Tài liệu Báo cáo khoa học: Catalytic mechanism of SGAP, a double-zinc aminopeptidase from Streptomyces griseus pdf

Catalytic mechanism of SGAP, a double-zinc
aminopeptidase from Streptomyces griseus
Yifat F. Hershcovitz
1
, Rotem Gilboa
2
, Vera Reiland
2
, Gil Shoham
2
and Yuval Shoham
1
1 Department of Biotechnology and Food Engineering and Institute of Catalysis Science and Technology,
Technion-Israel Institute of Technology, Haifa, Israel
2 Department of Inorganic Chemistry, The Laboratory for Structural Chemistry and Biology, The Hebrew University of Jerusalem, Israel
Aminopeptidases are exopeptidases that catalyze the
removal of N-terminal amino acids from peptides; they
are found in bacteria, plants and mammalian tissues.
Many aminopeptidases are metallo-enzymes, containing
two catalytic transition metals (usually zinc) in their act-
ive site [1–3]. The activity of these enzymes is associated
with many central biological processes, such as protein
maturation, protein degradation, hormone level regula-
tion, angiogenesis and cell-cycle control [4–8]. Not
surprisingly, aminopeptidases play an important role in
many pathological conditions, including cancer, cata-
ract, cystic fibrosis and HIV infection. Indeed, anti-
tumor drugs such as ovalicin and fumagillin were found
to inhibit aminopeptidases. In this regard, the natural
inhibitor for aminopeptidases, bestatin, was recently
shown to significantly decrease HIV infection by inhibit-

ing aminopeptidase activity [9–11]. Aminopeptidases
can be classified into clans and families based on their
amino acid sequence homology. Clan M contains
mainly metallopeptidase families, one of which is M28.
Keywords
aminopeptidase; catalytic mechanism;
catalytic residues; fluoride inhibition;
isotope effect
Correspondence
Y. Shoham, Department of Biotechnology
and Food Engineering, Technion,
Haifa 32000, Israel
Fax: +972 4 8293399
Tel: +972 4 8293072
E-mail:
(Received 30 April 2007, revised 28 May
2007, accepted 1 June 2007)
doi:10.1111/j.1742-4658.2007.05912.x
The catalytic mechanism underlying the aminopeptidase from Streptomyces
griseus (SGAP) was investigated. pH-dependent activity profiles revealed
the enthalpy of ionization for the hydrolysis of leucine-para-nitroanilide by
SGAP. The value obtained (30 ± 5 kJÆmol
)1
) is typical of a zinc-bound
water molecule, suggesting that the zinc-bound water ⁄ hydroxide molecule
acts as the reaction nucleophile. Fluoride was found to act as a pure non-
competitive inhibitor of SGAP at pH values of 5.9–8 with a K
i
of 11.4 mm
at pH 8.0, indicating that the fluoride ion interacts equally with the free

enzyme as with the enzyme–substrate complex. pH-dependent pK
i
experi-
ments resulted in a pK
a
value of 7.0, suggesting a single deprotonation step
of the catalytic water molecule to an hydroxide ion. The number of proton
transfers during the catalytic pathway was determined by monitoring the
solvent isotope effect on SGAP and its general acid–base mutant
SGAP(E131D) at different pHs. The results indicate that a single proton
transfer is involved in catalysis at pH 8.0, whereas two proton transfers are
implicated at pH 6.5. The role of Glu131 in binding and catalysis was
assessed by determining the catalytic constants (K
m
, k
cat
) over a tempera-
ture range of 293–329 °K for both SGAP and the E131D mutant. For the
binding step, the measured and calculated thermodynamic parameters for
the reaction (free energy, enthalpy and entropy) for both SGAP and the
E131D mutant were similar. By contrast, the E131D point mutation resul-
ted in a four orders of magnitude decrease in k
cat
, corresponding to an
increase of 9 kJÆmol
)1
in the activation energy for the E131D mutant,
emphasizing the crucial role of Glu131 in catalysis.
Abbreviations
AAP, Aeromonas proteolytica aminopeptidase; blLAP, bovine lens leucine aminopeptidase; Leu-pNA, leucine-para-nitroanilide; SGAP,

Streptomyces griseus aminopeptidase.
3864 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS
Family M28 is currently divided into five subfamilies,
M28A–M28E [12,13]. The M28 family includes several
bacterial aminopeptidases, such as M28A Streptomyces
griseus aminopeptidase [(SGAP) EC 3.4.11.10] and
M28E Aeromonas proteolytica aminopeptidase [(AAP)
EC 3.4.11.10]. In addition, the M28 family includes
important human aminopeptidases such as M28B glu-
tamate carboxypeptidase II (N-acetylated, alpha-linked
acidic dipeptidase, prostate-specific membrane antigen)
[9,13–23]. The crystal structure of several double-zinc
aminopeptidases has been determined, including that of
SGAP, AAP [24–30] and the bovine lens leucine ami-
nopeptidase [(blLAP) EC 3.4.11.1] [31–34]. Based on
biochemical and structural data, a general catalytic
mechanism was proposed for aminopeptidases that
involves an acidic residue acting as a general acid ⁄ gen-
eral base and a di-nuclear metal center participating in
binding the substrate and stabilizing the transition state
[2,14,35–37]. The main data presently available for
aminopeptidases and their catalytic mode of action are
summarized in several recent reviews [2,14,38].
SGAP is a monomeric (30 kDa) thermostable
enzyme that prefers large hydrophobic amino-terminus
residues in its peptide and protein substrates. This
enzyme contains two zinc ions in its active site and
was shown to be activated by calcium ions [39,40].
High-resolution crystal structures of SGAP and com-
plexes of the enzyme with reaction products were

determined [26–28] and used together with biochemical
data from SGAP and other double-zinc aminopeptid-
ases [2,14] in postulating a general catalytic mechanism
for this enzyme [27]. Recently, the SGAP gene was
cloned and expressed in Escherichia coli, enabling
researchers to verify, by site-directed mutagenesis, the
role of two main catalytic residues, Glu131 and
Tyr246 [36,41]. It was suggested that the acidic residue
(Glu131 in SGAP corresponding to Glu151 in AAP)
acts as a general base and generates the hydroxide
nucleophile from the zinc-bound water; the nucleophile
then attacks the carbonyl carbon of the target peptide
bond, leading to the formation of a gem-diolate inter-
mediate. Presumably, the abstracted proton is trans-
ferred by the acidic residue (Glu131) to the leaving
peptide amine group, resulting in the breakdown of
the intermediate. The second catalytic residue, Tyr246,
which so far was shown to be critical only in SGAP,
can form hydrogen bonds with the substrate carbonyl
oxygen and thus can stabilize the interaction between
this oxygen atom and one of the zinc ions in the active
site (Fig. 1) [2,14,27,42].
SGAP and AAP were shown to be quite similar in
size, sequence, thermostability and overall structure.
Nevertheless, a number of significant features differ-
entiate these apparently homologous enzymes, sug-
gesting that their exact catalytic mechanisms (and
probably those of the corresponding subfamilies,
M28A and M28E) are not completely identical. The
most significant differences between these two enzymes

