Figure 1

Ribbon representations of LysU (a) The 2.4 Å resolution crystal structure of the LysU dimer viewed down the molecular 2-fold axis, with the substrates lysine (pink) and AMP-PCP (cyan) shown in a space filling representation. Mg²⁺ ions are shown in gold. One complete monomer is shown in blue, whereas the other is coloured according to the domain structure. The N-terminal domain is shown in orange. Within the larger catalytic domain, the conserved core which is common to all class II aminoacyl-tRNA synthetases is shown in red, while the insertion sequence specific to LysRS is shown in purple. In the red monomer, the flipping loop (yellow) is located above the lysine substrate, while the motif 2 loop (green) is situated above the ATP. Strands C2 and C3, along with their symmetry related equivalents form part of a 6-stranded antiparallel β-sheet centred about the two-fold axis. The loop between strands C2-C3 is positioned above and interacts with the motif 2 loop of the opposite monomer. (b) The average structure of the 1 ns FO trajectory. Monomer 2 has been superimposed upon monomer 1 by fitting the core catalytic domain. The same colouring scheme is used. The movement of several loops and domains is apparent, resulting in asymmetry. The motif 2 loop of monomer 1 (green) shifts further over ATP substrate along with the C2-C3 loop of monomer 2. The helix-loop-helix insertion motif also shifts by a few angstroms. Less apparent from this viewpoint is the variation in position of the 4-helix bundle of the insertion, and a rigid body rotation of the N-terminal domain. This figure was created using Molscript [58] and RASTER3D [59].