7RSM

Crystal structure of pyrrolysyl-tRNA synthetase (N346D/C348S/Y384F) in complex with o-Chlorophenylalanine and AMP-PNP

Summary for 7RSM

• Entry DOI: 10.2210/pdb7rsm/pdb
• Descriptor: Pyrrolysine--tRNA ligase, PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER, 2-chloro-L-phenylalanine, ... (4 entities in total)
• Functional Keywords: trna synthetase, pylrs, o-chlorophenylalanine, rna binding protein
• Biological source: Methanosarcina mazei (Methanosarcina frisia)
• Total number of polymer chains: 4
• Total formula weight: 126236.76

Authors

Yang, K.,Liu, W. (deposition date: 2021-08-11, release date: 2022-07-20, Last modification date: 2023-11-15)

Primary citation

Vatansever, E.C.,Yang, K.S.,Geng, Z.Z.,Qiao, Y.,Li, P.,Xu, S.,Liu, W.R.
A Designed, Highly Efficient Pyrrolysyl-tRNA Synthetase Mutant Binds o-Chlorophenylalanine Using Two Halogen Bonds.
J.Mol.Biol., 434:167534-167534, 2022

PubMed Abstract: As one of the most valuable tools for genetic code expansion, pyrrolysyl-tRNA synthetase (PylRS) is structurally related to phenylalanyl-tRNA synthetase (PheRS). By introducing mutations that mimic ligand interactions in PheRS into PylRS, we designed a PylRS mutant. This mutant, designated as oClFRS, recognizes a number of o-substituted phenylalanines for their genetic incorporation at amber codon. Its efficiency in catalyzing genetic incorporation of o-chlorophenylalanine (o-ClF) is better than that for N-tert-butyloxycarbonyl-lysine catalyzed by PylRS. The crystal structure of oClFRS bound with o-ClF shows that o-ClF binds deeply into a hydrophobic but catalytically inactive pocket in the active site and involves two halogen bonds to achieve strong interactions. The shift of o-ClF to a catalytically active position in the oClFRS active site will be necessary for its activation. This is the first reported aminoacyl-tRNA synthetase that involves two halogen bonds for ligation recognition and might represent an alternative route to develop aminoacyl-tRNA synthetase mutants that are selective for noncanonical amino acids over native amino acids.

PubMed: 35278475
DOI: 10.1016/j.jmb.2022.167534

Experimental method

X-RAY DIFFRACTION (2.15 Å)