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
previous page 693 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online next page 695 Encyclopedia of Molecular Cell Biology and Molecular Medicine read online Home Toggle text on/off