Figure 1
Crystal structure of ZmASCH. (a) Structure-based sequence alignment of ZmASCH with other related proteins. Sequence alignment was performed using the Clustal Omega from the European Bioinformatics Institute. Identical residues are marked with an asterisk “*”, while strongly and weakly similar residues are marked with “:” and by “.”, respectively. The α-helices (cylinders) and β-strands (arrows) in the ZmASCH structure are numbered in order of their appearance. The Leu residues that were mutated to solve the phasing problem are indicated with boxes. Residues that were mutated for in vitro assays are enclosed in black boxes over a gray background. Abbreviations: ZsYTH, YTH from Z. rouxii; hYTH1, human YTH1; hYTH2, human YTH2; ZmASCH, ASCH from Z. mobilis ZM4. (b) A ribbon diagram of ZmASCH with non-protein molecules observed in the trigonal crystal system. The putative chloride ions (Cl) are represented by pink balls, and the bound polyethylene glycol 400 (P400) is shown as a space-filling model. The observed sulfate ion (SO4), and some residues that form the pocket and the surface cleft, are drawn as stick models. (c) Surface-potential map of the ZmASCH molecule in Fig. 1b. The surface electrostatic potential was calculated using the APBS server (http://www.poissonboltzmann.org/) and is visualized as a color ramp from blue (positive) to red (negative). This figure was rotated with respect to Fig. 1b, to clearly display the surface-potential in the pocket and on the nucleic acid-binding cleft. The surface pocket is marked with a yellow-dotted circle (pocket), and the positively-charged cleft on the surface is indicated with a red-dotted line (cleft). The bound P400 is depicted as a space-filling model and the sulfate ion (SO4) is depicted as stick models. Figures 1(a), 2, 4(a),(b),(c) were prepared by the PyMol molecular graphics program (Schrödinger, LLC).
