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Figure 1.
Figure 1. (a) Stereo view showing superimposed WT M.HhaI (grey
3MHT.pdb) and R165A M.HhaI (cyan) complexed to AdoHcy (yellow
in WT, orange in R165A), a DNA substrate (red in WT, violet in
R165A) and Val121, Arg165, and Glu119 in green in the WT M.HhaI
complex structure and in marine in the mutant complex
structure. The flipped out cytosine (red in WT, violet in R165A)
can be seen. The RMSD for both structures is 0.47 Å,
based on comparing the protein backbones. (b) The previously
characterized base flipping motif within the WT M.HhaI^26
showing contacts (dotted black lines) between the Arg165 and the
flipped out cytosine base within the active site. DNA
(magenta), and the flipped out cytosine base (salmon); Val121,
Arg165, and Glu119 (green), and the protein backbone (gray) are
shown. The distance unit is Å. (c) Stereo view shows
superimposing the core active sites of the WT M.HhaI/DNA/AdoHcy
(3MHT.pdb grey) and R165A M.HhaI/DNA/AdoHcy (cyan) ternary
structures. The flipped out cytosine base, Cys81, Glu119,
Val121, Arg163, Arg165, and Ala165 (thick lines), and the other
residues and protein backbone (transparent sticks and
transparent cartoon loops) are shown. (d) Stereo view showing
the flipped out cytosine base with the 2F[o]–F[c] map (mesh
in orange) contoured at 1.0 σ in the R165A M.HhaI/DNA/AdoHcy
complex structure. (e) Stereo view showing omit electron
density maps contoured at 1.0 σ, where the flipped out
cytosine base and the 5′ phosphate were omitted in the
structure factor calculation. The heteroatom colors are: red,
oxygen; blue, nitrogen; hot pink, phosphorus; purple, water;
and carbon atoms are shown in gray in all images. Figure 1.
(a) Stereo view showing superimposed WT M.HhaI (grey 3MHT.pdb)
and R165A M.HhaI (cyan) complexed to AdoHcy (yellow in WT,
orange in R165A), a DNA substrate (red in WT, violet in R165A)
and Val121, Arg165, and Glu119 in green in the WT M.HhaI complex
structure and in marine in the mutant complex structure. The
flipped out cytosine (red in WT, violet in R165A) can be seen.
The RMSD for both structures is 0.47 Å, based on comparing
the protein backbones. (b) The previously characterized base
flipping motif within the WT M.HhaI[4]^26 showing contacts
(dotted black lines) between the Arg165 and the flipped out
cytosine base within the active site. DNA (magenta), and the
flipped out cytosine base (salmon); Val121, Arg165, and Glu119
(green), and the protein backbone (gray) are shown. The distance
unit is Å. (c) Stereo view shows superimposing the core
active sites of the WT M.HhaI/DNA/AdoHcy (3MHT.pdb grey) and
R165A M.HhaI/DNA/AdoHcy (cyan) ternary structures. The flipped
out cytosine base, Cys81, Glu119, Val121, Arg163, Arg165, and
Ala165 (thick lines), and the other residues and protein
backbone (transparent sticks and transparent cartoon loops) are
shown. (d) Stereo view showing the flipped out cytosine base
with the 2F[o]–F[c] map (mesh in orange) contoured at 1.0 σ
in the R165A M.HhaI/DNA/AdoHcy complex structure. (e) Stereo
view showing omit electron density maps contoured at 1.0 σ,
where the flipped out cytosine base and the 5′ phosphate were
omitted in the structure factor calculation. The heteroatom
colors are: red, oxygen; blue, nitrogen; hot pink, phosphorus;
purple, water; and carbon atoms are shown in gray in all images.
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