The structural basis for seryl-adenylate and Ap4A synthesis by seryl-tRNA synthetase

AbstractBackground: Seryl-tRNA synthetase is a homodimeric class II aminoacyl-tRNA synthetase that specifically charges cognate tRNAs with serine. In the first step of this two-step reaction, Mg·ATP and serine react to form the activated intermediate, seryl-adenylate. The serine is subsequently transferred to the 3′-end of the tRNA. In common with most other aminoacyl-tRNA synthetases, seryl-tRNA synthetase is capable of synthesizing diadenosine tetraphosphate (Ap4A) from the enzyme-bound adenylate intermediate and a second molecule of ATP. Understanding the structural basis for the substrate specificity and the catalytic mechanism of aminoacyl-tRNA synthetases is of considerable general interest because of the fundamental importance of these enzymes to protein biosynthesis in all living cells.Results Crystal structures of three complexes of seryl-tRNA synthetase from Thermus thermophilus are described. The first complex is of the enzyme with ATP and Mn2+. The ATP is found in an unusual bent conformation, stabilized by interactions with conserved arginines and three manganese ions. The second complex contains seryl-adenylate in the active site, enzymatically produced in the crystal after soaking with ATP, serine and Mn2+. The third complex is between the enzyme, Ap4A and Mn2+. All three structures exhibit a common Mn2+ site in which the cation is coordinated by two active-site residues in addition to the α-phosphate group from the bound ligands.Conclusion Superposition of these structures allows a common reaction mechanism for seryl-adenylate and Ap4A formation to be proposed. The bent conformation of the ATP and the position of the serine are consistent with nucleophilic attack of the serine carboxyl group on the α-phosphate by an in-line displacement mechanism leading to the release of the inorganic pyrophosphate. A second ATP molecule can bind with its γ-phosphate group in the same position as the β-phosphate of the original ATP. This can attack the seryl-adenylate with the formation of Ap4A by an identical in-line mechanism in the reverse direction. The divalent cation is essential for both reactions and may be directly involved in stabilizing the transition state

SAXS investigation on the influence of oil dilution on morphological changes in a SBS block copolymer during the first draw cycle

Spin-cast films of one pure SBS and two oil-extended SBS samples were observed during first cycle drawing in the synchrotron radiation beam at Hasylab. For evaluation, from a two-dimensional Vidicon scattering picture the scattering curve was extracted by intersecting perpendicular to the observed layer lines. Using a method described in a preceding paper [1], the scattering curve is analyzed by fitting to one-dimensional two-phase models. Essential for a fit with parameters of physical sense is the assumption of at least two components. One of these two main components is identified with fibrils containing PS cylinders, the axes of which are orientated parallel; the other is identified with fibrils containing cylinders transverse to the drawing direction. For the mechanical properties of the thermoplastic rubber this splitting of cylinder orientation in the drawn state seems to be of some importance. Only the cylinders of the longitudinal component turn out to be rigid, while the cylinders of the transversal component appear to yield and even break. The amount of cylinders allotted to each of the two components in the drawn state varies as a function of the diluent. An extrapolation of topological parameters back to the undrawn state indicates a possible reason, a fair variation of the cylindrical particle dimensions within a "lattice cell" of only slighly varying dimensions. While paraffinic mineral oil dilution causes the cylinders lengths to decrease, thus improving cylinder orientability within the pseudo lattice cell, aromatic oil dilution increases the particles diameters. A remaining faint contribution to the scattering pattern that produces the layer lines is suggested not to be caused by a periodic structure, but by a single and precisely defined polybutadiene matrix length ("string") between two PS cylinders with a considerable height variance. © 1989 Steinkopff

A VIDICON SYSTEM FOR REAL TIME DIFFRACTION STUDIES

Un système à base d'un Vidicon à été développé pour des études de diffraction en temps réel sur l'anneau de stockage DORIS (DESY). Il est possible d'accumuler jusqu'à 256 diagrammes de 512x512 pixels avec une mémoire et une unité arithmétique. Avant transfert, la moyenne sur quatre points est calculée et on effectue une mise a l'échelle sur 256 niveaux de gris. Le temps minimum de transfer d'un diagramme de 256x256 pixels est environ 2 s.A Vidicon system has been developed for real time diffraction studies at the storage ring DORIS (DESY). Up to 256 digitized frames of 512x512x2 bytes can be accumulated by a memory and an arithmetic logic unit. Prior to storage on disc, every four pixels are averaged arid scaled to 256 grey levels. Minimum transfer time per frame of 256x256 pixels to disc is about 2 s