Bioorganic Chemistry
19
O
O
P
O
O
−
O
N
1
O
OH
P
O
O
−
O
O
N
2
OH
NN
H
HN
NH
+
O
O
P
O
O
−
O
N
1
HN
NH
HN
NH
+
O
O
PO
−
−
O
O
O
N
2
OH
+
O
O
P
O
O
−
O
N
1
HN
NH
+
O
P
O
O
−
O
NH
N
H
O
H
O
HO
N
2
OH
O
O
P
O
O
−
O
N
1
HN
NH
HN
NH
+
O
O
PO
−
−
O
OH
+
O
O
P
O
O
−
O
N
1
NN
H
O
OH
P
O
−
O
O
−
HN
NH
+
Fig. 14
The mechanism of catalysis of phosphodiester cleavage in single-stranded RNA by RNase A,
accomplished by coordinated acid–base chemistry of two histidines.
intermediate. In essentially the reverse
process,
another
active
site
histidine
(which is protonated) protonates the 5
0
-
OH of the other nucleotide. In doing
so, it allows the flow of electrons in the
phosphorus oxygen bond to migrate to the
(now) positively charged 5
0
-OH–histidine
complex.
The
result
of
this
electron
movement is the release of one of the
products, the free 5
0
-OH nucleotide, and
the formation of the cyclic phosphate
form of the 3
0
-OH phosphate. In the
same way that histidine A deprotonated
the 2
0
-OH for attack originally, in the
Fnal step, histidine B deprotonates a
water, essentially producing a nucleophilic
hydroxide anion. This then attacks the
cyclic phosphate intermediate. Histidine
A can now act as an acid and protonate
the 2
0
-OH. This again will allow the
electrons in that P
−
Ob
ondt
om
ig
r
a
t
e
toward the positive charge. The result is the
Fnal product, the 3
0
-phosphate nucleotide.
This
reaction
sequence
demonstrates
how
the
reactivity
of
speciFc
groups
can be signiFcantly altered by speciFc
electrostatic
interactions.
±urthermore,
enzymes
can
both
protonate
and
deprotonate virtually simultaneously, so
that if the reaction calls for it, electrons can
simultaneously be ‘‘pushed’’ and ‘‘pulled.’’
A rich area of bioorganic chemistry is in
the development of small molecules that
can in some way mimic the actions of
