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Figure 4.
Figure 4. Structural changes within the peptide binding pocket
during catalysis. a, The active site cleft showing the
location of the peptide substrate (pink) in the acyl -enzyme
complex at pH 5. The enzyme is shown as a gray space filling
model with Ser 195 (green), His 57 (purple) and Asp 102 (brown)
highlighted. b, Model of the protein -peptide complex at pH 5
(pink) overlaid with the model of the tetrahedral intermediate
(blue) (see Methods) . A circle highlights the active site Ser
residue under the bound peptide. Both Wat 318 and hydrogen bonds
between enzyme and peptide are red in the acyl -enzyme complex
and blue in the tetrahedral intermediate. During product
release, the loop formed by residues 217 -219 (immediately below
the binding pocket) moves so as to partially fill a space
previously occupied by the peptide. Arg 217 takes up a position
similar to that found in the native unliganded structure (1QNJ)5.
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