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Molecular modeling study of the editing active site of Escherichia coli leucyl‐tRNA synthetase: Two amino acid binding sites in the editing domain
Author(s) -
Lee Keun Woo,
Briggs James M.
Publication year - 2004
Publication title -
proteins: structure, function, and bioinformatics
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.699
H-Index - 191
eISSN - 1097-0134
pISSN - 0887-3585
DOI - 10.1002/prot.10300
Subject(s) - thermus thermophilus , homology modeling , docking (animal) , aminoacyl trna synthetase , transfer rna , amino acid , amino acyl trna synthetases , escherichia coli , proofreading , biology , protein structure , homology (biology) , active site , biochemistry , computational biology , enzyme , polymerase , rna , medicine , nursing , gene
Abstract Aminoacyl‐tRNA synthetases (aaRSs) strictly discriminate their cognate amino acids. Some aaRSs accomplish this via proofreading and editing mechanisms. Mursinna and coworkers recently reported that substituting a highly conserved threonine (T252) with an alanine within the editing domain of Escherichia coli leucyl‐tRNA synthetase (LeuRS) caused LeuRS to cleave its cognate aminoacylated leucine from tRNA Leu (Mursinna et al., Biochemistry 2001;40:5376–5381). To achieve atomic level insight into the role of T252 in LeuRS and the editing reaction of aaRSs, a series of molecular modeling studies including homology modeling and automated docking simulations were carried out. A 3D structure of E. coli LeuRS was constructed via homology modeling using the X‐ray structure of Thermus thermophilus LeuRS as a template because the E. coli LeuRS structure is not available from X‐ray or NMR studies. However, both the X‐ray T. thermophilus and homology‐modeled E. coli structures were used in our studies. Amino acid binding sites in the proposed editing domain, which is also called the connective polypeptide 1 (CP1) domain, were investigated by automated docking studies. The root mean square deviation (RMSD) for backbone atoms between the X‐ray and homology‐modeled structures was 1.18 Å overall and 0.60 Å for the editing (CP1) domain. Automated docking studies of a leucine ligand into the editing domain were performed for both structures: homology structure of E. coli LeuRS and X‐ray structure of T. thermophilus LeuRS for comparison. The results of the docking studies suggested that there are two possible amino acid binding sites in the CP1 domain for both proteins. The first site lies near a threonine‐rich region that includes the highly conserved T252 residue, which is important for amino acid discrimination. The second site is located in a flexible loop region surrounded by residues E292, A293, M295, A296, and M298. The important T252 residue is at the bottom of the first binding pocket. Proteins 2004;54:000–000. © 2004 Wiley‐Liss, Inc.