Figure 3
Comparison with R.PabI. (a) Characteristic structure of R.CcoLI. The structures of R.CcoLI protomer (chain A) and R.PabI protomer in the product DNA-binding state (PDB ID: 3WAZ, chain A) are superposed and are colored cyan and gray, respectively. Characteristic local structures in R.CcoLI that are not observed in R.PabI are indicated by red dotted squares (sites 1 and 2). The extended loops of R.CcoLI are indicated by orange dotted squares. (b) Structure of the insertion residues of R.CcoLI (site 1 in (A)). Residue numbers and secondary structures of R.CcoLI are labeled cyan. Residue numbers of R.PabI are labeled gray. (c) Structure of the N-terminal region of R.CcoLI (site 2 in (A)). Secondary structures of R.CcoLI and R.PabI are labeled cyan and gray, respectively. (d) Superposition of the dimeric structure of R.CcoLI (cyan) and those of R.PabI in the DNA-free state (PDB ID: 2DVY, green), the sequence-nonspecific DNA-binding state (5IFF, yellow), the intermediate state (PDB ID: 6L2O, salmon pink) and the product DNA-binding state (3WAZ, magenta).
