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Figure 2.
Fig. 2. A 30 Å long ammonia channel connects the two
remote active centers of GatCAB. (A) The active site of a
glutaminase reaction in GatA is composed of the conserved
Ser-cis-Ser-Lys catalytic scissors shown as magenta stick
representations. Residues involved in the hydrogen-bonded
network (dashed black lines) in the active site are labeled. A
plausible hydrolytic water molecule is colored light blue and is
on the opposite side of a supposed ammonia product (orange
sphere). The Fo-Fc electron density map (contoured at 3  ,
green mesh) calculated without the glutamine and Ser178 clearly
demonstrates the tetrahedral covalent intermediate of the
glutamine with Ser178. (B) The environment of the ADP binding
site shown together with the omit Fo-Fc electron density map (2
, blue). Residues
contributing to ADP (ball-and-stick) recognition are represented
as stick models with labels. Two water molecules (light blue
spheres) are coordinated to a magnesium ion (purple) and to
ß phosphate. (C) The putative ammonia channel was
calculated using the program CAVER (26), with the structure of
the water-omitted GatCAB/glutamine complex. Glu125B blocking the
ammonia transport route is shown in a space-filling
representation for clarity. The channel was filled with a row of
solvent molecules (light blue spheres), which interact with the
conserved polar residues (colored sticks) along the pathway. A
bound glutamine in GatA is drawn as spheres indicating the start
point of the channel. (D) Schematic representation of the
ammonia channel. Residues defining the channel are colored
corresponding to their properties: red, negative; blue,
positive; black, nonpolar side chain; gray, main chain.
Hydrolyzed ammonia is colored orange. Strictly conserved
residues are underlined and hydrogen-bonding distances are
indicated (Å). The presumed movement of the Glu125B gate
to open the ammonia channel is indicated by a black arrow.
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