Abstract
Many enzymes which catalyze the conversion of large substrates are made of several structural domains belonging to the same polypeptide chain. Transfer RNA (tRNA), one of the substrates of the multidomain aminoacyl-tRNA synthetases (aaRS), is an L-shaped molecule whose size in one dimension is similar to that of its cognate aaRS. Crystallographic structures of aaRS/tRNA complexes show that these enzymes use several of their structural domains to interact with their cognate tRNA. This mini review discusses first some aspects of the evolution and of the flexibility of the pentadomain bacterial glutamyl-tRNA synthetase (GluRS) revealed by kinetic and interaction studies of complementary truncated forms, and then illustrates how stable analogues of aminoacyl-AMP intermediates have been used to probe conformational changes in the active sites of Escherichia coli GluRS and of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) of Pseudomonas aeruginosa.
Highlights
Multidomain enzymes probably evolved from an ancestral domain containing the active site, to which were added during evolution of other domains which increased their catalytic efficiency, and/or improved their specificity for their substrate(s)
As noted by Schimmel, Giegé, Moras and Yokoyama in their 1993 review [6], the aminoacyl-tRNA synthetases (aaRS) structures are organized, to a rough approximation, into two major domains: one containing the active site which interacts with the ancestral part of Transfer RNA (tRNA) including the acceptor end, and one generally less or not conserved which provides for interactions with the second domain of tRNA, including the anticodon
Using a bioinformatic method named “computational solvent mapping”, Chuang et al [7] compared ten different crystallographic structures of a multidomain enzyme, and were able to detect significant changes in binding sites and interdomain crevices at a higher resolution than that provided by superposing these X-ray structures, revealing conformational changes even at an overall root mean square deviation (RMSD) that is close to the expected error in the atomic coordinates
Summary
This mini review discusses first some aspects of the evolution and of the flexibility of the pentadomain bacterial glutamyl-tRNA synthetase (GluRS) revealed by kinetic and interaction studies of complementary truncated forms, and illustrates how stable analogues of aminoacylAMP intermediates have been used to probe conformational changes in the active sites of Escherichia coli GluRS and of the nondiscriminating aspartyl-tRNA synthetase (ND-AspRS) of Pseudomonas aeruginosa. Multidomain enzymes probably evolved from an ancestral domain containing the active site, to which were added during evolution of other domains which increased their catalytic efficiency (kcat), and/or improved their specificity for their substrate(s).
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