Molecular Biology of the Cell by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morgan, Martin Raff, Keith Roberts, Peter Walter by by Bruce Alberts, Alexander Johnson, Julian Lewis, David Morg

146 Chapter 3: Proteins
SUBSTRATE
This substrate is an oligosaccharide of six sugars,
labeled A through F. Only sugars D and E are shown in detail.
PRODUCTS
The final products are an oligosaccharide of four sugars
(left) and a disaccharide (right), produced by hydrolysis.
A B C
O
D
O
R
O
CH 2 OH
O
E
O
F
A B C
O
D
O
R
H
O
H
O
CH 2 OH
O
E
O
F
CH 2 OH
R
side chain
on sugar E
CH 2 OH
R
ES
C
C
C
Glu35
Glu35
Glu35
C O
C O
C O
O
H O H O
O
H
H
HOCH 2
CH 2 OH
HOCH 2 H
CH 2 OH
HOCH 2 H H
CH 2 OH
O D O
E
O O O D O O E
O O
O D O O O
O
E
O
R
C
O
C
C
R
R
R
R
H C1 carbon
O
H
R
O
O C
O C
C
O C
Asp52
Asp52
C
O
Asp52
C
EP
In the enzyme–substrate complex (ES), the
enzyme forces sugar D into a strained
conformation. The Glu35 in the enzyme is
positioned to serve as an acid that attacks the
adjacent sugar–sugar bond by donating a proton
(H + ) to sugar E; Asp52 is poised to attack the
C1 carbon atom.
The Asp52 has formed a covalent bond between
the enzyme and the C1 carbon atom of sugar D.
The Glu35 then polarizes a water molecule (red ),
so that its oxygen can readily attack the C1
carbon atom and displace Asp52.
The reaction of the water molecule (red)
completes the hydrolysis and returns the enzyme
to its initial state, forming the final enzyme–
product complex (EP).
atoms that speed up a reaction by using charged groups to alter the distribution of
electrons in the substrates (Figure 3–52B). And as we have also seen, when a substrate
binds to an enzyme, bonds in the substrate are often distorted, changing the
MBoC6 m3.51/3.47
substrate shape. These changes, along with mechanical forces, drive a substrate
toward a particular transition state (Figure 3–52C). Finally, like lysozyme, many
enzymes participate intimately in the reaction by transiently forming a covalent
bond between the substrate and a side chain of the enzyme. Subsequent steps in
the reaction restore the side chain to its original state, so that the enzyme remains
unchanged after the reaction (see also Figure 2–48).
Tightly Bound Small Molecules Add Extra Functions to Proteins
Although we have emphasized the versatility of enzymes—and proteins in general—as
chains of amino acids that perform remarkable functions, there are many
instances in which the amino acids by themselves are not enough. Just as humans
Figure 3–51 Events at the active site
of lysozyme. The top left and top right
drawings show the free substrate and the
free products, respectively, whereas the
other three drawings show the sequential
events at the enzyme active site. Note
the change in the conformation of sugar
D in the enzyme–substrate complex; this
shape change stabilizes the oxocarbenium
ion-like transition states required for
formation and hydrolysis of the covalent
intermediate shown in the middle panel.
It is also possible that a carbonium ion
intermediate forms in step 2, but the
covalent intermediate shown in the middle
panel has been detected with a synthetic
substrate (Movie 3.9). (See D.J. Vocadlo et
al., Nature 412:835–838, 2001.)
–
+
+
–
(A) enzyme binds to two
substrate molecules and
orients them precisely to
encourage a reaction to
occur between them
(B) binding of substrate
to enzyme rearranges
electrons in the substrate,
creating partial negative
and positive charges
that favor a reaction
(C) enzyme strains the
bound substrate
molecule, forcing it
toward a transition
state to favor a reaction
Figure 3–52 Some general strategies of
enzyme catalysis. (A) Holding substrates
together in a precise alignment. (B) Charge
stabilization of reaction intermediates.
(C) Applying forces that distort bonds in the
substrate to increase the rate of a particular
reaction.