Fig. 1. The proposed catalytic mechanism of
SGAP. An acidic residue (Glu131) activates
a zinc-bound water molecule and an addi-
tional residue (Tyr246) polarizes the carbonyl
carbon and stabilizes the transition state.
Glu131 is thought to act as a general base
and to generate the hydroxide nucleophile
from the zinc-bound water; the nucleophile
then attacks the carbonyl carbon of the tar-
get peptide bond leading to the formation of
a gem-diolate intermediate. The abstracted
proton is presumably transferred by the aci-
dic residue (Glu131) to the amine group of
the leaving peptide bringing to the break-
down of the intermediate. Dashed lines indi-
cate stabilizing interactions and ⁄ or hydrogen
bonds in the catalytic pathway; Pep, the
incoming peptide ⁄ protein substrate.
Y. F. Hershcovitz et al. Mechanism of an aminopeptidase from S. griseus
FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS 3865
are that: (a) AAP is almost fully active (approximately
80%) [14,35,43–45], with only one zinc ion in the active
site, whereas the corresponding SGAP was shown to be
approximately 50% active, with 1 mol of Zn
2+
per mol
of enzyme [39]; (b) the activity of SGAP is modulated by
calcium ions bound in two specific sites, whereas AAP
does not bind Ca
2+

[10,28,46]; (c) in AAP, there is no
homologues residue to the SGAP catalytic residue,
Tyr246 [36]; (d) the binding affinities to the natural
inhibitors bestatin and amastatin are approximately
two-fold larger in AAP than in SGAP [10]; and (e) in
SGAP, the free amine group of the substrate forms
strong interactions with three protein residues near the
active site, whereas in AAP the free amine interacts with
the second zinc ion (Zn2) [24–28].
Open issues regarding the catalytic mechanism
underlying SGAP include the exact binding mode of
the hydroxide to the metal ions, the proton pathway in
catalysis and the specific involvement of the catalytic
residues in the enzymatic reaction. The two zinc ions
in the active metal center are thought to participate in
substrate binding by activating the water ⁄ hydroxide
nucleophile and stabilizing the transition state. Specif-
ically regarding SGAP, whether the water ⁄ hydroxide
molecule becomes terminally bound (bound to a single
zinc molecule) during the reaction pathway remains
unclear. In their biochemical studies on SGAP, Harris
and Ming [47] proposed that the bridging hydroxide
undergoes a single interaction at some point of the cat-
alytic reaction. A similar conclusion was derived for
the catalytic mechanism of AAP, in which the bridging
water molecule was thought to become terminally
bound following substrate binding [35]. This was based
on several lines of experimental evidence: (a) 80%
AAP activity was obtained with a single Zn ion bound;
(b) the mode of inhibition of external anions; and (c)

EPR data observed in the presence of the inhibitor
butane boronic acid [35,48]. However, according to
recent crystal structures of SGAP and its complexes, it
is suggested that the water ⁄ hydroxide molecule could
be maintained by the two zinc ions along the reaction
pathway [49], without traversing terminally bound
water ⁄ hydroxide species. A similar situation was pro-
posed for the hexameric aminopeptidase blLAP, based
on its crystal structure in complex with a transition
state analog [33,34].
In the present study, we utilized the inhibition by
external anions to study the binding mode of the
hydroxide ⁄ water molecule in the SGAP metal center. In
addition, proton transfer during catalysis was assessed
by measuring the isotope effect at different pHs, for
the native enzyme and its catalytic mutant E131D. The
exact mechanistic role of Glu131 was explored by
analyzing the temperature dependence of the kinetic
parameters. Interestingly, we found that fluoride is a
noncompetitive inhibitor of SGAP, in contrast to what
was published previously [47], suggesting that the
water ⁄ hydroxide molecule is bound similarly in the free
enzyme and in the enzyme–substrate complex.
Results
pH-dependent activity profile
The proposed catalytic mechanism for SGAP involves
a zinc-bound water ⁄ hydroxide as a nucleophile
(Fig. 1). Indeed, the crystal structures of SGAP dem-
onstrate that such a water molecule bridges between
the two active site zinc ions in an appropriate position,

where it acts as a nucleophile in the first stage of the
catalytic reaction [26,27]. To verify that the nucleophile
is generated from the zinc-bound water molecule, we
determined the pH dependence of k
cat
for the hydroly-
sis of leucine-para-nitroanilide (Leu-pNA) under satur-
ating substrate concentrations (4 mm) at 298, 303 and
308 °K (Fig. 2). At all three temperatures at pH values
below 7.0, logk
cat
was found to be strongly dependent
on the pH, providing slopes of 1.1–1.3. This behavior
(slopes of ± 1) is typical of monobasic acids and indi-
cates that a single ionization step controls the reaction
rate [50]. At pH values above 7.0, logk
cat
was less
affected by the pH. The point of intersection of the
two regions is the kinetic pK
a
of the ionizing groups
on the ES complex [51]. As the proton dissociation
constant is a thermodynamic parameter, a change in
temperature can result in alteration of the pH activity
curve. The pK
a
at each temperature was determined
and plotted against the inverse absolute temperature
(Fig. 3). From the pK

a
versus the 1 ⁄ T plot, the
enthalpy of ionization (DH
ion
) could be obtained,
resulting in a value of 30 ± 5 kJÆmol
)1
. This enthalpy
of ionization value is typical of a zinc-bound water
molecule [52]. Thus, the k
cat
dependence on the pH
could reflect the ionization of the zinc-bound water to
hydroxide.
Inhibition of SGAP by fluoride and phosphate
ions
Based on the crystal structures of native SGAP, the
metal center in the active site binds a water molecule
(or a hydroxide ion), which bridges almost symmetri-
cally between the two zinc ions [26–28]. To verify the
nature of the metal–water ⁄ hydroxide binding and to
determine whether one or both metal ions act as Lewis
acids in catalysis, we investigated the inhibition of
Mechanism of an aminopeptidase from S. griseus Y. F. Hershcovitz et al.
3866 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS
SGAP by fluoride and phosphate anions. Anions such
as fluoride and phosphate have been widely used to
probe the binding of water ⁄ hydroxide to metal ions in
the active site of metalloenzymes [53–58]. Inhibition of
SGAP by fluoride and phosphate anions was investi-

gated by determining the initial rates of the hydrolysis
of Leu-pNA as a function of the inhibitor concentra-
tion (0–80 mm NaF or 0–50 mm NaH
2
PO
4
) at several
substrate concentrations (0.1–10 mm). For both anions,
the resulting data were found to fit best to a noncom-
petitive mode of inhibition (Figs 4 and 5) [59]. In this
mode of inhibition, the inhibitor and the substrate
(Leu-pNA in this case) bind independently at different
sites, namely, the inhibitor binds equally well to the
free enzyme or to the enzyme–substrate complex, and
A
B
C
Fig. 2. pH dependence of the observed k
cat
of Leu-pNA hydrolysis
by SGAP at different temperatures. (A) 25 °C; (B) 30 °C; (C) 35 °C.
The plot used to estimate the pK
a
at each temperature.
Fig. 3. Plot of pK
a
versus the inverse temperature for the hydro-
lysis of Leu-pNA. The enthalpy of ionization, DH
ion
¼ 30 kJÆmol

