Aminoacetylation Reaction Catalyzed by Leucyl-tRNA Synthetase Operates via a Self-Assisted Mechanism Using a Conserved Residue and the Aminoacyl Substrate

A Multiple Proton Transfer Mechanism for the Charging Step of the Aminoacylation Reaction at the Active Site of Aspartyl tRNA Synthetase

Aspartyl-tRNA synthetase catalyzes the attachment of aspartic acid to its cognate tRNA by the aminoacylation reaction during the initiation of the protein biosynthesis process. In the second step of the aminoacylation reaction, known as the charging step, the aspartate moiety is transferred from aspartyl-adenylate to the 3'-OH of A76 of tRNA through a proton transfer process. We have investigated different pathways for the charging step through three separate QM/MM simulations combined with the enhanced sampling method of well-sliced metadynamics and found out the most feasible pathway for the reaction at the active site of the enzyme. In the charging reaction, both the phosphate group and the ammonium group after deprotonation can potentially act as a base for proton transfer in the substrate-assisted mechanism. We have considered three possible mechanisms involving different pathways of proton transfer, and only one of them is determined to be enzymatically feasible. The free energy landscape along reaction coordinates where the phosphate group acts as the general base showed that, in the absence of water, the barrier height is 52.6 kcal/mol. The free energy barrier is reduced to 39.7 kcal/mol when the active site water molecules are also treated quantum mechanically, thus allowing a water mediated proton transfer. The charging reaction involving the ammonium group of the aspartyl adenylate is found to follow a path where first a proton from the ammonium group moves to a water in the vicinity forming a hydronium ion (H₃O⁺) and NH₂ group. The hydronium ion subsequently passes the proton to the Asp233 residue, thus minimizing the chance of back proton transfer from hydronium to the NH₂ group. The neutral NH₂ group subsequently takes the proton from the O3' of A76 with a free energy barrier of 10.7 kcal/mol. In the next step, the deprotonated O3' makes a nucleophilic attack to the carbonyl carbon forming a tetrahedral transition state with a free energy barrier of 24.8 kcal/mol. Thus, the present work shows that the charging step proceeds through a multiple proton transfer mechanism where the amino group formed after deprotonation acts as the base to capture a proton from O3' of A76 rather than the phosphate group. The current study also shows the important role played by Asp233 in the proton transfer process.

Partitioning of the initial catalytic steps of leucyl-tRNA synthetase is driven by an active site peptide-plane flip

To correctly aminoacylate tRNA^Leu, leucyl-tRNA synthetase (LeuRS) catalyzes three reactions: activation of leucine by ATP to form leucyl-adenylate (Leu-AMP), transfer of this amino acid to tRNA^Leu and post-transfer editing of any mischarged product. Although LeuRS has been well characterized biochemically, detailed structural information is currently only available for the latter two stages of catalysis. We have solved crystal structures for all enzymatic states of Neisseria gonorrhoeae LeuRS during Leu-AMP formation. These show a cycle of dramatic conformational changes, involving multiple domains, and correlate with an energetically unfavorable peptide-plane flip observed in the active site of the pre-transition state structure. Biochemical analyses, combined with mutant structural studies, reveal that this backbone distortion acts as a trigger, temporally compartmentalizing the first two catalytic steps. These results unveil the remarkable effect of this small structural alteration on the global dynamics and activity of the enzyme.

Principles of chemical geometry underlying chiral selectivity in RNA minihelix aminoacylation

The origin of homochirality in L-amino acid in proteins is one of the mysteries of the evolution of life. Experimental studies show that a non-enzymatic aminoacylation reaction of an RNA minihelix has a preference for L-amino acid over D-amino acid. The reaction initiates by approaching of a 3'-oxygen of the RNA minihelix to the carbonyl carbon of an aminoacyl phosphate oligonucleotide. Here, employing molecular dynamics simulations, we examined the possible mechanisms that determine this chiral selectivity. The simulation system adopted a geometry required for the chemical reaction to occur more frequently with L-alanine than that with D-alanine. For L-alanine, the structure with this geometry was formed by a combination of stable dihedral angles along alanyl phosphate backbone with a canonical RNA structure, where the methyl group of alanine was placed on the opposite side of the approaching 3'-hydroxyl group with respect to the carbonyl plane. For D-alanine, the methyl group and the 3'-hydroxyl group were placed on the same side with respect to the carbonyl plane, which significantly decreased its ability to approach 3'-oxygen close to the carbonyl carbon compared to L-alanine. The mechanism suggested herein can explain experimentally observed chiral preferences.

Cyclization Reaction Catalyzed by Cyclodipeptide Synthases Relies on a Conserved Tyrosine Residue

Cyclodipeptide synthases (CDPSs) form various cyclodipeptides from two aminoacyl tRNAs via a stepwise mechanism with the formation of a dipeptidyl enzyme intermediate. As a final step of the catalytic reaction, the dipeptidyl group undergoes intramolecular cyclization to generate the target cyclodipeptide product. In this work, we investigated the cyclization reaction in the cyclodipeptide synthase AlbC using QM/MM methods and free energy simulations. The results indicate that the catalytic Y202 residue is in its neutral protonated form, and thus, is not likely to serve as a general base during the reaction. We further demonstrate that the reaction relies on the conserved residue Y202 serving as a proton relay, and the direct proton transfer from the amino group to S37 of AlbC is unlikely. Calculations reveal that the hydroxyl group of tyrosine is more suitable for the proton transfer than hydroxyl groups of other amino acids, such as serine and threonine. Results also show that the residues E182, N40, Y178 and H203 maintain the correct conformation of the dipeptide needed for the cyclization reaction. The mechanism discovered in this work relies on the amino groups conserved among the entire CDPS family and, thus is expected to be universal among CDPSs.

A water-mediated and substrate-assisted aminoacylation mechanism in the discriminating aminoacyl-tRNA synthetase GlnRS and non-discriminating GluRS

Computational methods have been used to elucidate key differences and similarities between the distinct aminoacyl-tRNA synthetases (aaRS) GlnRS and non-discriminating-GluRS.