Many paths to methyltransfer: a chronicle of convergence

Abstract

S-adenosyl-L-methionine (AdoMet) dependent methyltransferases (MTases) are involved in biosynthesis, signal transduction, protein repair, chromatin regulation and gene silencing. Five different structural folds (I-V) have been described that bind AdoMet and catalyze methyltransfer to diverse substrates, although the great majority of known MTases have the Class I fold. Even within a particular MTase class the amino-acid sequence similarity can be as low as 10%. Thus, the structural and catalytic requirements for methyltransfer from AdoMet appear to be remarkably flexible.

Fig. 1

The tertiary structures of the five classes of S-adenosyl-l-methionine (AdoMet)-dependent methyltransferases (MTases). In each case a representative tertiary structure (left) and topology diagram (right) is shown. (a) Class I: tertiary structures have been determined for >33 family members, most containing a seven-stranded β sheet flanked by α helices (enzyme:PDB code, M.HhaI:6MHT). (b) Class II: the reactivation domain of methionine synthase contains a series of long β strands and binds to AdoMet in a shallow groove on the surface of the domain (MetH:1MSK). (c) Class III: the bilobal structure of CbiF contains an AdoMet-binding site between the two αβα domains, and a groove in the N-terminal domain is proposed to be the active-site cleft (CbiF:1CBF). (d) Class IV: the SPOUT family of RNA MTases contains a novel knot structure (magenta) at the C terminus that contributes to the AdoHcy-binding site (YibK:1MXI). (Helices that are not conserved between family members are shown in pale pink in the topology diagram.) (e) Class V: the SET-domain containing histone-lysine N-MTase family is formed by the combination of three small β sheets. The AdoMet-binding site is formed on a shallow groove of the protein and the substrate active site is proximal to the C-terminal tail, which is also involved in a knot-like structure (Set7/9:1O9S). Figures were generated using PYMOL (http://www.pymol.org).

Fig. 2

The strong structural similarity within the Class I methyltransferases (MTases) can been seen in the alignment of 14 structures via their β strands. For clarity, only the peptide backbone of the catalytic core containing the main β sheet (green) and the first α helix (blue) is shown. The cofactor (AdoMet or AdoHcy) is shown in stick model with carbon (yellow), oxygen (red), nitrogen (blue) and sulfur (orange). Structures include protein isoaspartate O-MTase (PDB code: 1I1N), protein arginine N-MTase (1F3L), cyclopropane-fatty-acyl-phospholipid synthase (1KPH), catechol O-MTase (1VID), M.TaqI (2ADM), M.HhaI (6MHT), CheR (1AF7), FtsJ (1EIZ), isoliquiritigenin O-MTase (1FP1), ErmC′ (1QAN), VP39 (1VPT), PrmC (1NV8), mj0882 (1DUS), hypothetical rv2118c (1I9G).

Fig. 3

AdoMet. (a) Overlay of the S-adenosyl-l-methionine (AdoMet) or S-adenosyl-l-homocysteine (AdoHcy) conformations in different methyltransferase (MTase) classes. The molecules are aligned via the ribose rings, and show varying degrees of bend at the intersection between the adenosine and methionine moieties. Described in order of structural class, indicating enzyme PDB code:Class I, M.HhaI:6MHT (orange); Class II, MetH:1MSK (yellow); Class III, CbiF:1CBF (pink); Class IV, YbiK:1K2X (white), Class V, Rubisco:1MVL (blue). (b) AdoMet atomic nomenclature. The O4′-C1′-N9-C4 and C4′-C5′-Sδ-Cγ dihedrals are highlighted yellow and pink, respectively.

Fig. 4

Substrate-bound Class I methyltransferase (MTase) structures [protein, green; S-adenosyl-l-methionine (AdoMet) or S-adenosyl-l-homocysteine (AdoHcy), yellow; substrate, white]. (a) DNA adenine N6-MTase M.TaqI bound to adenosine (a combination of two PDB files: 2ADM and 1G38). (b) Protein glutamine N5-MTase PrmC/HemK bound to an AdoMet–AdoHcy mixture and partially methylated glutamine (1NV8). (c) Class V SET7/9 N-MTase bound to the lysine residue of a histone-tail peptide (1O9S). (d) DNA C5-cytosine MTase M.HhaI bound to a mixture of AdoMet and AdoHcy and partially methylated cytosine (6MHT). (e) Catechol O-MTase bound to magnesium (magenta) and 3,5-dinitrocatechol (1VID). (f) Chalcone O-MTase bound to two alternate conformations of 2′,4,4′-trihydroxychalcone (1FP1). (g) Protein isoaspartate O-MTase facilitates protein repair by binding the residues surrounding the mutant isoaspartate as if it were a β strand within the MTase structure (1JG3).