ATP binding by glutamyl‐tRNA synthetase is switched to the productive mode by tRNA binding

• Published in: The EMBO journal Vol. 22; no. 3; pp. 676 - 688
• Main Authors: Sekine, Shun‐ichi, Nureki, Osamu, Dubois, Daniel Y., Bernier, Stéphane, Chênevert, Robert, Lapointe, Jacques, Vassylyev, Dmitry G., Yokoyama, Shigeyuki
• Format: Journal Article
• Language: English
• Published: Chichester, UK John Wiley & Sons, Ltd 03.02.2003; Blackwell Publishing Ltd; Oxford University Press
• Subjects: Adenosine Triphosphate - metabolism; Amino Acid Sequence; Amino acids; aminoacylation; aminoacyl‐tRNA synthetase; ATP; Bacterial Proteins - chemistry; Bacterial Proteins - metabolism; Binding Sites; Crystallography, X-Ray; Genes, Bacterial; Glutamate-tRNA Ligase - chemistry; Glutamate-tRNA Ligase - genetics; Glutamate-tRNA Ligase - metabolism; Humans; Models, Molecular; Molecular Sequence Data; Molecular Structure; Protein Binding; Protein Structure, Tertiary; ribonucleoprotein; RNA, Bacterial - metabolism; RNA, Transfer - metabolism; Sequence Alignment; Thermus thermophilus - enzymology; Thermus thermophilus - genetics; tRNA; X‐ray crystallography
• ISSN: 0261-4189; 1460-2075
• DOI: 10.1093/emboj/cdg053

Aminoacyl‐tRNA synthetases catalyze the formation of an aminoacyl‐AMP from an amino acid and ATP, prior to the aminoacyl transfer to tRNA. A subset of aminoacyl‐tRNA synthetases, including glutamyl‐tRNA synthetase (GluRS), have a regulation mechanism to avoid aminoacyl‐AMP formation in the absence of tRNA. In this study, we determined the crystal structure of the ‘non‐productive’ complex of Thermus thermophilus GluRS, ATP and L‐glutamate, together with those of the GluRS·ATP, GluRS·tRNA·ATP and GluRS·tRNA·GoA (a glutamyl‐AMP analog) complexes. In the absence of tRNAGlu, ATP is accommodated in a ‘non‐productive’ subsite within the ATP‐binding site, so that the ATP α‐phosphate and the glutamate α‐carboxyl groups in GluRS· ATP·Glu are too far from each other (6.2 Å) to react. In contrast, the ATP‐binding mode in GluRS·tRNA· ATP is dramatically different from those in GluRS·ATP·Glu and GluRS·ATP, but corresponds to the AMP moiety binding mode in GluRS·tRNA·GoA (the ‘productive’ subsite). Therefore, tRNA binding to GluRS switches the ATP‐binding mode. The interactions of the three tRNAGlu regions with GluRS cause conformational changes around the ATP‐binding site, and allow ATP to bind to the ‘productive’ subsite.