Core structural components corresponding to conserved regions in the AAA+ multiple alignment. (a) Structural components of the DNA polymerase δ′ subunit (pdb: 1A5T). (b) Structural components of NSF–D2 (pdb: 1NSF). Four key conserved positions are indicated. (1) E133/K631 and (2) R158/A660 correspond to conserved (charged residue) positions in boxes VI and VII, respectively (see Fig.4 and text). (3) P167/I670 corresponds to a conserved hydrophobic position in box VII′ that presumably establishes an important contact with the amino-terminal region of the AAA+ module (Yu et al. 1998); in both Pol III d′ and NSF–D2 this hydrophobic residue contacts a Trp residue. (4) G199/K708 corresponds to a conserved basic residue position within the sensor-2 motif (see text). Each core structural element has the same color as the bar over the corresponding aligned region in Fig. 1. Unconserved regions are shown as single gray threads. ATP is colored cyan in b. The β-strand and three-helix bundle corresponding to the last four (orange, yellow, lime, and green) components and the box II (scarlet) component are distinct structural characteristics of the AAA+ class (see Fig. 3and text). Note, however, that the box II component is absent from Pol III δ′. These and the other structural images were created using the RASMOL program by Roger Sayle (GlaxoWellcome).