)1
,
was calculated from the slope of the line.
A
B
Fig. 4. Inhibition of SGAP by fluoride. (A) A representative plot of
the Lineweaver–Burk plot for determination of the mode of inhibi-
tion at various fluoride concentrations at pH 8. The plots fit the non-
competitive inhibition mode. The reaction solution contained 50 m
M
Mops, 20 lM ZnCl
2
and 1 mM CaCl
2
. Fluoride concentrations were
0.0 (j), 10 (h), 20 (d), 50 (s) and 80 (m)m
M NaF. (B) Dixon plot
for determination of noncompetitive inhibition.
Y. F. Hershcovitz et al. Mechanism of an aminopeptidase from S. griseus
FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS 3867
the substrate binds equally well to the free enzyme or
to the enzyme–inhibitor complex [42,60]. For purely
noncompetitive inhibition, a Dixon plot of 1 ⁄ V versus
the inhibitor concentration is expected to yield a
straight line for a given substrate concentration
(Figs 4B and 5B) [61]. Similar experiments with NaCl
instead of NaF or NaH
2
PO
4

ÆH
2
O resulted in no inhibi-
tion up to concentrations of 0.8 m NaCl at pH 8, indi-
cating that the reaction is not influenced by ionic
strength (at the tested concentrations) and, as expected,
the binding of Cl
–
to hard acids is much smaller than
that of F
–
[62]. Such a binding difference was also
reported for AAP [35] and is also expected for the zinc
ions of SGAP, which are situated in a generally positive
environment and hence behave as relatively hard Lewis
acids. To further confirm the displacement of the
hydroxide nucleophile by the fluoride anion, the pH
dependence of the pK
i
was determined. The purely
noncompetitive behavior of fluoride towards SGAP
was exhibited over a pH range of 5.9–8.0. However, the
pK
i
value remained constant at low pHs and decreased
at pH values above 7.0 (Fig. 6). The point of intersec-
tion of the two linear regions corresponded to pH 7.0.
These data fit a mechanism involving a deprotonation
step from a water molecule to produce a hydroxide ion
under conditions in which, at pH values > 7.0, the

fluoride ion (the inhibitor) can be replaced by a coordi-
nated water ⁄ hydroxide bound to the two zinc ions in a
noncompetitive mode [51,60].
Solvent isotope effect
The proposed catalytic mechanism of SGAP involves
two proton transfers, suggesting that the reaction rate
could be affected by solvent isotope effects, typical of
catalytic mechanisms involving general acids or general
bases. The magnitude of the solvent isotope effect
depends of course on the rate-limiting step in the reac-
tion, which could include the protonation or deproto-
nation steps and ⁄ or the generation of the nucleophile
and the collapse of the tetrahedral intermediate
(Fig. 1) [63]. To study the protonation events via the
catalytic pathway, and to confirm the role of Glu131
as a proton shuttle in catalysis, we carried out the
reaction in the presence of D
2
O. The k
cat
values for
both SGAP and the catalytic mutant, E131D, were
measured at different D
2
O ⁄ H
2
O ratios at pH values of
6.5 and 8.0. Data were plotted as the rate ratio V
n
⁄ V

1
versus the atom fraction of deuterium (n), where V
n
corresponds to the k
cat
value obtained at a particular
fraction of deuterium (n), and V
1
corresponds to the
k
cat
value in 100% D
2
O (Fig. 7). Interestingly, the
presence of D
2
O in solution reduced the catalytic
A
B
Fig. 5. Inhibition of SGAP by phosphate ion. (A) A representative
plot of a Lineweaver–Burk plot for determination of the mode of
inhibition at various phosphate ion concentrations (Na
2
H
2
PO
4
ÆH
2
O)

at pH 7.2. The plots fit noncompetitive inhibition mode. The reac-
tion solution contained 50 m
M Mops, 20 lM ZnCl
2
and 1 mM CaCl
2
.
Fluoride concentrations were 0.0 (j), 10 (h), 20 (d), 30 (s), 40 (m)
and 50 (n )m
M Na
2
H
2
PO
4
ÆH
2
O. (B) Dixon plot for determination of
noncompetitive inhibition.
Fig. 6. pH dependence of the fluoride ion inhibition Michaelis con-
stant (K
i
) for Leu-pNA hydrolysis by SGAP. The pK
i
at each tem-
perature was calculated from the data of initial velocities at
different substrate and NaF concentrations using GraFit, version 5.0
for noncompetitive inhibition.
Mechanism of an aminopeptidase from S. griseus Y. F. Hershcovitz et al.
3868 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS

activity for both SGAP and the catalytic mutant
E131D, resulting in solvent isotope effects of 1.67 and
2.52, respectively, at pH 8; and 2.10 and 2.92, respect-
ively, at pH 6.5 (Table 1). The profound solvent iso-
tope effect indicates that a proton transfer is involved
in the rate-limiting step of the reaction [64]. At pH 8.0,
for both SGAP and E131D, there was a linear correla-
tion between the rate ratio (V
n
⁄ V
1
) and the atom frac-
tion of deuterium (n), suggesting the involvement of a
single protonation step in the catalytic reaction at this
pH (Fig. 7A,C). However, at pH 6.5, the relation
between the rate ratio and the atom fraction of deuter-
ium, for both SGAP and E131D, fitted best to a poly-
nomial function. This suggests that, at pH 6.5, at least
two proton transfers are involved in the rate-limiting
steps of the reaction (Fig. 7B,D). To further analyze
the number of proton transfers in catalysis, the c
method of Albery [65] was applied. This method is
based on the observation that the maximum deviation
between theoretical proton-inventory curves V
n
(n) for
different mechanistic models occurs at the midpoint of
the isotopic solvent mixture (V
m
, n ¼ 0.5). Thus, it is

best to compare various models with the observed
midpoint solvent isotope effect, V
m
⁄ V
1
. Equations 1–3,
derived by Elrod et al. [65] were accordingly used to
calculate the predicted values of V
m
⁄ V
1
for three gen-
eral models.
One proton catalysis:
V
m
V
1
¼ð1 À n
m
Þ
V
0
V
1

þ n
m
ð1Þ
Two-proton catalysis (equal isotope effects):

