Introduction to Enzyme and Coenzyme Chemistry - E-Library Home

46 Chapter 3
E + S
E + S
ES'
ES
‘strained’ conformation
Figure 3.20 Rate acceleration from a strained ES 0 complex.
substrate to compensate for the adoption of an unfavourable conformation in
the strained part of the molecule.
To illustrate this concept, we shall look at the example of carboxypeptidase
A, a Zn 2þ -containing protease similar to thermolysin. When the X-ray crystal
structure of carboxypeptidase A was solved, it was found that in order to bind
the peptide substrate with the most favourable enzyme–substrate interactions, a
‘twist’ needed to be introduced into the scissile amide bond. In this conformation
the carbonyl group of the amide being hydrolysed was bound slightly out
of plane of the amide N2H bond, assisted by co-ordination to the active site
zinc ion. This has the eVect of reducing the overlap of the nitrogen lone pair of
electrons with the carbonyl p-bond, which requires the amide bond to be
planar. This makes the carbonyl much more reactive, more like a ketone
group than an amide, so it is much more susceptible to nucleophilic attack, in
this case by the carboxylate side chain of Glu-270. Figure 3.21 shows that in this
strained conformation the carbonyl oxygen has already moved some distance
towards where it will be in the transition state, so the energy diVerence between
the bound conformation and the transition state is reduced, hence we see rate
acceleration.
Thus, if an enzyme is able to bind its substrate in a less favourable but more
reactive conformation, then it is able to realise additional rate acceleration in
this way. Analysis of this type requires detailed insight from X-ray crystallography,
so it is not surprising that there are only a few well-documented
examples of this phenomenon. One other is that of lysozyme, which we shall
see in Chapter 5. However, it is possible that this strategy may be used in many
enzyme-catalysed reactions.
Zn 2+
O
O
H N
H N
H
normal planar conformation ‘strained’ conformation
Figure 3.21 Strained substrate conformation in carboxypeptidase A.
N
δ−
Zn 2+
O
δ−
O-Enz