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Figure 3.
Figure 3 Interactions at the active site. (A) Uroporphyrinogen I
product (green), wild-type URO-D (yellow). Protein residues are
shown if one atom from the residue lies within 4.0 Å of the
product in at least one of the structures. Also shown is Leu88.
The pyrrole rings are denoted A, B, C and D, with the D-ring
being the site where acetate and propionate groups are reversed
in the III-isomer product. Van der Waals' surfaces are shown
around the protein atoms, with residues nearer the viewer given
a more transparent surface. Hydrogen bonds are indicated with
dashed lines. The apparent hydrogen bond seen between Ala39 O
and the C-ring propionate indicates that this carboxylate is
protonated. (B) Same as (A), but for the III-isomer product
complex. The I- and III-isomer products superimpose very closely
following overlap on the protein C[  ]atoms.
The major differences are the conformations of Arg37 and Arg 41
side chains. (C) Comparison of product bound to various URO-D
variants. Structures were superimposed by overlap on the protein
C[ ]atoms.
The water molecules that lie roughly in the position of the
wild-type Asp86 side chains are shown explicitly. Color scheme
is indicated and is the same as in Figure 2B. This figure was
generated using Molscript (Kraulis, 1991) and Raster3D (Merritt
and Bacon, 1997).
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