Related Experiment Videos
Alanyl-tRNA synthetase crystal structure and design for acceptor-stem recognition
Manal A Swairjo1, Francella J Otero, Xiang-Lei Yang
1Skaags Institute for Chemical Biology, 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 crystal structure of Aquifex aeolicus alanyl-tRNA synthetase (AlaRS) reveals how it recognizes tRNA(Ala). This structure clarifies the "second genetic code" mechanism involving a key G:U base pair in the tRNA acceptor stem.
Area of Science:
- Molecular Biology
- Structural Biology
- Biochemistry
Background:
- The recognition of transfer RNA (tRNA) by aminoacyl-tRNA synthetases (aaRS) is crucial for protein synthesis.
- The alanine-specific tRNA (tRNA(Ala)) and alanyl-tRNA synthetase (AlaRS) system provided early evidence for a "second genetic code" based on tRNA acceptor stem identity elements.
- A single G:U base pair at a specific position in the tRNA acceptor stem is the primary determinant for AlaRS recognition.
Purpose of the Study:
- To elucidate the structural basis of tRNA(Ala) recognition by AlaRS.
- To understand the role of the key G:U base pair in the acceptor stem of tRNA(Ala).
- To provide insights into the mechanism of the "second genetic code".
Main Methods:
- Determination of a high-resolution (2.14 Å) crystal structure of a catalytic fragment of Aquifex aeolicus AlaRS.
- Analysis of the structural domains of AlaRS: catalytic, helical, and C-terminal.
- Computational docking of tRNA(Ala) onto the determined AlaRS structure.
Main Results:
- The crystal structure reveals three distinct domains in the AlaRS catalytic fragment: a class II catalytic domain, a helical domain with a hairpin motif for acceptor-stem binding, and a mixed alpha/beta C-terminal domain.
- Docking simulations show critical interactions between tRNA(Ala) and all three domains of AlaRS.
- The structural model is consistent with prior mutagenesis and functional data regarding tRNA(Ala) recognition.
- The structure suggests conformational flexibility in the C-terminal domain, potentially accommodating variations in the position of the identity G:U base pair observed in some tRNA(Ala) molecules.
Conclusions:
- The determined crystal structure of Aquifex aeolicus AlaRS provides a detailed molecular model for tRNA(Ala) recognition.
- The findings support the role of multiple AlaRS domains in binding tRNA(Ala) and highlight the importance of the G:U base pair.
- The suggested conformational flexibility may explain variations in tRNA identity determinants, offering a deeper understanding of the "second genetic code".