Figure 3.
Figure 3. Conformation of the active site and the L1 loop.
(a) Ribbon diagram of GlpG (molecule A) showing the open cavity
leading to the active site. All invariant residues among the
eight rhomboid homologs in Figure 2 are shown. Red side chains,
putative catalytic-dyad residues Ser201 and His254; gold side
chains, all other invariant residues; red spheres, three water
molecules in the cavity. Ser201 hydrogen-bonds to His254 as well
as a water molecule. (b) Stereo view of interactions surrounding
the conserved Trp-Arg motif in GlpG. Trp136 and Arg137 appear to
stabilize the conformation of the L1 loop by participating in a
network of hydrogen bonds as well as van der Waals interactions
with surrounding residues of the L1 loop. (c) Stereo view of
packing interactions between residues of the L1 loop and
residues in helix 3
and the L3 loop. This interface is dominated by extensive van
der Waals interactions. (d) Stereo comparison of packing
interactions involving the L1 loop in our structure and in that
reported recently^24. Coloring of our structure is as in a
except that all side chains are colored yellow. The main chain
and side chains of the published structure^24 are in gray. The
structure and the packing interactions are nearly identical
between these two structures.
The above figure is reprinted
by permission from Macmillan Publishers Ltd:
Nat Struct Mol Biol
(2006,
13,
1084-1091)
copyright 2006.
3
and the L3 loop. This interface is dominated by extensive van
der Waals interactions. (d) Stereo comparison of packing
interactions involving the L1 loop in our structure and in that
reported recently^24. Coloring of our structure is as in a
except that all side chains are colored yellow. The main chain
and side chains of the published structure^24 are in gray. The
structure and the packing interactions are nearly identical
between these two structures.