V
m
V
1
¼ð1 À n
m
Þ
V
0
V
1

1
2
þ n
m
"#
2
ð2Þ
Generalized solvation changes:
V
m
V
1
¼
V
0
V
1


ð1Àn
m
Þ
ð3Þ
At pH 8.0, the observed values, for both SGAP and
its catalytic mutant, E131D, fitted best the model of a
AC
BD
Fig. 7. Rate ratio (V
n
⁄ V
1
) as a function of
atom fraction of deuterium (n) for SGAP and
its mutant E131D. V
n
is the k
cat
value
obtained at a particular fraction of deuterium
(n), whereas V
1
is k
cat
in 100% deuterium
oxide. (A) SGAP pH 8.0; (B) SGAP pH 6.5;
(C) E131D pH 8.0; (D) E131D pH 6.5. The
activity was determined in Mops buffer at
the appropriate pH, in 20 l
M ZnCl

2
,1mM
CaCl
2
and 4 mM Leu-pNA in different ratios
of D
2
O ⁄ H
2
O. At pH 8.0 for SGAP and
E131D, the data fitted a linear regression
curve that describes a one-proton transfer
solvent isotope effect. At pH 6.5, a polyno-
mial function was fitted for both, describing
at least a two-proton transfer solvent iso-
tope effect.
Table 1. Experimental versus calculated midpoint solvent isotope for the hydrolysis of Leu-pNA by SGAP and its E131D catalytic mutant.
Enzyme V
0
⁄ V
1
Midpoint solvent
isotope effect V
m
⁄ V
1
Calculated midpoint solvent isotope effect
One proton Two protons Generalized solvations changes
SGAP pH 6.5 2.10 1.43 1.55 1.50 1.45
E131D pH 6.5 2.92 1.78 1.95 1.83 1.70

SGAP pH 8.0 1.67 1.35 1.34 1.31 1.29
E131D pH 8.0 2.52 1.83 1.76 1.67 1.59
Y. F. Hershcovitz et al. Mechanism of an aminopeptidase from S. griseus
FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS 3869
single proton transfer in catalysis [(Eqn (1)] At pH 6.5,
the values fitted best a model with two proton trans-
fers; however, they could also be fitted to a model
involving general solvation changes [Eqns (2) and (3)].
Thus, using two different data analysis approaches, the
solvent isotope effects observed for SGAP at pH 6.5
indicate that there are at least two proton transfers in
the catalytic pathway and that at this pH these proton
transfer steps limit the hydrolysis of the substrate
(Table 1).
Temperature dependence of k
cat
and K
m
To verify the exact role of Glu131, either in binding or
catalysis, the kinetic parameters (K
m
, k
cat
) were meas-
ured at temperatures between 293 and 329 °K for both
SGAP and its catalytic mutant E131D (Fig. 8). We
previously verified by differential scanning calorimetry
and activity measurements that the melting tempera-
ture of SGAP is 348 °K, and that both the native and
the mutant enzymes are completely active and stable

(at least for 20 min) at 329 °K. In principle, with a
rapid equilibrium mechanism (K
m
¼ K
d
) (dissociation
constant, k
-1
⁄ k
1
), the kinetic constant, K
m
, usually cor-
responds to the formation of the enzyme–substrate
complex, E + S fi (ES), whereas k
cat
characterizes
the bond breaking and ⁄ or making step during the
formation of the transition state, ES fi (ESÆÆEP)à.
Enzyme–substrate interaction E+Sfi (ES)
For rapid equilibrium systems where K
m
¼ K
d
, a plot
of ln(1 ⁄ K
m
) versus 1 ⁄ T provides the standard enthalpy
change (DH°) for the enzyme–substrate binding reac-
tion, E+Sfi (ES) (Fig. 8A,C). The free energy

value (DG°) for the binding can be calculated from the
standard free energy equation, DG° ¼ –RTln1 ⁄ K
m
, and
the corresponding entropy (DS°), can be extracted
from the standard Gibbs relationship, DG° ¼
DH° ) TDS°. Using these simple definitions, we could
calculate the main thermodynamic parameters, free
energy, enthalpy and entropy for the reaction catalyzed
by SGAP (Table 2). These parameters, as calculated
for the step involving the enzyme–substrate interaction,
appeared to be quite similar for SGAP and its catalytic
AB
CD
Fig. 8. Temperature dependence of the
kinetic parameters for SGAP hydrolysis of
Leu-pNA at pH 8. (A,C) Temperature
dependence of 1 ⁄ K
m
in SGAP and E131D,
respectively. (B,D) Arrhenius plot: tempera-
ture dependence of k
cat
in SGAP and
E131D, respectively. The plots were used to
determine the thermodynamic parameters
of the SGAP reaction steps.
Table 2. Thermodynamic parameters for the hydrolysis of Leu-pNA
by SGAP and its E131D mutant.
Reaction step SGAP E131D

Enzyme–substrate interaction DG° (kJÆmol
)1
) )2 )1.5
E+S fi (ES) DH° (kJÆmol
)1
) )39 )38
DS° (J ⁄ mol*K) )122 )121
Formation of the transition state DGà (kJÆmol
)1
) +59 +81
ES fi (ESÆÆEP)à DHà (kJÆmol
)1
) +29 +38
DSà (J ⁄ mol*K) )100 )144
E
a
(kJÆmol
)1
)3241
Mechanism of an aminopeptidase from S. griseus Y. F. Hershcovitz et al.
3870 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS
mutant E131D. For example, at 303 °K the K
m
values
were 0.45 and 0.58 mm, for SGAP and E131D,
respectively. Hence, the replacement of Glu131 by Asp
did not significantly affect the initial binding interac-
tion of the substrate with the enzyme.
Attaining the transition state ES fi (ESÆÆEP)à
As described above, k

cat
is directly correlated with the
generation rate of the transition state (ESÆÆEP)à.A
plot of log V
max
versus 1 ⁄ T provides the activation
energy (E
a
) for the step involving the generation of the
transition state. The first-order rate constant, k
cat
,ina
simple rapid equilibrium reaction refers to V
max
⁄ [E],
where the enzyme concentration does not change
throughout the experiment [66]. Thus, an Arrhenius
plot of lnk
cat
versus 1⁄ T yields the free activation
energy of the reaction [–E
a
⁄ R(R ¼ 8.3145 JÆK
)1
Æ
mol
)1
)] (Fig. 8B,D). The other thermodynamic con-
stants can be extracted from these data using the
equations DGà ¼ –RTln(k

cat
h ⁄ k
B
T), DHà ¼ Ea ) RT,
DSà ¼ (DHà ) D G à) ⁄ T, where k
B
, h and R are the
Boltzman, Planck and gas constants, respectively. The
resulting Arrhenius plot forms a straight line, suggest-
ing that the rate-limiting step does not change in the
tested range of temperatures (no protein melting) [60].
The calculated activation energies for SGAP and
E131D were 32 and 41 kJÆmol
)1
, respectively (Table 2).
Both values are within the range obtained for typical
enzymatic reactions (32–48 kJÆmol
)1
). The replacement
of Glu131 by Asp resulted in a significant increase of
9kJÆmol
)1
for the activation energy, indicating that
Glu131 plays a major role in forming the transition
state of the catalytic reaction.
Discussion
Involvement of a zinc-bound hydroxide as the
reaction nucleophile
Based on structural studies and ample biochemical evi-
dence, the crucial elements in the active site that play

