Enzyme Mechanisms

Enzymes function by a wide variety of mechanisms. We will cover a few examples to

illustrate the means that enzymes use to catalyze reactions.
Serine proteases
Peptide bond hydrolysis is a very common process. A wide variety of enzymes can
perform proteolytic reactions.
Members of one large family of protease are called serine proteases because of the
important serine at the active site. All of the serine proteases contain three residues
at their active site: a serine, a histidine, and an aspartate. These comprise the
characteristic catalytic triad. In the numbering scheme for chymotrypsin (a
numbering scheme which is typically used in studies of any of the mammalian
serine proteases), the residues are Ser195, His57, and Asp102. Note that these
residues are distributed throughout the 240 amino acid residues found in
chymotrypsin, but are located in close proximity in the active three-dimensional
conformation of the enzyme (see figure, below).
The serine proteases are synthesized as larger, inactive, precursors. As an example:
chymotrypsinogen is converted to chymotrypsin by two cleavage processes involving
excision of residues 12-15 and 147-148. Interestingly the structures of
chymotrypsinogen and chymotrypsin (including the catalytic residues) are almost
completely superimposable; the conformational change involved in the conversion
process appears to be fairly small. The implication is that relatively small structural
changes can cause dramatic changes in activity. (Note: some changes in other
aspects of the active site are observed. However, because the catalytic triad residues
are observed in their normal conformation, the zymogen forms of serine proteases
usually exhibit low levels of catalytic activity.)
Ser195

Residues
147-148
This
figure
shows
superimposed
structures of chymotrypsin (in blue,
from
PDB
ID
1CA0)
and
chymotrypsinogen (in red, from PDB
ID 2CGA). Note the overall similarity in
the structures, especially on the left side
of the figure and in the position of the
catalytic triad residues. The location of
the excised residues (12-15 and 147-148)
removed
in
the
conversion
of
chymotrypsinogen to chymotrypsin is
shown in orange.

His57
Asp102

Residues
12-15

Copyright 2000-2011 Mark Brandt, Ph.D.

27

Some bacterial serine proteases (e.g., Streptomyces griseus Protease A) are

structurally similar to the mammalian enzymes; the invention of the serine
protease structure therefore occurred prior to the divergence of prokaryotes and
eukaryotes. On the other hand, the Bacillus subtilus protease subtilisin, although it
has the same catalytic residues, has a completely different structure, suggesting
that serine protease mechanism has been invented more than once during
evolution.
The serine proteases differ in their sequence and in their substrate specificity: the
bacterial protease subtilisin (one of the major enzymes that resulted in the
advertising slogan the cleaning power of enzymes!) will cleave essentially any
substrate, while one of the enzymes in the clotting cascade, Factor Xa, requires a
four residue recognition sequence, Ile-Glu-Gly-Arg, in order to uniquely hydrolyze
its polypeptide substrate after the arginine.
Trypsin is specific for cleavage after lysine and arginine. Trypsin contains Asp189 in
the substrate side-chain binding pocket, and this residue forms an electrostatic
interaction with basic residues. However, the specificity is not completely dependent
on a single residue; mutating Asp189 to serine (the corresponding residue in
chymotrypsin) converts trypsin into a non-specific protease, rather than into an
enzyme with chymotrypsin-like specificity. (Even incorporating other mutations in
nearby residues is only partially effective at producing a chymotrypsin-like enzyme;
proteins are complex entities!)
Catalytic mechanism of serine proteases
Serine proteases increase the rate of peptide bond hydrolysis by ~1010 compared to
the uncatalyzed reaction. A variety of structural features are responsible for the
catalytic effectiveness of these enzymes. As mentioned above, the serine proteases
all have three residues that are critical for catalysis: a serine, a histidine, and an
aspartic acid. These are conserved in all of the serine proteases, and are
superimposable in the crystal structures of these proteins.
Steps in the catalytic process:
1) Substrate binding. Note that for the substrate peptide, the side-chain of the
amino acid residue immediately before the scissile peptide bond can bind to
the recognition site on the enzyme.
N

N
H

H
O
Peptide

C
R

Substrate side-chain
recognition site

28

R
O

Peptide

N
H

O H
Ser195

Copyright 2000-2011 Mark Brandt, Ph.D.

His57

O
Asp102

2) Nucleophilic attack. Serine195 acts as a nucleophile, facilitated by

Histidine57, which abstracts a proton from Ser195. The result of the
nucleophilic attack is a covalent bond between the Ser195 side-chain oxygen
and the substrate. The negative charge that develops on the peptide carbonyl
oxygen is stabilized by hydrogen bonds formed from two protease backbone
amide protons. This region of the protein is called the oxyanion hole,
because it stabilizes the negative charge on the oxygen; the oxyanion hole is
critical for catalysis. (Note: the oxyanion hole includes the backbone amide
proton from Ser195; the diagrams illustrating this discussion are thus
somewhat distorted from the three-dimensional structure.)
Oxyanion hole
N

N
H

H
O
Peptide

C
R

R
O

Peptide

N
H

O H

Ser195

Asp102

His57

3) Protonation. His57 donates a proton to the substrate amide nitrogen,

allowing release of the C-terminal part of the substrate as a free peptide.
Oxyanion hole
N
H
O
C

Peptide
R

N
H

H
O

Ser195

N
H

H N

Peptide

Peptide

N
H

Peptide

H
O

Ser195

HN

Asp102

His57

O
Asp102

His57

4) Ester hydrolysis. The final step is an attack by water on the ester bond
between the peptide and the Ser195 oxygen. This forms the second product
peptide with a normal carboxyl group, and regenerates the serine hydroxyl.
The second peptide then dissociates from the enzyme to allow another
Copyright 2000-2011 Mark Brandt, Ph.D.

