Figure 3.

Aspartate racemase and type II 3-deydrogenate dehyralase. A new circular permutation discovered between a) aspartate racemase (1iu9, chain A, top) and type II 3-dehydrogenate dehydralase (1h0r, chain A, bottom) superimpose well spatially with an RMSD of 1.49Å between 59 residues, with a significant p-value of 4.7 × 10^-4. b) These proteins are related by a circular permutation. The loop connecting helix 1 with strand 1 in aspartate racemase (in rectangle, top) becomes disconnected in type II 3-dehydrogenate dehydralase (in rectangle, bottom), but the N- and C- termini of aspartate racemase (in ellipse, top) becomes connected in dehydrogenate dehydralase (in ellipse, bottom) with an insertion (shown in green). For visualization, residues of aspartate racemase in the N-to-C direction before the cut in the dehydrogenate dehydralase are colored red, and residues after the cut are colored blue. c) The topology diagram of these two proteins. Here an ellipse represents a helix and a block arrow represents a strand.