an essential role in catalysis are the zinc-bound
water ⁄ hydroxide and the carboxylic group of Glu131
[26–28]. From a high-resolution crystal structure of
SGAP, it was demonstrated that, in its free native state,
a water ⁄ hydroxide molecule is held in position by close
interactions with the two active site zinc ions and the
acidic side chain of Glu131. To test whether this mole-
cule is in fact the active site nucleophile, we determined
the enthalpy of ionization (DH
ion
) of the hydrolysis of
Leu-pNA by SGAP, which was found to be 30 ± 5 kJÆ
mol
)1
. This value is in the range of the expected ioniza-
tion of a zinc-bound water ⁄ hydroxide in solution,
DH
ion
of 20–30 kJÆmol
)1
[52]. The enthalpy of ioniza-
tion of a carboxylic group is much lower, 5–10 kJÆ
mol
)1
; thus, the pK
a
of the acidic residue is less
sensitive to changes in temperature. In calculating
DH
ion

, it is assumed that the deprotonation of the zinc-
bound water molecule to the hydroxide nucleophile has
a greater effect on the reaction rate than the protona-
tion of the peptide bond nitrogen by Glu131. In this
regard, the isotope effect studies instead suggest that at
pH 8, the protonation of the peptide-bond nitrogen by
Glu131 is rate limiting (and not the ionization of the
zinc-bound water) (Table 1, Fig. 7). Thus, it is likely
that the rate-limiting step does change with pH. How-
ever, as can be seen in Fig. 2, the k
cat
values above
pH 7.5 contribute very little to the determined pK
a
(the
point of intersection between the two regions) and
therefore the DH
ion
value is valid.
Considering both the crystal structure of the ligand-
free SGAP, where a bridging water molecule was
found to be bound to the zinc ions of the active site,
and the observed DH
ion
value, it is likely that the zinc-
bound water molecule generates the catalytic nucleo-
phile of the hydrolytic reaction [26–28,36]. Thus, the
primary role of Glu131 is to stabilize the zinc-bound
water molecule and to extract a proton from the zinc-
bound water. An alternative nucleophile could, in prin-

ciple, be the negatively charged carboxylate group of
Glu131, as was once suggested for Glu270 of carb-
oxypeptidase A [67,68]. In this case, the enthalpy of
the reaction should have resembled more the ioniza-
tion enthalpy of the acidic residue (5–10 kJÆmol
)1
).
Similar enthalpy of ionization results were obtained
for other homologous metallopeptidases such as AAP
towards the substrate Leu-pNA (25 kJÆmol
)1
) [69], and
carboxypeptidase E towards the substrate dansyl-Phe-
Ala-Arg (28.9 kJÆmol
)1
) [52]. As expected, for both
enzymes, the zinc-bound water ⁄ hydroxide is thought
to act as the reaction nucleophile.
The binding mode of the water
⁄
hydroxide to the
di-zinc center
Inhibition of SGAP by fluoride anions was utilized to
assess the binding of the water ⁄ hydroxide to the active
metal center. Fluoride was found to act as a purely
noncompetitive inhibitor of SGAP under all the pH
conditions tested (5.9–8.0) with a K
i
value of 11.4 mm
at pH 8.0. A noncompetitive inhibition behavior indi-

cates that the inhibitor binds similarly to the free
enzyme and to the enzyme–substrate complex [42,61].
As fluoride is likely to replace the bound water, this
mode of inhibition suggests that binding of the
Y. F. Hershcovitz et al. Mechanism of an aminopeptidase from S. griseus
FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS 3871
water ⁄ hydroxide molecule to both zinc ions is the same
in the free enzyme as in the enzyme–substrate complex.
This notion is further supported by several lines of
evidence. In the high-resolution crystal structures
of SGAP, the water ⁄ hydroxide molecule is clearly
observed in contact with the two zinc ions [26,28,49].
In the structures of SGAP in complex with Met, Leu
and Phe, it is evident that each amino acid is bound to
the active site through the two oxygens of the carboxy-
late group [26,27]. These structures appear to resemble
either the transition state (a gem-diolate moiety) or the
product of the reaction (the free carboxylate group of
the cleaved amino acid residue). In both cases, one
of the oxygens (O2), which presumably originated
from the substrate carbonyl carbon of the peptide
bond, is connected to Zn2, whereas the other oxygen
(O1), which presumably originated from the hydroxide
nucleophile, is bound to both Zn ions (Zn1 and Zn2)
in SGAP [27]. The fact that, in the enzyme–product
complex, the coordination number of Zn2 is 5 (His247,
Glu132, Asp97 and the two carboxylate oxygens) sug-
gests that this coordination number is also maintained
in the transition state. Thus, fluoride appears to be
replacing a water molecule that is bound to both zinc

ions in the transition state.
Additional support that the hydroxide nucleophile in
the gem-diolate intermediate is stabilized by interac-
tions to both metals comes from the structures of
SGAP with its reaction products. From these struc-
tures, it is evident that the N-terminal amine group of
the products is stabilized by three residues, namely,
Glu131, Asp160 and the backbone carbonyl group of
Arg202, whereas, in the related aminopeptidase AAP
from A. proteolytica, the N-terminal amine is in con-
tact with one of the zinc ions [26,27]. This mode of
binding in SGAP still allows the oxygen atoms of the
gem-diolate intermediate to be stabilized by interacting
with both metals and Tyr246 [2,26,27]. Thus, the
catalytic mechanism of SGAP may not require that the
N-terminal of the leaving product will be bound to a
single zinc atom, as proposed for AAP [2,14,70].
Further support that the two zinc ions function as
Lewis acid-type catalysts comes from comparing the
structures of SGAP and blLAP (leucine aminopepti-
dase from bovine lens). Interestingly, the latter enzyme
utilizes a carbonate ion instead of a carboxylic residue
to stabilize the water molecule [34]. The position of
this carbonate ion in blLAP corresponds to the posi-
tion of Glu131 in SGAP. The crystal structure of
blLAP in complex with the transition state analog,
l-leucinephosphonic acid, revealed that the two oxy-
gens of the phosphate group are bound as a bidentate
ligand to one of the zinc ions (Zn1), and one of these
oxygens bridges between both Zn ions [33]. Based on

