Chemistry Reference
In-Depth Information
FIGURE 10.15
Schematic representation of the reaction steps proposed for RNase H. The substrate RNA is shown in pink and products in
purple. Coordination of metal ions is highlighted in dark blue, and scissile phosphate in red. Selected hydrogen bonds are shown as blue lines.
Black circles represent water molecules. The distance between the two metal ions is indicated in the enzyme
e
substrate, enzyme
e
intermediate,
and enzyme
e
product complexes.
(Adapted from
Nowotny & Yang, 2006
.
)
5
0
-phosphate group allows metal ion B to relax and attain a regular octahedral coordination with two new ligands
from water molecules.
In the classic two-metal polymerase/phosphodiesterase reactions, one ion activates a catalytic water or ribose
hydroxyl for nucleophilic attack, while the second coordinates the leaving group: both metal ions stabilise
the pentavalent transition state. Recent structural studies (
Schmidt, Burgin, Deweese, Osheroff, & Berger, 2010
:
pp. 974) have led to a novel variation of the classic two-metal mechanism for DNA cleavage by topoisomerases.
4
The proposed cleavage mechanism is indicated in
Figure 10.16
. Metal A and Arg781 stabilise the transition state,
whereas metal B and His736 anchor the (
1) phosphate.
Yet another superfamily, the nucleotidyl-transferase family, also utilises the two-metal-ion-dependent catalysis:
the members include transposases, retrovirus integrases, and Holliday junction resolvases.
5
Whereas, in the
nucleases, the Mg
2
รพ
ions are asymmetrically coordinated, and play distinct roles, in respectively activating the
e
4. These important enzymes are responsible for DNA supercoiling
5. It would simply befuddle the reader to explain what these enzymes do
e
suffice it to know that they cut and paste DNA fragments with as
much exquisite specificity, as we hopefully do with our word processers!
