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Positional recognition of a tRNA determinant dependent on a peptide insertion
Martha A Lovato1, Manal A Swairjo, Paul Schimmel
1Skaggs 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.
Molecular Cell
|April 1, 2004
Summary
The study reveals how Aquifex aeolicus AlaRS recognizes a key tRNA identity element. A specific protein insertion in Drosophila melanogaster mitochondrial AlaRS allows it to recognize a translocated G:U base pair in its cognate tRNA.
Area of Science:
- Biochemistry
- Molecular Biology
- Structural Biology
Background:
- The G3:U70 identity element in the tRNA acceptor stem is crucial for recognition by AlaRS across many organisms.
- Drosophila melanogaster mitochondrial tRNA(Ala) utilizes a G2:U71 base pair, a translocated version of the conserved identity element, for recognition.
Purpose of the Study:
- To elucidate the mechanism by which AlaRS recognizes the G3:U70 identity element.
- To understand how Drosophila melanogaster mitochondrial AlaRS recognizes the translocated G2:U71 identity element.
Main Methods:
- X-ray crystallography of Aquifex aeolicus AlaRS catalytic fragment.
- Sequence alignments of mitochondrial AlaRS enzymes.
- Site-directed mutagenesis involving deletion of a specific amino acid insertion in Dm mt AlaRS.
Main Results:
- The crystal structure of A. aeolicus AlaRS provides insights into G3:U70 recognition.
- Dm mt AlaRS differs from bacterial AlaRS by a 27-amino acid insertion.
- Deletion of this insertion enabled Dm mt AlaRS to preferentially recognize a G3:U70 substrate, indicating its role in positional switching.
Conclusions:
- The 27-amino acid insertion in Dm mt AlaRS acts as a hinge, enabling recognition of the translocated G2:U71 identity element.
- Structural and functional data reveal a mechanism for alternative identity element recognition in mitochondrial tRNA.
- This work highlights the adaptability of aminoacyl-tRNA synthetases in accommodating variations in tRNA structure.