Chemistry Reference
In-Depth Information
15.4 Advantages of Two - Metal-Ion Catalysis: Specifi city and Versatility
The exquisite sensitivity of metal ions to the local environment
16,18,105
provides a
means for nucleic acid enzymes to convert small conformational differences into
large catalytic rate changes. Three features of two-metal-ion mechanisms ensure the
substrate recognition and catalytic specifi city: (i) interdependence of substrate rec-
ognition and two-metal-ion binding, as illustrated in RNase H,
63
type II restriction
endonucleases,
67,78,81
ribozyme
106
and DNA polymerases
50,107
; (ii) usage of metal ions
with highly stringent coordination requirements to destabilize the enzyme-substrate
complex and promote product formation, as observed with RNase H
86
and (iii) reli-
ance on the electrostatic environment created by both the catalytic residues and the
nucleic acid substrate for nucleophile formation, and for metal ion movement during
the course of the phosphoryl transfer reaction.
Mg
2+
, known for its exquisite octahedral coordination geometry and narrow
distribution of coordination distance,
18
is most often used in two-metal catalysis.
Ca
2+
, because of its large atomic radius and indifference to ligand number and
coordination distance, usually does not support phosphoryl transfer reactions. Mn
2+
,
which is most similar to Mg
2+
in chemical nature, but has relaxed coordination
requirements, can replace Mg
2+
and allow phosphoryl transfer reactions to occur
with altered catalytic residues, nonideal substrates and reduced specifi city.
50,108 - 112
The natural abundance of cellular Mg
2+
over Mn
2+
thus furthers the substrate
specifi city of two - metal - ion catalysis.
The second advantage of two-metal-ion catalysis is its versatility and reversibil-
ity. The versatility is clearly demonstrated in DNA and RNA synthesis, where
polymerases have to incorporate various nucleotide building blocks ((d)NTPs) with
roughly equal effi ciency and yet in each reaction cycle select only the right one
according to the template base. Two-metal-ion catalysis, which allows the active site
to align correctly only upon association with a Watson-Crick base pair, enables
DNA and RNA polymerases to achieve high specifi city with a broad range of sub-
strates. Regarding reversibility, since two-metal-ion catalysis has no specifi c require-
ment for a general base or acid, it supports both making and breaking of DNA and
RNA. During DNA transposition and RNA splicing, a single active site with two
metal ions can carry out at least two consecutive phosphoryl transfer reactions.
63,84
In the fi rst reaction, DNA or RNA is cleaved to generate a 3
′
- OH (product), and
in the second reaction the 3
-OH is the nucleophile (substrate) and results in strand
transfer (Figure 15.1). The symmetric arrangement of the two metal ions in the
active site of Tn5 transposase and group I ribozyme (Figure 15.7) allows the metal
ions to alternate their roles in activating a nucleophile and stabilizing a pentacova-
lent intermediate in consecutive phosphoryl transfer reactions without releasing the
3
′
- OH.
64,101
′
15.4.1 One - Metal - Ion Catalysis
Exceptions to two - metal - ion catalysis are one - metal - ion and metal - ion - independent
catalysis utilized by certain nucleases and recombinases. To date, only reactions
resulting in 5
′
- OH and 3
′
-phosphate are known to be catalysed by enzymes that
