Fig. 6: Domain movements upon substrate binding.
Dimer structure of 50 ms (S) is superimposed on the core D4/D4 domains of the 50 ms (L) dimer by minimizing the root mean square deviation (RMSD) of the main-chain Cα positions. a RMSD values of Cα positions of the monomer (chain A) of the 50 ms (L) and (S) structures are plotted against the residue numbers. D2 (residues 9–91), D3 (residues 103–203), and D4 (residues 229–623) domains are indicated by blue, orange, and green bars, respectively, with residue numbers at both ends. Thin red lines indicates the average RMSD value (also mentioned in numbers) of each domain. Source data are provided as a Source Data file. b Array of dimers in the crystal lattice (thin gray line) is shown with the same color codes for each domain as indicated in panel (a), except for gray-colored domain D4, viewed in an orthoscopic manner with slight rotation (5°) around the a-axis. Four dimers in the unit cell are shown in darker colors. Small black arrows indicate the direction of the unit cell axes in the abc coordinate system. Enlarged window illustrates the movements of the D2 and D3 domains identified by comparing the 50 ms (L) and (S) structures. Two magenta arrows indicate the vectors of the mass center movements of D2 (blue; vector components: a = 0.139 Å, b = −0.053 Å, and c = 0.021 Å) and D3 (orange; a = −0.084 Å, b = −0.232 Å, and c = 0.0041 Å) against D4 (green) in the 50 ms (S) structure. To emphasize the moving direction, vector lengths are magnified by 40-fold at the mass centers calculated from the Cα positions of the domains. TPQpsb (magenta spheres) and substrate-binding pocket (white surface) are also overlaid.
