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Figure 1.
Figure 1. (a) The structure of PhoB RD. Richardson diagram of
PhoB RD. Helices are shown as blue ribbons (α1 to α5) and
β-strands as yellow arrows (β1 to β5). The N and C-terminal
ends are indicated (N and C, respectively). The green arrow
points to the active site cavity. Key residue side-chains
mentioned throughout the text are highlighted. (b) Dimers
interacting through the α1-Lβ5α5 interface. Cα plot showing
the superimposition of WT-RD (grey) and DAYC-Na (khaki) dimers.
Secondary structure elements belonging to the interface are
indicated; the distance between vicinal Lβ4α4 loops within a
dimer is shown. The green arrows point to the active site
cavities of each protomer within a dimer. The C and N-terminal
ends of the RDs are shown (N and C, respectively). In each case,
molecules A are on the left and molecules B on the right of the
dimer. (c) Packing of WT (grey) and DAYC (khaki) helix α4
against the protein core. Mutated residues or side-chains that
change the conformation are indicated twice, with colour coding
according the molecule they belong to. α-helices and β-strands
numbering is indicated. (d) Each constituting monomer within the
WT RD dimer (superimposed with its solid Connolly surface) has
been rotated vertically 90° from the position occupied in
(b) to grant insight into the interacting surface. The residues
of each molecule participating in direct contacts are shown and
labelled. The colour coding reflects conservation of each
position, ranging from 0% (light yellow) to 100% (intense
red). The approximate location of the active site cleft is
indicated by a green arrowhead. (e) DADE (green) and
BeF-RD[3]^36 (coral) active sites are superimposed (strands β1,
β3 and β4 where used for an optimal superposition of residues
in the active site). Mutated residues or side-chains that change
the conformation are indicated twice. The small spheres
represent water (W) molecules, which are numbered according to
the PDB. The M sphere represents the coordinated metal; the Be
sphere the Beryllium and F1, F2 and F3 the fluorine atoms in the
BeF[3]¯ molecule, an analogue of the activating phosphate
moiety. Electrostatic and hydrogen bond interactions are
represented by broken lines and, together with water oxygen
atoms, are coloured according to the PDB they belong to. W3 and
the interaction between the cation and Met55 carbonyl are not
shown for clarity. Secondary structure elements are indicated.
(f) DAYC (khaki) and BeF[3]-RD^36 (coral) are superimposed
around their active sites. The criteria of representation are
the same as for (e).
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