Fig. 4: Insulator loop and DNA recognition. | Communications Biology

Fig. 4: Insulator loop and DNA recognition.

From: Crystal structures of monomeric BsmI restriction endonuclease reveal coordinated sequential cleavage of two DNA strands

Fig. 4

A Comparison of the different positions of the Insulator loop. The wt.BsmI structure is represented in light colors, while the Nt*.BsmI one (similar to all the other mutants) is represented in darker colors. The Insulator loop is depicted in blue and its retraction movement away from the DNA is materialized by a double arrow in black. The pink spheres correspond to the calcium ions found in the wt.BsmI structure and their known glutamate ligands are in ball-and-stick representation. The DNA backbone is in grey. B Comparison of the DNA conformation with B-DNA. The Insulator loop of the wt.BsmI is represented in light blue in the context of the beta-sheet of the top-strand nicking domain (in light brown). The blue and yellow patches on the DNA backbone illustrate the position of the scissile phosphodiester bonds of the bottom and the top strand respectively. The light and dark purple DNA backbone corresponds respectively to the top and bottom strands of the cognate DNA in the ideal B-form. The Insulator loop opens up the minor groove of the DNA to bring into position the second nicking site.

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