|
Figure 2.
Fig. 2. Structural views and superpositions focusing on
enzyme and substrate residues and water molecules involved in
reaction. (A) Stereoviews comparing AAPR-trypsin (enzyme
carbons, green; substrate carbons and water molecule, yellow)
and leupeptin-trypsin (enzyme carbons, purple; substrate
carbons, orange) with a representative trypsin/inhibitor
Michaelis complex (enzyme carbons, gray; inhibitor carbons,
brick red) allow reconstruction of a probable reaction
coordinate for the acylation reaction. (B) Stereoviews comparing
AAPR-trypsin, AAPK-trypsin (enzyme carbons, light blue;
substrate carbons and water molecule, tan), and
leupeptin-trypsin structures allow reconstruction of a probable
reaction coordinate for water attack in the deacylation
reaction. (C) Stereoviews comparing AAPR-trypsin and
guanidinobenzoyl-trypsin (enzyme carbons, teal; inhibitor
carbons, brown) reveal differences in attack trajectory possibly
responsible for the great differences in reactivity between
these substrates. (D and E) AAPR-trypsin (D) and AAPK-trypsin
(E), stick diagrams overlaid with 2F[o]-F[c] density maps
contoured at 1  (gray mesh) and
F[o]-F[c] maps scaled at 3 (green mesh) reveal
dual conformations of His-57, as well as well defined density
for water S-25. (F) Stereoviews of superimposed acyl-enzyme
structures of different serine proteases, demonstrating a
conserved position for the proposed hydrolytic water. Carbons
and the attacking water molecule are colored differently for
each structure: suc-AAPR-trypsin (green), suc-AAPK-trypsin
(yellow), Ac-NPI-elastase [aqua; PDB ID code 1GVK (28)], and
 -chymotrypsin [magenta;
PDB ID code 2GCT (29)].
|
