 protein show more divergence in their position in the binding site than do the residues that make specific interactions, even when the sequences are identical (Figure 4D). D

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Figure 4. CARM1−peptide interactions. (A) Hydrogen bonds (dashed lines) to arginine side chains irrespective of methylation state and a water mediated interaction are conserved in all structures. H-bonds are shown for the H3 R17 structure. (B) Nomenclature and schematic for CARM1− peptide interactions. Dashed lines indicate conserved hydrogen bonds; wavy lines indicate nonconserved interactions. (C) Three conserved hydrogen bonds are seen between CARM1 residue side chains and the peptide backbone C-terminal to the arginine residue. An additional interaction with Tyr476 is seen only in a subset of structures. (D) Overlay of five peptide structures shows conservation of the core binding mode despite differing primary sequences. All figures utilize the following color scheme: H3 R17 = green; H3 R17(Me) = cyan; PABP1 R455 = magenta; PABP1 R455(Me) = yellow; PABP1 R460(Me) = coral.

Figure 5. Superposition of the CARM1−H3 R17 complex (green/yellow) with peptide complexes. (A) PRMT1 (PDB 1OR8); (B) PRMT5-MEP50 (PDB 4GQB). PRMT1 and PRMT5 complexes are gray; residues involved in arginine recognition are shown in stick representation and are labeled with CARM1/PRMT1 or PRMT5 residue numbers.

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Figure 6. Superpositions of the CARM1−H3 R17(Me) complex (green/yellow) with CARM1 inhibitor structures. Overlap between the peptide substrate and known inhibitors (2Y1X = gray; 2Y1W = purple) is shown.

affinity for the CARM1 enzyme than the unmethylated or singly methylated substrates by 3 orders of magnitude (S. Jacques, unpublished data). Although no dimethylated H3 peptides were attempted in this study, results with PABP1 peptides are consistent with this finding. Arg455 was seen in the CARM1 binding site when this residue was unmethylated and monomethylated. However, the peptide with asymmetrically dimethylated Arg455 resulted in a different arginine residue, monomethylated Arg460, bound in the CARM1 substrate site. This shift in residue binding may be due to the nucleoside analog used in the experiments. The structures presented in this study were crystallized with sinefungin, an analog of the substrate SAM. Models of the dimethylated state indicate the asymmetrically methylated arginine would clash with the donor methyl of SAM and the NH3 group of sinefungin. Therefore, the fact that the dimethylated residue was not found in the binding site of sinefungin containing CARM1 crystals is not surprising. As noted earlier, no peptide was seen in structures where SAH was found in the SAM binding site. Therefore, the structure of the ternary product state of the asymmetric reaction of CARM1 or any PRMT enzyme remains unknown. Additionally, these data are suggestive that PABP1 peptides, like the H3 peptides, also have a preferred substrate residue for catalysis, but further enzymatic studies on PABP1 peptides or PABP1 protein would be needed to confirm this hypothesis. Sequence Independent Interactions May Be Thematic to Family. The CARM1−peptide complexes give the first clear view of the interactions between a type I enzyme and residues beyond the arginine substrate. For PRMT1, density for the peptide outside the arginine channel was ambiguous;19 only Cα atoms were modeled, and thus analysis of protein−peptide interactions could not be completed. In contrast, the hydrogen bond pattern for the CARM1 substrates show conservation of key interactions with backbone atoms and some flexibility in the binding mode based on peptide sequence. A predominance of backbone interactions was also noted in the PRMT5−

binding site would be seen with a CARM1−peptide−SAH complex. Overlays of the peptide structures with crystal structures of CARM1 inhibitors18 show that some of the interactions are conserved between the different scaffolds (Figure 6). The pyrazole series compound engages the same residues in the arginine channel as the substrate, with only minor changes in the position of Glu257 to accommodate the differing geometries of the headgroup. In contrast, the N-methylethanamine group makes only two hydrogen bonds, thus engaging only a subset of residues compared to the arginine, and the vector of the hydrogen bond to His414 is quite different. Interestingly, the terminal methyl groups of both compounds occupy a similar position in the binding site as the methylated arginine. No interactions outside the arginine pocket are shared by the inhibitors and the peptide; however, there were limited polar interactions between the protein and the compounds in these regions. Structural Results Consistent with CARM1 Substrate Preference. The methylation reaction of CARM1 with the H3 peptide has recently been extensively studied and showed Arg17 of histone H3 is preferred for methylation over Arg26 (S. Jacques, unpublished data). The results of this study support this work, as Arg17 was found in the CARM1 binding site when the unmethylated peptide was used and both Arg17 and Arg26 were available for binding to CARM1. Kinetic studies also showed that CARM1 methylates peptide substrates containing a monomethylated arginine residue as well as the unmethylated residue (S. Jacques, unpublished data). The structures of both the singly methylated and unmethylated H3 peptides showed little difference in the position of the substrate or the surrounding residues, with no structural clashes. Information on catalytic efficiency cannot be obtained through analysis of a crystal structure; however, the results of the structures of the H3 peptide are consistent with the kinetic findings. In contrast, characterization of dimethylated H3 peptides indicates the asymmetric product at Arg17 has a much lower F

