Essential Cell Biology 5th edition

How Proteins Work
147
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 BC
O
R
D
O
CH 2 OH
O
CH 2 OH
O
E
R
O
F
side chain
on sugar E
A BC
O
R
D
O
CH 2 OH
H
O
H
O
CH 2 OH
O
E
R
O
F
STEP 1:
SUBSTRATE BINDING
STEP 5:
PRODUCT RELEASE
O
Glu 35
C
Glu 35
C
Glu 35
C
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
D O
E
O O O D O O E
O O
O D O O O
O
E
R
C
O
C
C
R
R
R
R
H C1 carbon
O
H
R
O
O C
O C
C
O C
Asp 52
Asp 52
C
O
Asp 52
C
O
STEP 2: FORMATION OF ES
In the enzyme–substrate complex (ES), the
lysozyme forces sugar D into a strained
conformation. The Glu 35 in the active site is
positioned to serve as an acid that attacks the
adjacent sugar–sugar bond by donating a proton
(H + ) to sugar E; Asp 52 is poised to attack the
C1 carbon atom of sugar D.
STEP 3: TRANSITION STATE
The Asp 52 has formed a covalent bond between
the enzyme and the C1 carbon atom of sugar D.
The Glu 35 then polarizes a water molecule (red),
so that its oxygen can readily attack the C1
carbon atom of sugar D and displace Asp 52.
STEP 4: FORMATION OF EP
The water molecule splits: its –OH group attaches
to sugar D and its remaining proton replaces the
proton donated by Glu 35 in step 2. This
completes the hydrolysis and returns the enzyme
to its initial state, forming the final enzyme–
product complex (EP).
Figure 4−39 Enzymes bind to, and chemically alter, substrate molecules. In the active site of lysozyme, a
covalent bond in a polysaccharide molecule is bent and then broken. The top row shows the free substrate and
the free products. The three lower panels ECB5 depict 04.39sequential events at the enzyme active site, during which a
sugar–sugar covalent bond is broken. Note the change in the conformation of sugar D in the enzyme–substrate
complex compared with the free substrate. This conformation favors the formation of the transition state shown
in the middle panel, greatly lowering the activation energy required for the reaction. The reaction, and the
structure of lysozyme bound to its product, are shown in Movie 4.8 and Movie 4.9. (Based on D.J. Vocadlo et al.,
Nature 412:835–838, 2001.)
Binding to the enzyme also changes the shape of the substrate, bending
bonds so as to drive the bound molecule toward a particular transition
state (Figure 4−40C). Finally, like lysozyme, many enzymes participate
intimately in the reaction by briefly forming a covalent bond between
the substrate and an amino acid side chain in the active site. Subsequent
steps in the reaction restore the side chain to its original state, so that the
enzyme remains unchanged after the reaction and can go on to catalyze
many more reactions.
Many Drugs Inhibit Enzymes
Many of the drugs we take to treat or prevent illness work by blocking the
activity of a particular enzyme. Cholesterol-lowering statins inhibit HMG-
CoA reductase, an enzyme involved in the synthesis of cholesterol by
the liver. Methotrexate kills some types of cancer cells by shutting down
dihydrofolate reductase, an enzyme that produces a compound required