Crystal structure of the human PRMT5:MEP50 complex

Abstract

Protein arginine methyltransferases (PRMTs) play important roles in several cellular processes, including signaling, gene regulation, and transport of proteins and nucleic acids, to impact growth, differentiation, proliferation, and development. PRMT5 symmetrically di-methylates the two-terminal ω-guanidino nitrogens of arginine residues on substrate proteins. PRMT5 acts as part of a multimeric complex in concert with a variety of partner proteins that regulate its function and specificity. A core component of these complexes is the WD40 protein MEP50/WDR77/p44, which mediates interactions with binding partners and substrates. We have determined the crystal structure of human PRMT5 in complex with MEP50 (methylosome protein 50), bound to an S-adenosylmethionine analog and a peptide substrate derived from histone H4. The structure of the surprising hetero-octameric complex reveals the close interaction between the seven-bladed β-propeller MEP50 and the N-terminal domain of PRMT5, and delineates the structural elements of substrate recognition.epigenetics | protein-protein complex | A9145C P osttranslational methylation of lysine and arginine residues by protein lysine methyltransferases and protein arginine methyltransferases (PRMTs) alters the activity and interactions of substrate proteins, with crucial consequences to diverse cellular functions (1-3). Histone methylation is an epigenetic mark that plays a vital role in normal cell function, and whose dysregulation is associated with several diseases (4).The PRMT family of methyltransferases belongs to the largest class (class I) of S-adenosylmethionine (AdoMet)-dependent methyltransferase enzymes, responsible for the transfer of a methyl group from AdoMet to the arginine side-chains of histones and other proteins. PRMTs are further subdivided into type I, type II, type III, and type IV enzymes based on their patterns of arginine methylation. Eleven human PRMTs have been identified to date (5), and they all methylate the terminal guanidino nitrogen atoms of arginine residues. Type I PRMT enzymes (PRMT1, -2, -3, -4, -6, and -8) generate ω-NG-monomethyl and ω-NG,NG-asymmetric di-methyl arginines, whereas PRMT5 is a type II PRMT that catalyzes the formation of ω-NG-monomethyl and ω-NG,N′G-symmetric di-methyl arginine residues. PRMT7 was initially thought to have type II activity, but recent evidence suggests that it may be a type III enzyme that is only able to monomethylate substrates to form ω-NG-monomethyl arginine (6). A type IV enzyme that catalyses the formation of δ-N-methyl arginine has been identified in yeast (7). All PRMTs share the highly conserved methyltransferase catalytic domain, and several PRMTs contain additional domains that modulate their activity and specificity. PRMT2, PRMT3, and PRMT9 contain SH3, zinc finger, and TRP2 domains, respectively, and PRMT5 contains a largely uncharacterized N-terminal region.In contrast to type I PRMTs, PRMT5 functions as part of various high molecular weight protein complexes that invariably contain the WD-repe...

Structural basis for substrate recognition by the human N-terminal methyltransferase 1

“…These unique features of NTMT1 are in striking contrast to lysine/arginine methyltransferases, such as PRMT5, in which a substrate-binding groove is formed on the surface of these enzymes, and the target histone arginine H4R3 is inserted into a narrow channel to reach the SAM-binding pocket ( Fig. 3C; Antonysamy et al 2012). Therefore, our crystal structures of these NTMT1 ternary complexes described above explain the specificity of NTMT1 in catalyzing α-N-terminal methylation.…”

“…(C) The catalytic pocket of PRMT5. PRMT5 (PDB: 4GQB) (Antonysamy et al 2012) is shown in electrostatic surface representation, and the cofactor SAM analog A9145C and the histone H4R3 peptide are shown as green and yellow sticks, respectively. (D) Catalytic mechanism for the α-N-terminal methylation.…”

Mammalian Protein Arginine Methyltransferase 7 (PRMT7) Specifically Targets RXR Sites in Lysine- and Arginine-rich Regions

“…Thus, the singly methylated species was actually a mixture of peptides Table 1) were methylated by PRMT7 as described in Fig. 3 legend. A-H show PRMT7-catalyzed methylation products of H2B (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37) with monomethylation on different arginine residues, and Arg-29 and Arg-31 should be the major methylation sites on H2B. Additionally, the fragmentation pattern for the methylated H2B(23-37)R29K peptide is more consistent with the Arg-31 site of methylation (Fig.…”

“…Methylation assays were then carried out with the previously characterized substrates GST-GAR, a protein containing the first 148 amino acids of human fibrillarin (5,21), and synthetic peptides derived from the N terminus of human histone H4 (22,23,(25)(26)(27). Using amino acid analysis employing high resolu- tion cation exchange chromatography, we were able to clearly separate MMA, SDMA, and ADMA and capture femtomole levels of methylation products from [ 3 H]AdoMet.…”

“…Fig. 9A shows an example of the 5-charge state of H2B (23)(24)(25)(26)(27)(28)(29)(30)(31)(32)(33)(34)(35)(36)(37) with an m/z of 388.03, which was deconvoluted to the monoisotopic mass of the peptide (1935.12 Da). After the reaction was catalyzed by PRMT7, Fig.…”