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Structural biology and chemistry of protein arginine methyltransferases - PubMed

  • ️Wed Jan 01 2014

Review

. 2014 Dec 19;5(12):1779-1788.

doi: 10.1039/c4md00269e. Epub 2014 Sep 12.

Affiliations

Review

Structural biology and chemistry of protein arginine methyltransferases

Matthieu Schapira et al. Medchemcomm. 2014.

Abstract

Protein arginine methyltransferases (PRMTs), an emerging target class in drug discovery, can methylate histones and other substrates, and can be divided into three subgroups, based on the methylation pattern of the reaction product (monomethylation, symmetrical or asymmetrical dimethylation). Here, we review the growing body of structural information characterizing this protein family, including structures in complex with substrate-competitive and allosteric inhibitors. We outline structural differences between type I, II and III enzymes and propose a model underlying class-specificity. We analyze the structural plasticity and diversity of the substrate, cofactor and allosteric binding sites, and propose that the conformational dynamics of PRMTs can be exploited towards the discovery of allosteric inhibitors that would antagonize conformationally active states.

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Figures

Fig. 1
Fig. 1. Structural overview of Type I PRMTs. (A) Domain architecture of human PRMTs. The C-terminal Rossman fold and β-barrel of PRMT7, shown in lighter colors, have low sequence similarity with template sequences, and are catalytically inactive. Dashed lines indicate putative structural elements for which no structural data is available. (B) Canonical dimeric arrangement of Type I PRMTs, illustrated by the structure of CARM1 (PDB code 3B3F). In CePRMT7, the C-terminal catalytic core replaces the second subunit. (C) Connolly surface representation of CARM1 colored by electrostatic potential highlighting the cofactor and substrate binding sites. (D) Schematic representation illustrating the structural mechanism of Type I PRMTs: folding of the α-helix on the cofactor completes the formation of the substrate binding site.
Fig. 2
Fig. 2. Structural dynamics of the Type I α-helix. The α-helix observed in Type I PRMTs is structurally dynamic and can adopt strikingly divergent conformations in the active (A – PDB: 3B3F) and inactive (B – PDB: ; 3B3J) states, correlating with distinct positioning of distant structural modules, such as the PH domain of CARM1 (shown), the SH3 domain of PRMT2, or the ZnF domain of PRMT3, relative to the catalytic domain. (C) Substrate specificity of Rossman-fold methyltransferases may rely on the nature of a regulatory element (red; inactive state: blue) N-terminal to the conserved Rossman fold (yellow). PDB codes: active CARM1: ; 3B3F; inactive CARM1: ; 3B3J; PRMT5: ; 4GQB; active DOT1L: ; 1NW3; inactive DOT1L: ; 4ER5; DNMT1: ; 3PTA; NSUN4: ; 4FP9; COMT: ; 1VID. (C is inspired from ref. 40).
Fig. 3
Fig. 3. Structural overview of PRMT5. (A) The structure core of CARM1 is shown as a reference [PDB: 3B3F]. (B) PRMT5 monomers have a conserved catalytic core composed of a Rossman fold and a β-barrel; specific structural features include a TIM barrel that recruits MEP50, and a linker region that contributes to cofactor and substrate binding. Interactions between the TIM barrel and Rossman fold + linker mediate dimerization; orthogonal stacking of dimers produces the PRMT5 tetramer [; 4GQB].
Fig. 4
Fig. 4. Structural determinants for product specificity of Type I, II and III PRMTs. Type I and II PRMTs asymmetrically and symmetrically dimethylate arginine side-chains respectively, while Type III PRMTs mono-methylate only. The conserved “double-E loop” glutamates are shown, along with residues dictating class specificity in the crystal structures of CARM1 [PDB: 2Y1X], PRMT5 [; 4GQB] and TbPRMT7 [; 4M38]. The substrate arginine (positioned manually in the case of CARM1 by superimposing the guanidinium group on the alanine moiety of a co-crystallized inhibitor [; 2Y1X]) is shown in magenta. Orange: residues from the α-helix of CARM1 and TbPRMT7, and from the linker region of PRMT5.
Fig. 5
Fig. 5. Structural plasticity of the cofactor and substrate binding sites. The conformationally dynamic α-helix of CARM1 [PDB code 2Y1W] (A) and the corresponding linker domain of PRMT5 [; 4GQB] (B) contribute to the formation of both cofactor and substrate binding pockets. The cofactor binding pocket is absent in the inactive state of CARM1 [; 3B3J] (C), and a novel pocket is formed at the interface of the α-Y helix and the structure core.
Fig. 6
Fig. 6. Structural diversity of the cofactor and substrate binding pockets. (A) Clustering of human methyltransferases in the protein databank based on the structural similarity of their cofactor site (Molsoft's APF method was used). (B) Side-chains within 5 Å of the cofactor in the CARM1 structure (PDB code ; 3B3F) were extracted from a multiple sequence alignment of Type I PRMTs. Sequence conservation at these positions was used for color-coding. Conserved residues forming direct hydrogen-bonds with the cofactor are marked with an “*”. Positions with significant sequence variability are highlighted in magenta (CARM1 numbering). (C) The same procedure as in (B) was applied to the substrate binding pocket, defined by side-chains within 5 Å of 2 substrate competitors co-crystallized to CARM1 (PDB codes ; 2Y1W and ; 2Y1X). (PNMT: phenylethanolamine N-methyltransferase).
Fig. 7
Fig. 7. Allosteric inhibition of PRMT3. (A and B) An allosteric PRMT3 inhibitor binds in a cavity of the β-barrel, at the base of the dimerization arm, and is buttressed against the α-helix (orange) of the other PRMT3 subunit. The cofactor-binding pocket is highlighted by a cofactor molecule (blue), and the substrate binding pocket by a substrate competitor (magenta) co-crystallized to CARM1 (superimposed CARM1 structure not shown). Both the cofactor and CARM1 inhibitor are shown as references, but are absent from the PRMT3 structure. (C) Entrance to the allosteric pocket is occluded by R396 in the absence of the inhibitor. (D) Sequence diversity of residues lining the allosteric pocket (constructed as in Fig. 6).
Fig. 8
Fig. 8. The PRMT pocketome. ICMPocketFinder (Molsoft, San Diego) was used to map pockets present in PRMT structures. Blue: merged cofactor and substrate binding pockets. Green: experimentally validated PRMT3 allosteric pocket. Orange: unexplored allosteric pocket observed in PRMT1, PRMT3 and PRMT6. Red: novel CARM1 pocket formed by the inactive α-helix. Light blue: pocket formed at the interface of the C-terminal β-barrel and pseudo-dimerization arm of CePRMT7 (C-terminal pseudo-PRMT core shown in white). PDB codes: PRMT1: 1OR8; PRMT3: ; 3SMQ; CARM1 (active): ; 2Y1W; CARM1 (inactive): ; 3B3J; PRMT5: ; 4GQB; PRMT6: ; 4HC4; CePRMT7: ; 3WSS. Red: α-helix of Type I/III PRMTs and linker domain of PRMT5.

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