this structure, the proposed catalytic mechanism for
blLAP indicates that both zinc ions function as Lewis
acids and a bridging hydroxide acts as a nucleophile
by attacking the substrate carbonyl carbon [33–35].
The importance of both zinc ions for the catalytic
activity of SGAP is also supported by previous kinetic
studies in which it was demonstrated that a single zinc
ion in the catalytic site provides only 50% of activity
[39]. Taken together, apparently the water ⁄ hydroxide
molecule is bound to both zinc ions in the free enzyme
similarly as in the enzyme–substrate complex, provi-
ding noncompetitive inhibition by fluoride. A similar
mode of inhibition was suggested for other metallo-
enzymes such as the purple acid phosphatase from
bovine spleen and porcine uterus, in which tetrahedral
oxyanions were found to bound in a noncompetitive
mode by bridging two iron ions in the active site [55].
Note that Harris and Ming [47] suggested a different
mode of SGAP inhibition by fluoride. In their study,
fluoride appeared to act as an uncompetitive inhibitor,
whereas phosphate ions exhibited noncompetitive inhi-
bition, suggesting that fluoride and phosphate ions
bind differently [71]. At this stage, we do not have a
simple explanation for these contradictory results,
other than assuming that they originate from different
experimental conditions. In AAP, fluoride was found
to act as an uncompetitive inhibitor, suggesting that
the hydroxyl nucleophile may be terminally bound fol-
lowing substrate binding [35]. Phosphate ions appear
to act as noncompetitive inhibitors of SGAP, as was

also demonstrated previously by Harris and Ming [47].
However, this result is somewhat puzzling because the
phosphate ion is too large to simply replace the water
molecule. Indeed, crystal structures of SGAP in com-
plex with phosphate reveal that the ion, located in the
zinc center, occupies both the space of the water mole-
cule and the substrate carbonyl group. Similarly, the
location of phosphate was also observed in the human
membrane-bound glutamate carboxypeptidase II, in
which the Zn[ ]O(phosphate) distances are between
1.75 and 1.93 A
˚
[23]. To explain these results, Harris
and Ming suggested that in solution the phosphate ion
actually binds at a different location.
The number of proton transfers in the reaction
The number of proton transfers during the catalytic
pathway of SGAP was studied in detail by monitoring
the solvent isotope effect on SGAP and its general
acid–base mutant E131D, both under different pH con-
ditions. At pH 8, the observed isotope effect values
were 1.67 and 2.52 for SGAP and the E131D mutant,
Mechanism of an aminopeptidase from S. griseus Y. F. Hershcovitz et al.
3872 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS
respectively. Comparison of the observed midpoint-
values derived from the rate ratio plots (Fig. 7) to the
theoretically calculated values (proton inventory proce-
dure) (Table 1) suggests that a single proton transfer is
involved in catalysis at pH 8. At this pH, the bridging
water molecule is likely to be ionized; thus, the reaction

is controlled (rate limiting) by other critical proton
transfers in the reaction, the proton transfer from
Glu131 (acting here as a general acid) to the nitrogen of
the amine leaving group. The isotope effect on E131D
was considerably higher than that observed on SGAP
at pH 8 (Table 1). This emphasizes the importance of
the acidic residue (E131) in facilitating the proton trans-
fer to the leaving group at the product generation step
of the reaction, and is consistent with the four orders of
magnitude decrease in k
cat
observed for E131D [36].
At pH 6.5, the resulting isotope effect values were 2.1
and 2.9 for SGAP and the E131D mutant, respectively,
and the calculated midpoint values for both forms of
the enzymes fitted at least two proton transfers in the
catalytic pathway (Table 1, Fig. 7). At pH 6.5, the zinc-
bound water molecule is less likely to be ionized, and
therefore an additional proton transfer is required,
resulting in at least two proton transfers in the reaction.
Interestingly, the solvent isotope effect observed for
E131D was somewhat higher under both pH conditions.
This presumably reflects the additional energetic barrier
required for catalysis in the catalytic mutant, thus provi-
ding further support that Glu131 is involved in both
proton transfers. Similar trends in proton transfer were
obtained with AAP, in which two proton transfers
were observed at pH 6.5 and one proton transfer was
observed at the higher pH, for both the wild-type and
the corresponding E151D catalytic mutant [37]. Taken

together, these results suggest that Glu131 and Glu151
play a similar role in SGAP and AAP, respectively.
The role of Glu131
Glu131 in SGAP was previously shown to act as one of
the catalytic residues, together with Tyr246 [36]. To ver-
ify the specific involvement of Glu131 in binding
and ⁄ or catalysis, the kinetic parameters of SGAP and
its E131D mutant were determined at several tempera-
tures. By knowing the temperature dependence of
K
m
(binding) and k
cat
(catalysis), it is possible to extract
the thermodynamic properties of the main reaction
steps (i.e. formation of the activated complex,
E+Sfi (EÆÆS)à), and the bond-breaking ⁄ making
step, ES fi (ESÆÆEP)à. The measured and calculated
thermodynamic parameters of the reaction (i.e. free
energy, enthalpy and entropy) for both SGAP and
the E131D catalytic mutant were quite similar for the
binding step (Table 2). Thus, the E131D replacement
appears to affect very little the interaction of the
enzyme with its substrate. This is also consistent with
the K
m
values obtained for SGAP and the catalytic
mutant [36]. By contrast, the E131D replacement resul-
ted in a decrease of four orders of magnitude in k
cat

,
corresponding to an increase of 9 kJÆmol
)1
in the acti-
vation energy for E131D (Table 2), emphasizing the
crucial role of Glu131 in catalysis. These results make
sense in terms of the geometry changes involved. For
example, shortening the carboxylic side chain by
approximately 1.5 A
˚
in the position of the catalytic
carboxylic group resulted in a large increase in the acti-
vation energy [36]. Interestingly, the transition state
entropy, DSà, of E131D, is 44 JÆmol
)1Æ
K
)1
lower than
that of SGAP. The activated state can be viewed as an
unstable transient phase in which bonds and their orien-
tations are disordered [60]. It is possible that, in SGAP,
the transition state is characterized by significantly
more freedom compared with the catalytic mutant.
Conclusions
The results of the present study substantiate several
catalytic features that characterize the mechanism of
action of SGAP. Taking together with the structural
data we can state: (a) the catalytic nucleophile is a
zinc-bound hydroxide; (b) Glu131 is involved in the
deprotonation of the zinc-bound water to form the

nucleophilic hydroxide and less involved in substrate
binding; and (c) the two zinc ions in the active site par-
ticipate in stabilizing the hydroxide nucleophile during
catalysis. The overall catalytic mechanism of SGAP
appears to be quite similar to the mechanism proposed
for AAP. However, the two enzymes differ in several
aspects, including the exact role of the two active site
zinc ions in catalysis, the detailed sequence of zinc-
coordination changes during catalysis and the mode of
inhibition of anions such as fluoride and phosphate.
Experimental procedures
Purification of SGAP
The cloning of the SGAP gene, site-directed mutagenesis
and the expression and purification of the recombinant pro-
teins were performed as previously described [36].
Enzymatic assay
The aminopeptidase enzymatic activity was determined at
30 °C in a continuous assay using Leu-pNA (Sigma, St
Louis, MO, USA) as a substrate. The reactions were
Y. F. Hershcovitz et al. Mechanism of an aminopeptidase from S. griseus
FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS 3873
carried out directly in 1-mL cuvettes, positioned in a tem-
perature-controlled cuvette-holder hooked to a regulated
water-bath. A termocouple sensor was placed inside the cu-
vette to verify the exact temperature in the cuvette. The
assay solution (650 lL total volume) contained 50 mm
Mops, pH 8, 1 mm CaCl
2
(SGAP was shown to be activa-
ted by Ca