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ACS Chemical Biology Table 1. Crystallographic Data Collection and Refinement Statistics for CARM1-Sinefungin Structures peptide data collection space group cell dimensions a, b, c (Å) α, β, γ (deg) resolution range (Å) (highest resolution shell) Rmerge overalla (%) I/σ(I) completeness overall (%) multiplicity reflections (unique) refinement number of reflections Rwork (%)b/Rfree (%) RMS deviations from ideal values bond lengths (Å) bond angles (deg) Φ, Ψ angle distribution for residuesc in preferred regions (%) in allowed regions (%) outliers (%)

apo

H3 R17

H3 R17(Me)

PABP1 R455

PABP R455(Me)

PABP1 R460(Me)

P21212

P21212

P21212

P21212

P21212

P21212

74.9, 97.9, 207.4 90.0, 90.0, 90.0 50.00−1.95 (2.02−1.95) 0.091 (0.532) 18.1 (3.0) 99.2 (99.7) 4.7 110778

75.7, 98.8, 208.7 90.0, 90.0, 90.0 50.00−2.05 (2.12−2.05) 0.079 (0.644) 13.8 (2.2) 89.9 (89.9) 3.5 88915

75.4, 98.4, 203.4 90.0, 90.0, 90.0 50.00−2.40 (2.49−2.40) 0.101 (0.623) 13.6 (2.4) 98.9 (97.5) 3.9 62299

74.9, 98.3, 207.5 90.0, 90.0, 90.0 50.00−1.96 (2.08−1.96) 0.103 (0.770) 14.9 (3.2) 99.0 (97.0) 7.4 110682

74.9, 98.3, 207.5 90.0, 90.0, 90.0 50.00−1.94 (2.06−1.94) 0.120 (0.771) 11.5 (2.6) 90.0 (92.5) 4.7 103564

75.2, 98.7, 207.7 90.0, 90.0, 90.0 48.10−2.07 (2.19−2.07) 0.119 (0.709) 10.7 (2.2) 98.9 (98.9) 4.0 94364

105181 19.7/23.0

84566 21.1/26.2

59187 20.7/25.7

109355 20.2/24.4

97410 20.6/24.5

89629 20.0/24.7

0.01 1.5

0.01 1.4

0.004 1.0

0.01 1.4

0.01 1.4

0.01 1.4

96.4 3.3 0.3

95.8 3.4 0.8

96.0 3.6 0.4

96.3 3.0 0.7

95.9 2.8 1.3

95.9 3.4 0.6

Rmerge = Σhkl [(Σi |Ii − ⟨I⟩|)/ Σi Ii]. bRvalue = Σhkl ||Fobs| − |Fcalcd||/Σhkl |Fobs|. Rfree is the cross-validation R factor computed for the test set of 5% of unique reflections. cRamachandran statistics as defined in COOT.30 a

peptide structure,20 although the pattern of hydrogen bonds and overall conformations of the peptides are dissimilar due to the structural differences between CARM1 and PRMT5 in this region (Figure 5B). Given the large number of substrates for PRMT enzymes, this combination of backbone recognition and plasticity seen in the CARM1 binding site may be a key feature of this family of enzymes. Differences between Catalytic Domain and Full Length Protein. The analysis of CARM1’s interactions with peptides is limited to the protein construct that is used to solve the structure. The crystallization construct used in most CARM1 structures and in this study is a truncated construct missing both the N- and C-terminal domains. In this construct, residues beyond Ala21 in the H3 peptides are not visible in the electron density; these residues are presumed to be disordered and therefore not contributing significantly to the binding mode. Interestingly, the enzyme kinetic results show that H3 peptides truncated at residue Ala25 are not active as substrates (S. Jacques, unpublished data). Full length CARM1 was used in the enzymology experiments; therefore, it is possible that the missing domains in the crystallization construct are important for substrate recognition, and additional interactions are made in the context of the full length protein. As noted earlier, the Cterminus of this CARM1 construct is near the C-terminus of the peptide, and therefore it is possible that the C-terminus plays an additional role in substrate recognition. The construct used for crystallization is enzymatically active (C. Sneeringer, unpublished data), but further studies on H3 substrates using the crystallography construct would be needed to understand the role of the missing domains on substrate utilization. A crystal structure of the full length protein bound to substrate would be valuable to discern additional elements in substrate recognition. However, given the conserved conformation of the substrate arginine residue in the binding site and surrounding amino acids, it is unlikely that the additional domains would

