Functional group recognition at the aminoacylation and editing sites of E. coli valyl-tRNA synthetase

Breaking the Stereo Barrier of Amino Acid Attachment to tRNA by a Single Nucleotide

“…This yielded a k cat /K m for the wild-type tRNA ending in A76 of 4.95 mM K1 s K1 , in good agreement with the published value of 3.23 mM K1 s K1 . 22 The 2 0 -dA76 derivative was inactive, while the 3 0 -dA76 derivative had a k cat /K m of 0.52 mM K1 s K1 , about 11% of that of the wild-type and consistent with a published report. 22 The U73 variant of tRNA Val ending in A76 had an approximate k cat /K m of 2.1 mM K1 s K1 , which was 2.4-fold below that of the wild-type tRNA and was consistent with the published decrease of two-to threefold.…”

“…22 The 2 0 -dA76 derivative was inactive, while the 3 0 -dA76 derivative had a k cat /K m of 0.52 mM K1 s K1 , about 11% of that of the wild-type and consistent with a published report. 22 The U73 variant of tRNA Val ending in A76 had an approximate k cat /K m of 2.1 mM K1 s K1 , which was 2.4-fold below that of the wild-type tRNA and was consistent with the published decrease of two-to threefold. 20 Interestingly, the activity of the 2 0 -dA76 derivative of the U73 variant was elevated to that of the 3 0 -dA76 derivative (0.08 mM K1 s K1 ).…”

“…At tRNA concentrations at least 20-fold below the published K m (4.3 mM) of the wild-type tRNA, 22 the initial rate of aminoacylation was used to derive an approximation of the k cat /K m parameter. This yielded a k cat /K m for the wild-type tRNA ending in A76 of 4.95 mM K1 s K1 , in good agreement with the published value of 3.23 mM K1 s K1 .…”

The Dimethylsulfoniopropionate (DMSP) Lyase and Lyase-Like Cupin Family Consists of Bona Fide DMSP lyases as Well as Other Enzymes with Unknown Function

“…Specifically, the native function seems to coincide with substrate structure dictating enzyme reactivity (rather than the substrates’ inherent reactivity or coincidental changes in substrate structure). − The rationale behind substrate profiling is that, if a given substrate were the enzyme’s native substrate, the enzyme’s active-site would largely be shaped to fit this particular substrate. Thus, relatively small changes in the substrate’s structure are expected to induce relatively large drops in activity. ,− True, the essence of enzyme promiscuity is acceptance of alternative substrates, sometimes with little resemblance to the original substrate and also in a selective manner . Nonetheless, selectivity with respect to the native substrate is observed in most enzymes including promiscuous ones, and especially in enzymes that evolved for one particular substrate (in contrast to broad-specificity enzymes).…”

Structural Basis for Non-cognate Amino Acid Discrimination by the Valyl-tRNA Synthetase Editing Domain

“…In the post-transfer editing the non-cognate amino acid may be hydrolyzed from the ribose 2Ј-OH in ValRS (and LeuRS), but in IleRS it may be hydrolyzed from the ribose 3Ј-OH (5,15,16). Actually, some of the editing site residues are distinctly conserved between ValRS and IleRS (Fig.…”