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Figure 1.
Figure 1 Stereoview ribbon representation of the Yuh1–Ubal
complex. (A) Ubal is not shown in this panel. Sidechains of the
active-site residues Gln84, Cys90, His166 and Asp181 (red) are
labeled Q, C, H and D. N- and C-termini are labeled. The
disordered segment (residues 63–77) is indicated with the
adjacent ordered residues labeled in magenta. The
active-site-crossover loop is colored yellow. Secondary
structures were as defined by PROMOTIF (Hutchinson and Thornton,
1996). Strands are colored green and the helices blue. Helix 4,
which contains the active-site nucleophile Cys90, is colored
cyan. This helix undergoes a severe kink, indeed PROMOTIF
defines residues 90–100 and 103–105 as separate helices. We
describe this as one continuous helix in order to maintain
consistency of nomenclature with UCH-L3, which also has a severe
kink in the corresponding part of helix 4. The following are
labeled on the figure: strand 0 (S0, residues 11–12), strand 1
(S1, 31–36), strand 2 (S2, 54–60), strand 2^1 (S2^1,
81–82), strand 2^2 (S2^2, 128–129), strand 3 (S3,
165–172), strand 4 (S4, 176–180), strand 5 (S5, 189–193),
strand 6 (S6, 227–233); helix 1 (H1, residues 15–25), helix
2 (H2, 44–46), helix 4 (H4, 90–105), helix 5 (H5,
111–122), helix 6 (H6, 132–143), helix 7 (H7, 205–221).
Helices are alpha-type, except for helix 2 and residues
102–105 of helix 4, which adopt the 3[10] conformation. There
is a turn of alpha helix (residues 146–150) within the
active-site-crossover loop. (B) Same as (A), but including the
Ubal shown in magenta. The sidechains of Ubal residues discussed
in the text are shown in orange and labeled. Figures 1, 4, 5 and
6 were produced with the programs MOLSCRIPT (Kraulis, 1991) and
RASTER 3D (Bacon and Anderson, 1988).
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