Identification of Amino Acids in the N-terminal Domain of Atypical Methanogenic-type Seryl-tRNA Synthetase Critical for tRNA Recognition*

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American Society for Biochemistry and Molecular Biology

RESUMO

Seryl-tRNA synthetase (SerRS) from methanogenic archaeon Methanosarcina barkeri, contains an idiosyncratic N-terminal domain, composed of an antiparallel β-sheet capped by a helical bundle, connected to the catalytic core by a short linker peptide. It is very different from the coiled-coil tRNA binding domain in bacterial-type SerRS. Because the crystal structure of the methanogenic-type SerRS·tRNA complex has not been obtained, a docking model was produced, which indicated that highly conserved helices H2 and H3 of the N-terminal domain may be important for recognition of the extra arm of tRNASer. Based on structural information and the docking model, we have mutated various positions within the N-terminal region and probed their involvement in tRNA binding and serylation. Total loss of activity and inability of the R76A variant to form the complex with cognate tRNA identifies Arg76 located in helix H2 as a crucial tRNA-interacting residue. Alteration of Lys79 positioned in helix H2 and Arg94 in the loop between helix H2 and β-strand A4 have a pronounced effect on SerRS·tRNASer complex formation and dissociation constants (KD) determined by surface plasmon resonance. The replacement of residues Arg38 (located in the loop between helix H1 and β-strand A2), Lys141 and Asn142 (from H3), and Arg143 (between H3 and H4) moderately affect both the serylation activity and the KD values. Furthermore, we have obtained a striking correlation between these results and in vivo effects of these mutations by quantifying the efficiency of suppression of bacterial amber mutations, after coexpression of the genes for M. barkeri suppressor tRNASer and a set of mMbSerRS variants in Escherichia coli.

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