29

catalytic cycle to begin.

N

N
H

O
C

Peptide

O
O

H
O

Ser195

Peptide

H
R

N
H

H
O H

Asp102
Ser195

His57

OH

His57

As is apparent in the series of drawings above, Ser195 is the residue that performs
the actual catalysis, while the other residues seem to be important for positioning of
the serine and for stabilizing the intermediate states. Aspartate102 is relatively far
from the substrate; Asp102 helps position His57, and raises the pKa of His57to allow
the histidine to act as a base. This is important to the catalytic process: mutation of
Asp102 to asparagine decreases the kcat by ~10,000-fold.
The serine protease reaction mechanism involves a covalent intermediate between
Ser195 and the substrate. Although polypeptides do (very slowly) hydrolyze in
aqueous solution, the hydrolysis reaction does not involve the formation of a
covalent bond with a passing serine side-chain. Thus, the serine protease
mechanism involves the use of an alternative pathway from that used in the
uncatalyzed reaction.
The serine protease mechanism does, however, involve stabilization of the
transition state. This has been observed in mutant studies in which all of the
catalytic triad residues were mutated. Although the reaction mechanism might be
interpreted to predict that the loss of the active site serine would inactivate the
enzyme, in fact, the triple mutant (where all three of the catalytic triad residues are
changed to other residues) retains some ability to catalyze the reaction, and
increases the rate of hydrolysis by ~5 x 104-fold over the uncatalyzed reaction. This
appears to be the result of the binding of the transition state to the enzyme, and in
particular to the precise positioning of the oxyanion hole which allows the
stabilization of the charged transition state. (Although all proteins contain peptide
backbones, in general proteins lack the precise three-dimensional structure to
catalyze reactions, which is why all proteins do not act as proteases.)
Serine proteases are very useful as model enzymes for studying catalytic processes,
because they use a variety of techniques for accelerating the reaction rate. They use
acid-base catalysis (the histidine abstraction of the serine proton, and the histidine
donation of the proton to allow release of the first peptide). Serine proteases also
use charge stabilization (in particular, the oxyanion hole) and geometric factors (in
particular the better fit of the tetrahedral alkoxide intermediate than the planar
carbonyl structures) to lower the energy of the transition state, and use covalent
catalysis to assist in the reaction.

Copyright 2000-2011 Mark Brandt, Ph.D.

30

Asp102

How do we know all this?

The serine proteases have been heavily studied. We will return to the serine
protease mechanism later when we discuss inhibition, but one feature of research
into the mechanism deserves some emphasis. The formation of the covalent enzymesubstrate intermediate was first proposed after a series of studies by B.S. Hartley
and B.A. Kilby in 1954. They used a model substrate (p-nitrophenylacetate) to
examine the kinetics of the reaction. Chymotrypsin has a low kcat for pnitrophenylacetate, which simplifies some of the analysis. The model substrate also
has the advantage of forming a colored product p-nitrophenolate. They discovered
that some p-nitrophenolate was released rapidly (burst phase kinetics) prior to the
establishment of the steady state.
Normal enzyme kinetic measurements involve a brief period following addition of
the enzyme, in which the enzyme-substrate complex forms. This pre-steady state
condition is followed by the linear formation of product with time characteristic of
steady state conditions. (The length of time required for steady state formation is
somewhat exaggerated in the graph below).

[Product]

Steady
state

Time

[Product]

In the case of the serine proteases, a brief period of rapid product formation also
occurs prior to establishment of steady state conditions. The amount of product
formed in this burst phase corresponded to about 1 mole of product per mole of
enzyme, suggesting that the enzyme rapidly formed a product, but then became
trapped in a non-catalytic state that cycled back to the catalytic state more slowly.

Steady
state

~1 mole product
per mole enzyme

Burst phase
Time

Copyright 2000-2011 Mark Brandt, Ph.D.

