Biology Reference
In-Depth Information
sequence of this RNA binding domain is conserved among AMV and
related viruses (ilarviruses).
27
It has been demonstrated that the argi-
nine at the center of this sequence (position 17 in the AMV coat pro-
tein) is crucial for RNA binding.
27-31
Circular dichroism studies and
the observation that crystallization of the coat protein requires prote-
olytic cleavage of the N-terminus suggest that the N-terminal RNA
binding domain of the AMV coat protein is unstructured in the
absence of RNA.
32-34
The recent co-crystal structure of the RNA signal sequence and a
26-amino acid peptide based on the AMV coat protein N-terminus
provides a first glance at how RNA and protein interact in this virus
to ensure correct packaging.
35
The structure also reveals the sig-
nificance of the AUGC repeats found in the 3´ UTRs of all AMV
genomic RNAs.
The structure illustrates that the RNA and the coat protein N-ter-
minus co-fold to form a novel structure in which the peptide and the
RNA adopt conformations that substantially differ from their unbound
forms (Fig. 5). The core of the peptide that contains the recognition
sequence PTxRSxxY takes on an
-helical structure followed by an L-
turn, which puts all crucial amino acids in direct contact with the
RNA. The 29-nucleotide RNA segment undergoes a conformational
transition that leads to the formation of base pairs between neighbor-
ing AUGC repeats (Fig. 5). In this unusual arrangement, the uridine
in position 844 and the cytosine in position 846 pair with adenine 865
and guanine 867, respectively. The resulting G:C pair is a
Watson-Crick type base pair; however, the A:U pair adopts the non-
canonical reverse Watson-Crick topology (Fig. 5). The two new base
pairs form a continuation of the first stem (nt 847-864) and an iden-
tical arrangement is seen at the base of stem 2. The formation of these
base pairs significantly distorts the structure of the AMV RNA. The
AUGC repeat that is located in between the two stem-loops (nt
865-868) participates in base pairing interactions at the bottom of
both stems. A direct consequence of this is that alternating bases in the
AUGC sequence are pointing into opposite directions. The resulting
stacking arrangement of the bases introduces a kink into the RNA
backbone.
α
