Alanyl-tRNA Synthetase Crystal Structure and Design for Acceptor-Stem Recognition

• Published in: Molecular cell Vol. 13; no. 6; pp. 829 - 841
• Main Authors: Swairjo, Manal A., Otero, Francella J., Yang, Xiang-Lei, Lovato, Martha A., Skene, Robert J., McRee, Duncan E., de Pouplana, Lluis Ribas, Schimmel, Paul
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 26.03.2004
• Subjects: Alanine-tRNA Ligase - chemistry; Alanine-tRNA Ligase - genetics; Amino Acid Motifs; Amino Acid Sequence; Aquifex aeolicus; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Base Pairing; Binding Sites; Cloning, Molecular; Crystallography, X-Ray; Escherichia coli - enzymology; Escherichia coli - genetics; Hydrophobic and Hydrophilic Interactions; Kinetics; Models, Molecular; Protein Structure, Secondary; Protein Structure, Tertiary; RNA, Bacterial - metabolism; Sequence Homology, Amino Acid; Substrate Specificity
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/S1097-2765(04)00126-1

Early work on aminoacylation of alanine-specific tRNA (tRNA Ala) by alanyl-tRNA synthetase (AlaRS) gave rise to the concept of an early “second genetic code” imbedded in the acceptor stems of tRNAs. A single conserved and position-specific G:U base pair in the tRNA acceptor stem is the key identity determinant. Further understanding has been limited due to lack of a crystal structure of the enzyme. We determined a 2.14 Å crystal structure of the 453 amino acid catalytic fragment of Aquifex aeolicus AlaRS. It contains the catalytic domain characteristic of class II synthetases, a helical domain with a hairpin motif critical for acceptor-stem recognition, and a C-terminal domain of a mixed α/β fold. Docking of tRNA Ala on AlaRS shows critical contacts with the three domains, consistent with previous mutagenesis and functional data. It also suggests conformational flexibility within the C domain, which might allow for the positional variation of the key G:U base pair seen in some tRNA Alas.