4TVA

Universal Pathway for Post-Transfer Editing Reactions: Insight from Crystal structure of TthPheRS with Puromycine

Summary for 4TVA

• Entry DOI: 10.2210/pdb4tva/pdb
• Related: 3HFZ
• Descriptor: Phenylalanine--tRNA ligase alpha subunit, Phenylalanine--tRNA ligase beta subunit, PHENYLALANINE, ... (5 entities in total)
• Functional Keywords: puromycine, editing, trna, phers, ligase-antibiotic complex, ligase/antibiotic
• Biological source: Thermus thermophilus; More
• Cellular location: Cytoplasm: P27001 P27002
• Total number of polymer chains: 2
• Total formula weight: 126666.55

Authors

Safro, M.,Klipcan, L.,Tworowski, D.,Peretz, M. (deposition date: 2014-06-26, release date: 2015-03-18, Last modification date: 2023-09-27)

Primary citation

Tworowski, D.,Klipcan, L.,Peretz, M.,Moor, N.,Safro, M.G.
Universal pathway for posttransfer editing reactions: Insights from the crystal structure of TtPheRS with puromycin.
Proc.Natl.Acad.Sci.USA, 112:3967-3972, 2015

PubMed Abstract: At the amino acid binding and recognition step, phenylalanyl-tRNA synthetase (PheRS) faces the challenge of discrimination between cognate phenylalanine and closely similar noncognate tyrosine. Resampling of Tyr-tRNA(Phe) to PheRS increasing the number of correctly charged tRNA molecules has recently been revealed. Thus, the very same editing site of PheRS promotes hydrolysis of misacylated tRNA species, associated both with cis- and trans-editing pathways. Here we report the crystal structure of Thermus thermophilus PheRS (TtPheRS) at 2.6 Å resolution, in complex with phenylalanine and antibiotic puromycin mimicking the A76 of tRNA acylated with tyrosine. Starting from the complex structure and using a hybrid quantum mechanics/molecular mechanics approach, we investigate the pathways of editing reaction catalyzed by TtPheRS. We show that both 2' and 3' isomeric esters undergo mutual transformation via the cyclic intermediate orthoester, and the editing site can readily accommodate a model of Tyr-tRNA(Phe) where deacylation occurs from either the 2'- or 3'-OH. The suggested pathway of the hydrolytic reaction at the editing site of PheRS is of sufficient generality to warrant comparison with other class I and class II aminoacyl-tRNA synthetases.

PubMed: 25775602
DOI: 10.1073/pnas.1414852112

Experimental method

X-RAY DIFFRACTION (2.597 Å)