Structural Studies of Lysyl-tRNA Synthetase:  Conformational Changes Induced by Substrate Binding

• Published in: Biochemistry (Easton) Vol. 39; no. 42; pp. 12853 - 12861
• Main Authors: Onesti, Silvia, Desogus, Gianluigi, Brevet, Annie, Chen, Josiane, Plateau, Pierre, Blanquet, Sylvain, Brick, Peter
• Format: Journal Article
• Language: English
• Published: United States American Chemical Society 24.10.2000
• Subjects: Adenosine Triphosphate; Adenosine Triphosphate - chemistry; Adenosine Triphosphate - metabolism; Binding Sites; Biochemistry, Molecular Biology; conformation; Crystallization; Crystallography, X-Ray; Escherichia coli; Escherichia coli - enzymology; Isoenzymes; Isoenzymes - chemistry; Isoenzymes - metabolism; Life Sciences; Lysine; Lysine - chemistry; Lysine - metabolism; Lysine-tRNA Ligase; Lysine-tRNA Ligase - chemistry; Lysine-tRNA Ligase - metabolism; Models, Molecular; Peptide Fragments; Peptide Fragments - chemistry; Peptide Fragments - metabolism; Protein Conformation; Protein Structure, Tertiary; RNA, Transfer; RNA, Transfer - chemistry; RNA, Transfer - metabolism; Substrate Specificity; tRNA Lys
• ISSN: 0006-2960; 1520-4995
• DOI: 10.1021/bi001487r

Lysyl-tRNA synthetase is a member of the class II aminoacyl-tRNA synthetases and catalyses the specific aminoacylation of tRNALys. The crystal structure of the constitutive lysyl-tRNA synthetase (LysS) from Escherichia coli has been determined to 2.7 Å resolution in the unliganded form and in a complex with the lysine substrate. A comparison between the unliganded and lysine-bound structures reveals major conformational changes upon lysine binding. The lysine substrate is involved in a network of hydrogen bonds. Two of these interactions, one between the α-amino group and the carbonyl oxygen of Gly 216 and the other between the carboxylate group and the side chain of Arg 262, trigger a subtle and complicated reorganization of the active site, involving the ordering of two loops (residues 215−217 and 444−455), a change in conformation of residues 393−409, and a rotation of a 4-helix bundle domain (located between motif 2 and 3) by 10°. The result of these changes is a closing up of the active site upon lysine binding.