Positional recognition of a tRNA determinant dependent on a peptide insertion.
The crystal structure of a catalytic fragment of Aquifex aeolicus AlaRS and additional data suggest how the critical G3:U70 identity element of its cognate tRNA acceptor stem is recognized. Though this identity element is conserved from bacteria to the cytoplasm of eukaryotes, Drosophila melanogaster mitochondrial (Dm mt) tRNA(Ala) contains a G:U base pair that has been translocated to the adjacent 2:71 position. This G2:U71 is the major determinant for identity of Dm mt tRNA(Ala). Sequence alignments showed that Dm mt AlaRS is differentiated from G3:U70-recognizing AlaRSs by an insertion of 27 amino acids in the region of the protein that contacts the acceptor stem. Precise deletion of this insertion from Dm mt AlaRS gave preferential recognition to a G3:U70-containing substrate. Larger or smaller deletions were ineffective. The crystal structure of the orthologous A. aeolicus protein places this insertion on the surface, where it can act as a hinge that provides positional switching of G:U recognition.
Lovato
Martha A
MA
Skaggs Institute for Chemical Biology and the Departments of Molecular Biology and Chemistry, The Scripps Research Institute, BCC-379, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA.
Swairjo
Manal A
MA
Schimmel
Paul
P
D000412:Alanine-tRNA Ligase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D000818:Animals; D020029:Base Pairing; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D004331:Drosophila melanogaster / Q000235:genetics; D007700:Kinetics; D008954:Models, Biological; D008969:Molecular Sequence Data; D016254:Mutagenesis, Insertional; D009690:Nucleic Acid Conformation; D010455:Peptides / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D012313:RNA / Q000737:chemistry; D012329:RNA, Bacterial / Q000737:chemistry*; D000077278:RNA, Mitochondrial; D017384:Sequence Deletion; D013379:Substrate Specificity; D014178:Translocation, Genetic
D010455:Peptides; D012329:RNA, Bacterial; D000077278:RNA, Mitochondrial; D012313:RNA; D000412:Alanine-tRNA Ligase