TRYPTOPHANYL-TRANSFER-RNA SYNTHETASE CRYSTAL-STRUCTURE REVEALS AN UNEXPECTED HOMOLOGY TO TYROSYL-TRANSFER-RNA SYNTHETASE

Background: Tryptophanyl-tRNA synthetase (TrpRS) catalyzes activation of tryptophan by ATP and transfer to tRNA(Trp), ensuring translation o f the genetic code for tryptophan. Interest focuses on mechanisms for specific recognition of both amino acid and tRNA substrates. Results: Maximum-entropy methods enabled us to solve the TrpRS structure. Its t hree parts, a canonical dinucleotide-binding fold, a dimer interface, and a helical domain, have enough structural homology to tyrosyl-tRNA synthetase (TyrRS) that the two enzymes can be described as conformati onal isomers. Structure-based sequence alignment shows statistically s ignificant genetic homology. Structural elements interacting with the activated amino acid, tryptophanyl-5'AMP, are almost exactly as seen i n the TyrRS:tyrosyl-5'AMP complex. Unexpectedly, side chains that reco gnize indole are also highly conserved, and require reorientation of ' specificity-determining' helix containing a conserved aspartate to ass ure selection of tryptophan versus tyrosine. The carboxy terminus, whi ch is disordered and therefore not seen in TyrRS, forms part of the di mer interface in TrpRS. Conclusions: For the first time, the Bayesian statistical paradigm of entropy maximization and likelihood scoring ha s played a critical role in an X-ray structure solution. Sequence rela tedness of structurally superimposable residues throughout TrpRS and T yrRS implies that they diverged more recently than most aminoacyl-tRNA synthetases. Subtle, tertiary structure changes are crucial for speci fic recognition of the two different amino acids. The conformational i somerism suggests that movement of the KMSKS loop, known to occur in t he TyrRS transition state for amino acid activation, may provide a bas is for conformational coupling during catalysis.