significantly alter the core binding mode of the substrate arginine and surrounding residues detailed in this study. Impact on Inhibitor Design. The crystal structure of a substrate bound to an enzyme can be useful in the design of inhibitors for that specific target. However, a substrate complex will only provide a snapshot of the structure; the dynamics of the protein and the residues that result in alternate conformations that are also amenable to inhibition are not easily captured and may be difficult to predict. For example, Phe327, shown to be critical in targeting symmetric dimethylation in PRMT5,22 occupies very different conformations in the peptide structure20 and the EPZ015666 complex.23 In contrast, comparison of the published CARM1 inhibitors and these peptide complexes show only minor changes to the positions of select residues in the arginine channel. Given the lack of conformational flexibility in the binding pocket, design of arginine channel moieties that engage additional residues that hydrogen bond to the substrate could result in new inhibitory scaffolds for CARM1. Some differences in side chain conformation are seen in the peptide binding site, and given the structural changes seen in this region with varying peptide sequences in this limited study, one could expect the dynamics in this region of the protein to be more significant. Targeting areas of similarity between the diverse peptide sequences described here, including hydrogen bond donors and acceptors, may also be useful for inhibitor design. Additional structures of CARM1 with inhibitors will also be useful in understanding the limits of mobility for this protein. Conclusion. In summary, structures of CARM1 with the substrate analog sinefungin and three distinct peptide sequences have been solved. The structures are the first for a type I PRMT enzyme that show detailed binding interactions beyond the arginine pocket. Comparison of the three diverse sequences provides insight into the flexibility of the CARM1 enzyme that allows the enzyme to act on multiple protein G

DOI: 10.1021/acschembio.5b00773 ACS Chem. Biol. XXXX, XXX, XXX−XXX

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substrates, and shows how key interactions beyond the arginine are largely sequence independent. Additionally, the insights provided by CARM1 may be useful for inhibitor design for this enzyme.

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The authors declare the following competing financial interest(s): P.A.B.-S., S.L.J., A.D., S.R., O.M., and R.A.C. are employees and stockholders of Epizyme, Inc.

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ACKNOWLEDGMENTS The authors thank W. Wei, F. Jiang, and Y. Xia for help with crystallization and structure determination and colleagues at Epizyme for helpful discussions.

METHODS

Protein Production. A truncated CARM1 construct containing amino acids 134−479 with an N-terminal hexahistidine tag and TEV protease cleavage site was expressed in Hi Five cells at a multiplicity of infection of 1:200 for 72 h using standard procedures for baculovirus expression. Cell pellets were resuspended in 50 mM Tris, 300 mM NaCl, and 10% (v/v) glycerol at a pH of 7.8 (buffer A) with Roche protease inhibitor cocktail added. Cells were lysed by sonication, and lysate was clarified using centrifugation. Protein was purified using nickel affinity chromatography using buffer A with step increases of 20, 50, and 250 mM imidazole, with CARM1 eluting in the final step. After cleavage with TEV protease, leaving residual amino acids ArgSer-Val N-terminal to residue 134 of CARM1, the protein was then passed over another nickel affinity column using buffer A. Finally, the protein was passed over a size exclusion column in buffer containing 20 mM Tris, 50 mM NaCl, and 1 mM βME at a pH of 7.2. Protein was concentrated to >15 mg mL−1 using a 30 kD MWCO concentrator, aliquoted, frozen in liquid nitrogen, and stored at −80 °C until needed for crystallization. Protein was >95% pure when visualized by SDSpage gel. Crystallography. CARM1 was diluted to 2 mg mL−1 with storage buffer prior to crystallization efforts. Sinefungin was solubilized at 100 mM in DMSO and peptide was solubilized in protein buffer before addition to CARM1 protein at final concentrations of 0.5 and 2 mM, respectively. Vapor diffusion methods utilizing hanging drop trays with a 0.5 mL reservoir were used for crystallization. Typically, 2 μL of protein was added to 1 μL of well solution containing 0.2 M ammonium sulfate, 0.1 M Tris at a pH of 8.5, and 18% (w/v) PEG 3350. Trays were incubated at 18 °C. Crystals were cryoprotected in a solution containing 85% (v/v) mother liquor and 15% (v/v) glycerol prior to freezing in liquid nitrogen. All data sets were collected at synchrotron sources at −180 °C. Data reduction and scaling were performed using either XDS24 and AIMLESS25 or HKL2000.26 Structure determination was performed using previously solved structures of CARM1 and visual inspection of difference density maps. Sinefungin dictionaries were generated using ProDrg27 within the CCP4 software package,28 and ligand fitting of sinefungin and peptide was performed manually. Structure refinement was performed using iterative cycles of refinement and model building using REFMAC529 and COOT,30 respectively. Analysis of the structures shows greater than 99% of all residues are in preferred or allowed regions of the Ramachandran plot. Data collection and refinement statistics are shown in Table 1.

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ASSOCIATED CONTENT

Accession Codes

All structures have been deposited in the Protein Data Bank (SFG = 5DXJ; H3 R17 = 5DX0; H3 R17(Me) = 5DWQ; PABP1 R455 = 5DX1; PABP1 R455(Me) = 5DX8; PABP1 R460(Me) = 5DXA).

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REFERENCES

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AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Present Addresses †

Agile Biostructures, Wellesley, MA Genentech, San Francisco, CA § Raze Therapeutics, Cambridge, MA ‡

Funding

All efforts were funded by Epizyme. H

DOI: 10.1021/acschembio.5b00773 ACS Chem. Biol. XXXX, XXX, XXX−XXX

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DOI: 10.1021/acschembio.5b00773 ACS Chem. Biol. XXXX, XXX, XXX−XXX