Figure 1 - full size


Figure 1.
Fig. 1. (a) Ribbon diagram of HincII dimer (subunits shown in light and dark green) showing bound DNA (pale beige, red, and blue), site of Gln138 (cyan) intercalation, position of Ca^2+ (yellow) in the two active sites, and center step of the recognition sequence (red, blue). (b) The numbering scheme used throughout the paper for the HincII recognition sequence. Y indicates either C or T, R indicates either G or A. (c) Structure of the pyrimidine–purine step as found in the structure of wild-type HincII bound to cognate DNA containing GTCGAC (left) and in B-form DNA (right). The Y7 is unstacked from R8 within the same strand in the HincII bound DNA, and the center step purines (R8 and R8′) have increased stacking across the DNA duplex, forming a cross-strand purine stack (CSPS). (d) Overlay of portions of the structures of wtHincII/CG/Ca^2+ (white) and Q138F/TA/Ca^2+ (cocrystal) (color); nuc, putative water nucleophile of the DNA-cleavage reaction; SP, phosphate at the scissile phosphodiester bond. Arrows emphasize the largest structural differences: the side chain of residue 138 sits differently between the adjacent cytosine bases at the site of intercalation and the main chain around Phe138 is shifted away from the DNA to accommodate this different position (1). As a result, the side chain of Ala137 no longer makes a van der Waals contact to the DNA (2), which may be the reason for the altered pucker of the deoxyribose at Cyt10 from C1′exo to C2′endo (3). The different pucker at Cyt 0 causes a twisting of the sugar–phosphate backbone of the DNA strand (4) propagating to the phosphate between the Pyr7 and Pur8, potentially resulting in the O5′ of Ade9 jutting into the space normally occupied by the side chain of Thr130 (5). To avoid the steric conflict, the phosphate of Ade9 is rotated, blocking the position of the putative nucleophilic water (6).

The above figure is reprinted from an Open Access publication published by Elsevier: J Mol Biol (2008, 383, 186-204) copyright 2008.