Figure 5: Analysis of loops within UbL–UBA proteins.
From: Rad23 escapes degradation because it lacks a proteasome initiation region
Homologues of Rad23, Dsk2 and Ddi1 were retrieved from species selected broadly from evolution (see Supplementary Information). The loops within these proteins are defined as sequences that fall between motifs found in the SMART59 and Pfam41 databases. (a) Schematic of UbL–UBA proteins. Domains and loops represented are not to scale. In addition to UbL and UBA, abbreviations include ST2 (Sti1/Sti1 pair) and ASP (Asp_protease). Note that Rad4-binding domain (RBD) corresponds to the Pfam domain XPC. (b) Relative conservation of domains and loops. Conservation was evaluated by aligning individual domains with Clustal W60, extracting the pairwise percent conservation and averaging. Domains are represented by horizontal segments. Rad23 is shown in red, Dsk2 class I and II are shown in dark and light blue, respectively, and Ddi1 is shown in green. To align all of the UBA domains in the schematic, break points are introduced into the traces for class I Dsk2 and Ddi1. (c) Plot of loop lengths. The colour scheme for the loops is continued from b. Black dots indicate the average loop length.
