1JJC

Crystal structure at 2.6A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese

Summary for 1JJC

• Entry DOI: 10.2210/pdb1jjc/pdb
• Related: 1B7O 1B7Y 1EIY 1PYS
• Descriptor: PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN, PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN, ADENOSINE-5'-[PHENYLALANINYL-PHOSPHATE], ... (6 entities in total)
• Functional Keywords: heterodimer, phenylalanyl-trna, thermus thermophilus, ligase
• Biological source: Thermus thermophilus; More
• Cellular location: Cytoplasm: Q5SGX2 Q5SGX1
• Total number of polymer chains: 2
• Total formula weight: 126675.25

Authors

Safro, M.G.,Fishman, R.,Moor, N.,Ankilova, V. (deposition date: 2001-07-04, release date: 2001-11-02, Last modification date: 2023-08-16)

Primary citation

Fishman, R.,Ankilova, V.,Moor, N.,Safro, M.
Structure at 2.6 A resolution of phenylalanyl-tRNA synthetase complexed with phenylalanyl-adenylate in the presence of manganese.
Acta Crystallogr.,Sect.D, 57:1534-1544, 2001

PubMed Abstract: 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.

PubMed: 11679717
DOI: 10.1107/S090744490101321X

Experimental method

X-RAY DIFFRACTION (2.6 Å)