2+
ions) [10,46] and 0.02 mm ZnCl
2
, which were
mixed together with the appropriate diluted enzyme and
substrate concentrations in the range 0.1–10 K
m
. After the
reaction was initiated by adding the substrate, the increase
in absorbance at 405 nm was monitored continuously using
an Ultrospec 2100 spectrophotometer (Pharmacia, Uppsala,
Sweden). At 405 nm, the extinction coefficient for para-
nitroanilide at pH 8, and 30 °C was De ¼ 10.2 mm
)1
Æcm
)1
.
The catalytic constants, K
m
, k
cat
and K
i
were determined by
analysis with GraFit, version 5.0 using the appropriate inhi-
bition equations when required [59]. In these experiments
the experimental error was ± 5%. The inhibitors NaF and
NaH
2
PO

4
ÆH
2
O were added in concentrations in the range
0–80 mm and 0–50 mm, respectively, and the reactions were
initiated by adding together the substrate and the inhibitor.
Mops buffer (50 mm) was used for all pHs and the extinc-
tion coefficient of leucine-para-nitroanilide was corrected
for each of the pH values.
Solvent isotope effect
Enzyme samples [SGAP or SGAP(E131D)] were lyophilized
and reconstituted with fresh 99.9% D
2
O (Sigma). The reac-
tion solution, containing Mops buffer, ZnCl
2
, CaCl
2
and
the substrate Leu-pNA (4 mm), was composed with 99.9%
D
2
O. Adjusting the pH of the reaction solution was per-
formed accordingly with NaOD or DCl, both with
99%+ deuterium content (Acros Organics, Geel, Belgium).
The kinetic assays were performed at either pH 8.0 or 6.5
at 30 °C. Solutions containing different ratios of H
2
O ⁄ D
2

O
were used to determine the k
cat
values. These solutions were
prepared by diluting a ten-fold concentrated stock solution
of the enzymatic solution in D
2
O with the appropriate
amounts of D
2
O and H
2
O.
Acknowledgements
This study was supported by the Otto Meyerhof
Minerva Center for Biotechnology, Technion, estab-
lished by the Minerva Foundation (Munich, Ger-
many). Y. S. holds the Erwin and Rosl Pollak Chair in
Biotechnology.
References
1 Delange RJ & Smith EL (1971) Leucine aminopepti-
dase and other N-terminal exopeptidases. Enzymes 3,
81–118.
2 Lowther WT & Matthews BW (2002) Metallo-
aminopeptidases: common functional themes in
disparate structural surroundings. Chem Rev 102,
4581–4608.
3 Christianson DW & Cox JD (1999) Catalysis by metal-
activated hydroxide in zinc and manganese metallo-
enzymes. Annu Rev Biochem 68, 33–57.

4 Bauvois B (2004) Transmembrane proteases in cell
growth and invasion: new contributors to angiogenesis?
Oncogene 23, 317–329.
5 Sanderink GJ, Artur Y & Siest G (1988) Human amino-
peptidases: a review of the literature. J Clin Chem Clin
Biochem 26, 795–807.
6 Taylor A (1993) Aminopeptidases: structure and func-
tion. FASEB J 7, 290–298.
7 Taylor A (1993) Aminopeptidases: towards a mechan-
ism of action. Trends Biochem Sci 18, 167–171.
8 Taylor. A (1996) Aminopeptidases, occurence, regula-
tion and nomenclature. In: Aminopeptidases (Taylor A,
ed.), pp. 1–20. AG Landes Co, Austin, TX.
9 Holz RC, Bzymek KP & Swierczek SI (2003) Co-cata-
lytic metallopeptidases as pharmaceutical targets. Curr
Opin Chem Biol 7, 197–206.
10 Papir G, Spungin-Bialik A, Ben-Meir D, Fudim E,
Gilboa R, Greenblatt HM, Shoham G, Lessel U,
Schomburg D, Ashkenazi R et al. (1998) Inhibition of
Streptomyces griseus aminopeptidase and effects of cal-
cium ions on catalysis and binding. Eur J Biochem 258,
313–319.
11 Pulido-Cejudo G, Conway B, Proulx P, Brown R &
Izaguirre CA (1997) Bestatin-mediated inhibition of leu-
cine aminopeptidase may hinder HIV infection. Antiviral
Res 36 , 167–177.
12 Barrett AJ (2001) Proteolytic enzymes: nomenclature
and classification. In Proteolytic Enzymes (Beynon B &
Bond JS, eds), pp. 12–21. Oxford University Press,
New York, NY.

13 Rawlings ND, Morton FR & Barrett AJ (2006) MER-
OPS: The Peptidase Database. Nucleic Acids Res. 34,
D270–D272. Available at .
14 Holz RC (2002) The aminopeptidase from Aeromonas
proteolytica: structure and mechanism of co-catalytic
metal centers involved in peptide mechanism. Coord
Chem Rev 232, 5–26.
15 Mahadevan D & Saldanha JW (1999) The extracellular
regions of PSMA and the transferrin receptor contain
an aminopeptidase domain: implications for drug
design. Protein Sci 8, 2546–2549.
16 Speno HS, Luthi-Carter R, Macias WL, Valentine SL,
Joshi ART & Coyle JT (1999) Site-directed mutagenesis
of predicted active site residues in glutamate carboxy-
peptidase II. Mol Pharmacol 55, 179–185.
17 Davis MI, Bennett MJ, Thomas LM & Bjorkman PJ
(2005) Crystal structure of prostate-specific membrane
Mechanism of an aminopeptidase from S. griseus Y. F. Hershcovitz et al.
3874 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS
antigen, a tumor marker and peptidase. Proc Natl Acad
Sci USA 102, 5981–5986.
18 Pangalos MN, Neefs JM, Somers M, Verhasselt P, Bek-
kers M, van der Helm L, Fraiponts E, Ashton D &
Gordon RD (1999) Isolation and expression of novel
human glutamate carboxypeptidases with N-acetylated
alpha-linked acidic dipeptidase and dipeptidyl peptidase
IV activity. J Biol Chem 274, 8470–8483.
19 Slusher BS, Thomas A, Paul M, Schad CA & Ashby
CR Jr (2001) Expression and acquisition of the condi-
tioned place preference response to cocaine in rats is

