Figure 3 - full size

 

Figure 3.
Figure 3. (a) Superimposed structures of PfuLig (blue) and hLigI (orange) around the AMP-binding region. The structures were overlapped manually by fitting the adenyl ring moiety of AMP, colored blue (Pfu) and orange (human). Residues in motif VI, except for RE(D)DK, are depicted as alanine. The bound DNA substrate in hLigI is depicted by a sheet representation and is colored pink. (b) Ribbon diagrams of the adenylation domains from PfuLig and hLigI, flanked by surface representations of motif VI (PfuLig) and the upstream region of the substrate DNA (hLigI), in which the colors of the atoms (nitrogen, blue; oxygen, red) are mapped onto the surface. Since the distribution patterns of the charged atoms on the surfaces of motif VI and the DNA are similar to each other, the replacement of motif VI with DNA may easily occur. Helix A3 of the adenylation domain is responsible for interacting with the acidic portions of both motif VI and DNA, so the C-terminal region of helix A3 should have an abundance of basic residues in the Pfu and human forms, but not in the ChV and T7 forms, implying that this feature is specific for the ligases that adopt an open-closed exchange mechanism with a C-terminal extension helix. (c) Superimposed structures of the RE(D)DK motifs from the closed (PfuLig, cyan) and the open (hLigI, orange) forms. This Figure was prepared by minimizing the distances between the corresponding atom pairs, except for the side-chains of D532 and E880.

The above figure is reprinted by permission from Elsevier: J Mol Biol (2006, 360, 956-967) copyright 2006.