Biology Reference
In-Depth Information
cleavage reactions. As a class, the nucleolytic ribozymes all appear to use general acid-
base catalysis; guanine nucleobases in particular are very common participants.
1. INTRODUCTION
The hairpin
1-3
andVarkudsatellite(VS)
4
ribozymes are members of the
class of nucleolytic ribozymes that cleave or ligate RNA at a specific site within
the ribozyme.
5
The other members of this class are the hammerhead, hepatitis
delta virus (HDV), and GlmS ribozymes. The biological role of these cleavage
and ligation events is the processing of replication intermediates, except for the
GlmS ribozyme which effects gene control by cleavage of mRNA.
6
The nucleolytic ribozymes carry out cleavage at a specific site by a trans-
esterification reaction in which the 2
0
-O attacks the adjacent phosphorus
with concomitant departure of the 5
0
-O to leave a 2
0
,3
0
-cyclic phosphate
(
Fig. 3.1
). Ligation is simply the reverse reaction in which the 5
0
-O attacks
the phosphorus with departure of the 2
0
-O to open the cyclic phosphate.
The reactions follow an S
N
2 mechanism with inversion of configuration
at the phosphate. The reactions are accelerated by at least 10
5
-fold when
B
1
B
1
B
1
O
O
O
HX
O
O
O
:X
O
O
O
H
O
P
P
O
P
cl
eavag
e
O
O
O
O
YH
O
O
ligation
B
2
B
2
B
2
O
Y:
HO
O
O
O
OH
O
OH
O
OH
Figure 3.1 The proposed chemical mechanism of nucleolytic ribozymes cleavage by
general acid
-
base catalysis. The transesterification reaction proceeds by attack of the
2
0
-O nucleophile to generated a cyclic 2
0
,3
0
-cyclic phosphate in the cleavage reaction
(highlighted red), or by attack of the 5
0
-O in the reverse ligation reaction (blue). In
the cleavage reaction, the 2
0
-O nucleophile is deprotonated by a general base, and
the 5
0
-O leaving group is protonated by a general acid. In the ligation reaction, the
roles of general base and acid are reversed to deprotonate the 5
0
-O nucleophile and
protonate the 2
0
-O leaving group.
Search WWH ::
Custom Search