Biology Reference
In-Depth Information
Fig. 4.
Structure of the MS2 coat protein — RNA complex.
be crucial for specific binding. Additional backbone contacts are largely
with phosphates. However, there is one hydrogen bond between the
2´OH of U-5 and the carboxylate group of Glu 63.
17
The phosphate
interactions are mainly mediated by hydrogen bonds and ion pairs
with lysine and arginine side chains.
Among the base-specific contacts between RNA and protein,
the interactions with the bulged A-10 and A-4 in the loop are
especially intriguing. Two very similar binding pockets, one on
each subunit of the protein dimer, are used to recognize these two
bases and are partly responsible for the high specificity of the inter-
action. In both pockets the base is sandwiched between the aliphatic
part of the side chain of lysine 61 and the methyl group of threo-
nine 59 on one side, and the side chain of valine 29 on the other
(Fig. 4). Even though the three-dimensional structure of the
binding pockets is quite similar, the two adenine bases are bound
differently. A-4 is oriented such that its N1 is bound to Serine 47,
while N6 and N7 are bound to threonine 45. On the other hand,
A-10 is bound to Ser 47 via its N3, while its N1 and N6 form
hydrogen bonds with threonine 45. These differences are caused
by the asymmetry. The binding pockets are highly conserved in
related phages.
21,22
