How glutaminyl-tRNA synthetase selects glutamine

AbstractBackground: Aminoacyl-tRNA synthetases covalently link a specific amino acid to the correct tRNA. The fidelity of this reaction is essential for accurate protein synthesis. Each synthetase has a specific molecular mechanism to distinguish the correct pair of substrates from the pool of amino acids and isologous tRNA molecules. In the case of glutaminyl-tRNA synthetase (GlnRS) the prior binding of tRNA is required for activation of glutamine by ATP. A complete understanding of amino acid specificity in GlnRS requires the determination of the structure of the synthetase with both tRNA and substrates bound.Results: A stable glutaminly-adenylate analog, which inhibits GlnRS with a Ki of 1.32 μM, was synthesized and cocrystallized with GlnRS and tRNA2Gln. The crystal structure of this ternary complex has been refined at 2.4 å resolution and shows the interactions made between glutamine and its binding site.Conclusions: To select against glutamic acid or glutamate, both hydrogen atoms of the nitrogen of the glutamine sidechain are recognized. The hydroxyl group of Tyr211 and a water molecule are responsible for this recognition; both are obligate hydrogen-bond acceptors due to a network of interacting sidechains and water molecules. The prior binding of tRNAGln that is required for amino acid activation may result from the terminal nucleotide, A76, packing against and orienting Tyr211, which forms part of the amino acid binding site

Deep-sea Ordovician lingulide brachiopods and their associated burrows suggest an early colonization of proximal turbidite systems

Abstract Trace fossils from Ordovician deep-marine environments are typically produced by a shallow endobenthos adapted to live under conditions of food scarcity by means of specialized grazing, farming, and trapping strategies, preserved in low-energy intermediate to distal zones of turbidite systems. High-energy proximal zones have been considered essentially barren in the early Paleozoic. We report here the first trace and body fossils of lingulide brachiopods in deep-marine environments from an Upper Ordovician turbidite channel-overbank complex in Asturias, Spain. Body and trace fossils are directly associated, supporting the interpretation of a lingulide tracemaker. Ellipsoidal cross-section, cone-in-cone spreite, and spade morphologies suggest the specimens belong to Lingulichnus verticalis. The oblique orientation in both trace and body fossils is the result of tectonic deformation. The organisms were suspension feeders showing escape, dwelling, and equilibrium behaviours controlled by sedimentation rates associated with turbidite deposition. These trace fossils and their in situ producers represent the oldest evidence of widespread endobenthos colonization in high-energy, proximal areas of turbidite systems, expanding the bathymetric range of Lingulichnus and the variety of behaviours and feeding styles in early Paleozoic deep-marine environments