2IY5

PHENYLALANYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS complexed with tRNA and a phenylalanyl-adenylate analog

Summary for 2IY5

• Entry DOI: 10.2210/pdb2iy5/pdb
• Related: 1B70 1B7Y 2AKW 2ALY 2AMC
• Descriptor: PHENYLALANYL-TRNA SYNTHETASE ALPHA CHAIN, PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN, TRNAPHE, ... (6 entities in total)
• Functional Keywords: class ii aminoacyl-trna synthetase, ligase, rbd domin, magnesium, sh3 domain, phenylalanyl-trna synthetase, thermus thermophilus, protein biosynthesis, metal-binding, nucleotide-binding, rna-binding, atp-binding, trna-binding, helix-turn-helix motif, aminoacyl-trna synthetase
• Biological source: THERMUS THERMOPHILUS; More
• Total number of polymer chains: 3
• Total formula weight: 151035.14

Authors

Moor, N.,Kotik-Kogan, O.,Tworowski, D.,Sukhanova, M.,Safro, M. (deposition date: 2006-07-12, release date: 2006-09-06, Last modification date: 2023-12-13)

Primary citation

Moor, N.,Kotik-Kogan, O.,Tworowski, D.,Sukhanova, M.,Safro, M.
The crystal structure of the ternary complex of phenylalanyl-tRNA synthetase with tRNAPhe and a phenylalanyl-adenylate analogue reveals a conformational switch of the CCA end.
Biochemistry, 45:10572-10583, 2006

PubMed Abstract: The crystal structure of the ternary complex of (alphabeta)(2) heterotetrameric phenylalanyl-tRNA synthetase (PheRS) from Thermus thermophilus with cognate tRNA(Phe) and a nonhydrolyzable phenylalanyl-adenylate analogue (PheOH-AMP) has been determined at 3.1 A resolution. It reveals conformational changes in tRNA(Phe) induced by the PheOH-AMP binding. The single-stranded 3' end exhibits a hairpin conformation in contrast to the partial unwinding observed previously in the binary PheRS.tRNA(Phe) complex. The CCA end orientation is stabilized by extensive base-specific interactions of A76 and C75 with the protein and by intra-RNA interactions of A73 with adjacent nucleotides. The 4-amino group of the "bulged out" C75 is trapped by two negatively charged residues of the beta subunit (Glubeta31 and Aspbeta33), highly conserved in eubacterial PheRSs. The position of the A76 base is stabilized by interactions with Hisalpha212 of motif 2 (universally conserved in PheRSs) and class II-invariant Argalpha321 of motif 3. Important conformational changes induced by the binding of tRNA(Phe) and PheOH-AMP are observed in the catalytic domain: the motif 2 loop and a "helical" loop (residues 139-152 of the alpha subunit) undergo coordinated displacement; Metalpha148 of the helical loop adopts a conformation preventing the 2'-OH group of A76 from approaching the alpha-carbonyl carbon of PheOH-AMP. The unfavorable position of the terminal ribose stems from the absence of the alpha-carbonyl oxygen in the analogue. Our data suggest that the idiosyncratic feature of PheRS, which aminoacylates the 2'-OH group of the terminal ribose, is dictated by the system-specific topology of the CCA end-binding site.

PubMed: 16939209
DOI: 10.1021/bi060491l

Experimental method

X-RAY DIFFRACTION (3.1 Å)