Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
The crystal structure of phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus, a class II aminoacyl-tRNA synthetase, complexed with phenylalanyl-adenylate (Phe-AMP) was determined at 2.6 A resolution. Crystals of native PheRS were soaked in a solution containing phenylalanine and ATP in the presence of Mn(2+) ions. The first step of the aminoacylation reaction proceeds within the crystals, resulting in Phe-AMP formation at the active site. Specific recognition of the phenylalanine portion of the Phe-AMP is achieved by interactions of the phenyl ring of Phe-AMP with two neighbouring residues, Phealpha258 and Phealpha260. No manganese ions were observed within the active site; their role in the formation of the transition state may be assigned to a number of polar residues and water molecules. In the anomalous Fourier difference map, a divalent metal ion was detected at the interface of the alpha- and beta-subunits at a short distance from motif 3 residues participating in the substrate binding. A sulfate ion, which was identified on the protein surface, may mediate the interactions of PheRS with DNA. Visible conformational changes were detected in the active-site area adjacent to the position of the Phe-AMP, compared with the structure of PheRS complexed with a synthetic adenylate analogue (phenylalaninyl-adenylate). Based on the known structures of the substrate-free enzyme and its complexes with various ligands, a general scheme for the phenylalanylation mechanism is proposed.
Fishman
R
R
Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Ankilova
V
V
Moor
N
N
Safro
M
M
D000215:Acylation; D000249:Adenosine Monophosphate / Q000031:analogs & derivatives* / Q000737:chemistry*; D003460:Crystallization; D018360:Crystallography, X-Ray; D004247:DNA / Q000378:metabolism; D019281:Dimerization; D008345:Manganese / Q000737:chemistry*; D008958:Models, Molecular; D010652:Phenylalanine-tRNA Ligase / Q000737:chemistry*; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D013431:Sulfates / Q000378:metabolism; D016963:Thermus thermophilus / Q000201:enzymology*
D013431:Sulfates; C042022:phenylalanyl-AMP anhydride; C026617:phenylalanyl adenylate; D000249:Adenosine Monophosphate; D008345:Manganese; D004247:DNA; D010652:Phenylalanine-tRNA Ligase