31

The mechanism that Hartley and Kilby proposed to explain the burst phase kinetics
was that a covalent intermediate was formed between the enzyme and the acetate
from the substrate, rapidly releasing the colored p-nitrophenolate. The acetylatedenzyme intermediate then slowly hydrolyzed to regenerate active enzyme. The
initial burst of p-nitrophenolate production occurred at a high rate because it
preceded the rate-limiting step for the reaction. Once the majority of the enzyme
had become acetylated, the release of p-nitrophenolate became dependent on the
rate-limiting step, which is the hydrolysis of the covalent bond formed to the
enzyme.
NO2

Chymotrypsin

p-nitrophenylate

+
NO2

O
H3C

Chymotrypsin

O
O

H3C

hydrolysis
O

Chymotrypsin
H3C

p-nitrophenylacetate

When using normal polypeptide substrates, this burst phase kinetics can also occur.
For most peptide substrates, however, the burst phase tends to be less obvious,
because chymotrypsin cleaves polypeptides more effectively than it cleaves the
model substrate p-nitrophenylacetate. These types of kinetic studies, when properly
performed, allow insights into the enzyme mechanism, and have been the source of
much of the available information regarding enzyme catalysis.

Energy

The diagram below summarizes the reaction pathway for serine protease peptide
bond cleavage. Note that the highest energy peak in the serine protease reaction
pathway corresponds to the covalent intermediate hydrolysis process, which is the
slowest step in the reaction.
Uncatalyzed
(X)
hydrolysis
Serine
protease-catalyzed
hydrolysis

E+
H2O
+
S
ES
E-S E-P2
+ P1

H2O
+
E-P2

EP2

Progress of Reaction

Copyright 2000-2011 Mark Brandt, Ph.D.

32

E
+
P

Aspartyl proteases
Although serine proteases constitute a large family of enzymes with differing
specificity, the serine-dependent catalytic triad is only one of many possible
mechanisms for hydrolyzing peptide bonds. We will examine one other mechanism
for proteolysis (a number of others exist).
Aspartyl proteases comprise another family of proteolytic enzymes. This family
includes the stomach digestive enzyme pepsin, the highly specific protease renin
(the plasma enzyme that converts the circulating precursor angiotensinogen to the
hormone angiotensin), and the HIV protease (the enzyme that cleaves HIV
proteins during construction of the viral particle). Aspartyl proteases contain two
aspartate residues at the active site; in some cases, as in the HIV protease structure
shown below, each monomer provides one of the two aspartate residues in the
dimeric protein complex. While their catalytic mechanism differs considerably from
that of the serine proteases, the end result, the hydrolysis of a peptide bond within
the substrate to release two polypeptide products, is the same.
HIV Protease
(from PDB ID 1HVH)

Asp25

Catalytic mechanism
The mechanism is different from that of the serine proteases. In the aspartyl
proteases, the substrate never forms a covalent bond with the enzyme. Instead, the
first step of the reaction (following substrate binding) is a nucleophilic attack by a
water molecule on the substrate due to proton abstraction from the water by one of
the aspartate from the enzyme.
H

Peptide

H
N

Peptide

Peptide

H
N

Peptide

C
HO O R

H
O
O

H O

Copyright 2000-2011 Mark Brandt, Ph.D.

O
O H

33

One aspartate therefore acts as a base, while the water forms a covalent bond to the
substrate. Note that while one aspartate removes a proton from the water molecule;
the other aspartate acts as an acid, by releasing a proton to the carbonyl oxygen of
the polypeptide substrate.
In the next step, one aspartate residue acts as a base again, removing a proton from
one of the hydroxyls that have been formed on the former carbonyl carbon. At the
same time, the carbon-nitrogen bond breaks, with the nitrogen taking a proton from
the other active site aspartate.
H

Peptide

H
N

Peptide

C
HO O R

Peptide

H
C

O HN

OH

Peptide

H
O

O
O H

O
O

H O

This results in the formation of the carboxylic acid at one end of the new peptide,
and the free amino group at the end of the other new peptide.
The aspartyl protease mechanism requires that the environment of the protein
result in the two aspartate residues being 50% protonated. Since the typical pKa of
aspartate residues is about 4, this means that either the external pH must be fairly
low (as is the case for pepsin, a stomach enzyme that is most active at pH of about
2), or the environment of the active site must raise the pKa of the aspartate
residues enough to allow the partial protonation of the aspartate residues required
for activity (as is the case for the renin and the HIV protease, which are active at
pH of 7.4).

Copyright 2000-2011 Mark Brandt, Ph.D.

34

Summary
In order to recognize a substrate the enzyme must have a structure that is capable
of binding to the substrate. However, many enzymes alter their structure upon
substrate binding.
Enzymes alter reaction rates by a variety of methods. These methods include
increasing the local concentration of the substrate molecules by confining them to a
small volume, positioning the substrates in appropriate orientations for the reaction
to occur, inducing strain in the substrate, donating or abstracting protons,
stabilizing charge development, and interacting covalently with the substrate.
The variety of methods used result in enhanced reaction rates because of a
decreased energy of the most energetic transition state in the pathway. This is
possible because the enzyme binds to the transition state more tightly than to its
substrate or products.
Serine proteases, and to a lesser extent, aspartyl proteases, have been used as
models for studying the effect of protein structure on specific catalytic processes.
Serine proteases and aspartyl proteases catalyze peptide bond hydrolysis by
different mechanisms; both mechanisms take advantage of acid-base catalysis, but
the serine proteases form a covalent intermediate with their substrate, while the
aspartyl proteases do not.

Copyright 2000-2011 Mark Brandt, Ph.D.

35