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Figure 7.
Fig. 7. Proposed reactions at the synthetase active site. (a)
Superposition of synthetase active sites from crystal structures
with informative ligands. The A. aeolicus GatCAB with ATP,
Mn^2+, and Asp (this work) is shown in green with yellow C atoms
for the ligands; the S. aureus GatCAB with ADP and Mg^2+^14 in
orange with orange C for the ligands; and the M.
thermautotrophicus GatDE with tRNA^15 in magenta with yellow C
for tRNA. Mn^2+ ions are shown as purple spheres, Mg^2+ in
orange, and water molecules as red spheres. Substrates ATP, ADP,
Asp, and 3′-CCA of tRNA^Gln are represented as sticks.
Residues interacting with substrates are represented by thick
lines. The ammonia channel (gray surface) enters the synthetase
active site from the right and is continuous with the tRNA
binding site. (b) Model for the activation reaction. ATP is
positioned as in the structure reported here. The terminus of
Asp-tRNA^Asn was modeled based on the GatDE–tRNA complex in
which the 3′-terminal A was disordered. The Asp carboxyl group
is coordinated by the metal in the permanent site, as in the Asp
complex. (c) Model for the amidation complex. The activated
substrate, phosphoryl-Asp-tRNA^Asn, is shifted so that both
phosphate and O^δ coordinate the permanent metal, thereby
positioning the Asp C^γ atom at the exit of the ammonia tunnel,
ready to receive ammonia from the amidase active site. (d)
Schematic diagram of the reaction steps depicted in (b) and (c).
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