2DXI

2.2 A crystal structure of glutamyl-tRNA synthetase from Thermus thermophilus complexed with tRNA(Glu), ATP, and L-glutamol

Summary for 2DXI

• Entry DOI: 10.2210/pdb2dxi/pdb
• Related: 1G59 1GLN 1J09 1N75 1N77 1N78 2CUZ 2CV0 2CV1 2CV2
• Descriptor: tRNA, glutamyl-tRNA synthetase, MAGNESIUM ION, ... (6 entities in total)
• Functional Keywords: ligase, rna, structural genomics, nppsfa, national project on protein structural and functional analyses, riken structural genomics/proteomics initiative, rsgi, ligase-rna complex, ligase/rna
• Biological source: Thermus thermophilus; More
• Cellular location: Cytoplasm: P27000
• Total number of polymer chains: 4
• Total formula weight: 157517.39

Authors

Sekine, S.,Yokoyama, S.,RIKEN Structural Genomics/Proteomics Initiative (RSGI) (deposition date: 2006-08-28, release date: 2006-10-31, Last modification date: 2023-11-15)

Primary citation

Sekine, S.,Shichiri, M.,Bernier, S.,Chenevert, R.,Lapointe, J.,Yokoyama, S.
Structural bases of transfer RNA-dependent amino acid recognition and activation by glutamyl-tRNA synthetase
Structure, 14:1791-1799, 2006

PubMed Abstract: Glutamyl-tRNA synthetase (GluRS) is one of the aminoacyl-tRNA synthetases that require the cognate tRNA for specific amino acid recognition and activation. We analyzed the role of tRNA in amino acid recognition by crystallography. In the GluRS*tRNA(Glu)*Glu structure, GluRS and tRNA(Glu) collaborate to form a highly complementary L-glutamate-binding site. This collaborative site is functional, as it is formed in the same manner in pretransition-state mimic, GluRS*tRNA(Glu)*ATP*Eol (a glutamate analog), and posttransition-state mimic, GluRS*tRNA(Glu)*ESA (a glutamyl-adenylate analog) structures. In contrast, in the GluRS*Glu structure, only GluRS forms the amino acid-binding site, which is defective and accounts for the binding of incorrect amino acids, such as D-glutamate and L-glutamine. Therefore, tRNA(Glu) is essential for formation of the completely functional binding site for L-glutamate. These structures, together with our previously described structures, reveal that tRNA plays a crucial role in accurate positioning of both L-glutamate and ATP, thus driving the amino acid activation.

PubMed: 17161369
DOI: 10.1016/j.str.2006.10.005

Experimental method

X-RAY DIFFRACTION (2.2 Å)