ArticleThe Journal of biological chemistry2014
Enhanced amino acid selection in fully evolved tryptophanyl-tRNA synthetase, relative to its urzyme, requires domain motion sensed by the D1 switch, a remote dynamic packing motif.
Article in The Journal of biological chemistry, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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25 citing papers in PubMed, 39 citations in OpenAlex.
- Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies.Structural dynamics (Melville, N.Y.) · 2025Article
- A genomic database furnishes minimal functional glycyl-tRNA synthetases homologous to other, designed class II urzymes.Nucleic acids research · 2024Article
- Base Pairing Promoted the Self-Organization of Genetic Coding, Catalysis, and Free-Energy Transduction.Life (Basel, Switzerland) · 2024Review
- Domain acquisition by class I aminoacyl-tRNA synthetase urzymes coordinated the catalytic functions of HVGH and KMSKS motifs.Nucleic acids research · 2023Article
- High-throughput thermal denaturation of tryptophanyl-tRNA synthetase combinatorial mutants reveals high-order energetic coupling determinants of conformational stability.Structural dynamics (Melville, N.Y.) · 2023Article
- A Leucyl-tRNA Synthetase Urzyme: Authenticity of tRNA Synthetase Catalytic Activities and Promiscuous Phosphorylation of Leucyl-5'AMP.International journal of molecular sciences · 2022Article
- Multidimensional Phylogenetic Metrics Identify Class I Aminoacyl-tRNA Synthetase Evolutionary Mosaicity and Inter-Modular Coupling.International journal of molecular sciences · 2022Article
- Reciprocally-Coupled Gating: Strange Loops in Bioenergetics, Genetics, and Catalysis.Biomolecules · 2021Review
- Impedance Matching and the Choice Between Alternative Pathways for the Origin of Genetic Coding.International journal of molecular sciences · 2020Article
- The structural basis of the genetic code: amino acid recognition by aminoacyl-tRNA synthetases.Scientific reports · 2020Article
- Escapement mechanisms: Efficient free energy transduction by reciprocally-coupled gating.Proteins · 2020Article
- Backbone Brackets and Arginine Tweezers delineate Class I and Class II aminoacyl tRNA synthetases.PLoS computational biology · 2018Article
- High-Dimensional Mutant and Modular Thermodynamic Cycles, Molecular Switching, and Free Energy Transduction.Annual review of biophysics · 2017Review
- Augmenting the anisotropic network model with torsional potentials improves PATH performance, enabling detailed comparison with experimental rate data.Structural dynamics (Melville, N.Y.) · 2017Article
- Combining multi-mutant and modular thermodynamic cycles to measure energetic coupling networks in enzyme catalysis.Structural dynamics (Melville, N.Y.) · 2017Article
- Coding of Class I and II Aminoacyl-tRNA Synthetases.Advances in experimental medicine and biology · 2017Review
- An Ancestral Tryptophanyl-tRNA Synthetase Precursor Achieves High Catalytic Rate Enhancement without Ordered Ground-State Tertiary Structures.ACS chemical biology · 2016Article
- Aminoacyl-tRNA Synthetases in the Bacterial World.EcoSal Plus · 2016Review
- A modified PATH algorithm rapidly generates transition states comparable to those found by other well established algorithms.Structural dynamics (Melville, N.Y.) · 2016Article
- Functional Class I and II Amino Acid-activating Enzymes Can Be Coded by Opposite Strands of the Same Gene.The Journal of biological chemistry · 2015Article
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6 authors at 3 institutions in 2 countries.
Funding
Abstract
We previously showed (Li, L., and Carter, C. W., Jr. (2013) J. Biol. Chem. 288, 34736-34745) that increased specificity for tryptophan versus tyrosine by contemporary Bacillus stearothermophilus tryptophanyl-tRNA synthetase (TrpRS) over that of TrpRS Urzyme results entirely from coupling between the anticodon-binding domain and an insertion into the Rossmann-fold known as Connecting Peptide 1. We show that this effect is closely related to a long range catalytic effect, in which side chain repacking in a region called the D1 Switch, accounts fully for the entire catalytic contribution of the catalytic Mg(2+) ion. We report intrinsic and higher order interaction effects on the specificity ratio, (kcat/Km)Trp/(kcat/Km)Tyr, of 15 combinatorial mutants from a previous study (Weinreb, V., Li, L., and Carter, C. W., Jr. (2012) Structure 20, 128-138) of the catalytic role of the D1 Switch. Unexpectedly, the same four-way interaction both activates catalytic assist by Mg(2+) ion and contributes -4.4 kcal/mol to the free energy of the specificity ratio. A minimum action path computed for the induced-fit and catalytic conformation changes shows that repacking of the four residues precedes a decrease in the volume of the tryptophan-binding pocket. We suggest that previous efforts to alter amino acid specificities of TrpRS and glutaminyl-tRNA synthetase (GlnRS) by mutagenesis without extensive, modular substitution failed because mutations were incompatible with interdomain motions required for catalysis.
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