|
Figure 6.
Figure 6. The Putative Catalytic Center of KsgA
(A)
Stereo view showing the superposition of tetraloop structures
with the KsgA-RNA-SAH complex. SAH is shown as spheres (carbon
in gray, nitrogen in blue, oxygen in red, and sulfur in yellow).
KsgA is shown as a ribbon diagram in gray. RNAs are illustrated
as tube-and-stick models with the positions of A1518 and A1519
indicated by spheres. RNA in KsgA-RNA-SAH is shown in orange, a
structure of product RNA with dimethylated A1518 and A1519 (PDB
ID code 2AW7) in cyan, and a model for substrate RNA with
unmethylated adenosines (PDB ID code 1AFX) in magenta.
(B)
Stereo view showing the superposition of the putative catalytic
center of KsgA as observed in the ternary KsgA-RNA-SAH complex
(green) with the catalytic center assembly of M·TaqI as
observed in the M·TaqI-DNA-NEA structure (PDB ID code
1G38; yellow). The alignment was based on the cofactor SAH
(stick model with carbon in green, nitrogen in blue, oxygen in
red, and sulfur in yellow) and the cofactor analog NEA (stick
model with carbon in yellow). The target adenine dA606 for
M·TaqI is shown as a stick model in magenta, whereas the
A1518 and A1519 for KsgA are shown as stick models in red. The
contact between atom N6 of dA606 in the M·TaqI complex
and atom S of SAH in the KsgA complex is indicated with a dashed
line in black.
(C) A close-up stereo view showing the
details of the adenine-binding site. The amino acid side chains
in motif IV (N105, P106, P107, and Y108) and motif VIII (F196)
in M·TaqI are shown as line models in yellow. The
corresponding side chains in KsgA (N101, L102, P103, Y104, and
F166) are shown in green. The adenine substrate is shown in
magenta.
|