blocked by selective inhibitors of the enzyme N-acety-
lated-alpha-linked-acidic dipeptidase (NAALADASE).
Synapse 41, 22–28.
20 Slusher BS, Vornov JJ, Thomas AG, Hurn PD,
Harukuni I, Bhardwaj A, Traystman RJ, Robinson
MB, Britton P, Lu XC et al. (1999) Selective inhibi-
tion of NAALADase, which converts NAAG to
glutamate, reduces ischemic brain injury. Nat Med 5,
1396–1402.
21 Tiffany CW, Lapidus RG, Merion A, Calvin DC &
Slusher BS (1999) Characterization of the enzymatic
activity of PSM: comparison with brain NAALADase.
Prostate 39, 28–35.
22 Witkin JM, Gasior M, Schad C, Zapata A, Shippenberg
T, Hartman T & Slusher BS (2002) NAALADase (GCP
II) inhibition prevents cocaine-kindled seizures. Neuro-
pharmacology 43, 348–356.
23 Mesters JR, Barinka C, Li W, Tsukamoto T, Majer P,
Slusher BS, Konvalinka J & Hilgenfeld R (2006) Struc-
ture of glutamate carboxypeptidase II, a drug target in
neuronal damage and prostate cancer. EMBO J 25,
1375–1384.
24 Chevrier B, D’Orchymont H, Schalk C, Tarnus C &
Moras D (1996) The structure of the Aeromonas proteo-
lytica aminopeptidase complexed with a hydroxamate
inhibitor. Involvement in catalysis of Glu151 and two
zinc ions of the co-catalytic unit. Eur J Biochem 237,
393–398.
25 Chevrier B, Schalk C, D’Orchymont H, Rondeau J-M,
Moras D & Tarnus C (1994) Crystal structure of Aero-

monas proteolytica aminopeptidase: a prototypical mem-
ber of the co-catalytic zinc enzyme family. Structure 2,
283–291.
26 Gilboa R, Greenblatt HM, Perach M, Spungin-Bialik
A, Lessel U, Wohlfahrt G, Schomburg D, Blumberg S
& Shoham G (2000) Interactions of Streptomyces griseus
aminopeptidase with a methionine product analogue: a
structural study at 1.53A resolution. Acta Cryst D 56,
551–558.
27 Gilboa R, Spungin-Bialik A, Wohlfahrt G, Schomburg
D, Blumberg S & Shoham G (2001) Interactions of Strep-
tomyces griseus aminopeptidase with amino acid reaction
products and their implications toward a catalytic mech-
anism. Proteins: Struct Funct Genet 44, 490–504.
28 Greenblatt HM, Almog O, Maras B, Spungin-Bialik A,
Barra D, Blumberg S & Shoham G (1997) Streptomyces
griseus aminopeptidase: X-ray crystallographic structure
at 1.75A resolution. J Mol Biol 265, 620–636.
29 Reiland V, Fundoiano-Hershcovitz Y, Golan G, Gilboa
R, Shoham Y & Shoham G (2004) Preliminary crystal-
lographic characterization of BSAP, an extracellular
aminopeptidase from Bacillus subtilis. Acta Cryst D 60,
2371–2376.
30 Rowsell S, Pauptit RA, Tucker AD, Melton RG, Blow
DM & Brick P (1997) Crystal structure of carboxypepti-
dase G2, a bacterial enzyme with applications in cancer
therapy. Structure 5
, 337–347.
31 Burley SK, David PR, Sweet RM, Taylor A & Lips-
comb WN (1992) Structure determination and refine-

ment of bovine lens leucine aminopeptidase and its
complex with bestatin. J Mol Biol 224, 113–140.
32 Burley SK, David PR, Taylor A & NLW (1990)
Molecular structure of leucine aminopeptidase at 2.7A
resolution. Proc Natl Acad Sci USA 87, 6878–6882.
33 Strater N & Lipscomb WN (1995) Transition state ana-
logue L-leucinephosphonic acid bound to bovine lens
leucine aminopeptidase: X-ray structure at 1.65A resolu-
tion in a new crystal form. Biochemistry 34, 9200–9210.
34 Strater N & Lipscomb WN (1995) Two-metal ion mech-
anism of bovine lens leucine aminopeptidase: active site
solvent structure and binding mode of L-leucinal, a
gem-diolate transition state analogue, by X-ray crystal-
lography. Biochemistry 34, 14792–14800.
35 Chen G, Edwards T, D’souza VM & Holz RC (1997)
Mechanistic studies on the aminopeptidase from Aero-
monas proteolytica: a two-metal ion mechanism for
peptide hydrolysis. Biochemistry 36, 4278–4286.
36 Fundoiano-Hershcovitz Y, Rabinovitch L, Langut Y,
Reiland V, Shoham G & Shoham Y (2004) Identification
of the catalytic residues in the double-zinc aminopepti-
dase from Streptomyces griseus. FEBS Lett 571, 192–196.
37 Bzymek KP & Holz RC (2004) The catalytic role of
glutamate 151 in the leucine aminopeptidase from Aero-
monas proteolytica. J Biol Chem 279, 31018–31025.
38 Weston J (2005) Mode of action of bi- and trinuclear
zinc hydrolases and their synthetic analogues. Chem Rev
105, 2151–2174.
39 Ben-Meir D, Spungin A, Ashkenazi R & Blumberg S
(1993) Specificity of Streptomyces griseus aminopepti-

dase and modulation of activity by divalent metal ion
binding and substitution. Eur J Biochem 212, 107–112.
40 Spungin A & Blumberg S (1989) Streptomyces griseus
aminopeptidase is a calcium-activated zinc metallopro-
tein. Purification and properties of the enzyme. Eur J
Biochem 183, 471–477.
41 Ni SX, Cossar D, Man A, Norek K, Miller D,
Kearse C & Tsvetnitsky V (2003) Purification and
characterization of recombinant Streptomyces griseus
aminopeptidase. Protein Expr Purif 30, 62–68.
Y. F. Hershcovitz et al. Mechanism of an aminopeptidase from S. griseus
FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS 3875
42 Fersht A (1999) The basic equations of enzyme kinetics.
In Structure and Mechanism in Protein Science (Fersht
A, ed.). WH Freeman, New York, NY.
43 Prescott JM, Wilkes SH, Wagner FW & Wilson KJ
(1971) Aeromonas aminopeptidase. Improved isolation
and some physical properties. JBiolChem246, 1756–1764.
44 Bayliss ME & Prescott JM (1986) Modified activity of
Aeromonas aminopeptidase: metal ion substitutions and
role of substrates. Biochemistry 25, 8113–8117.
45 Prescott JM, Wagner FW, Holmquist B & Vallee BL
(1985) Spectral and kinetic studies of metal-substituted
Aeromonas aminopeptidase: nonidentical, interacting
metal-binding sites. Biochemistry 24, 5350–5356.
46 Arima J, Uesugi Y, Uraji M, Yatsushiro S, Tsuboi S,
Iwabuchi M & Hatanaka T (2006) Modulation of Strep-
tomyces leucine aminopeptidase by calcium: identification
and functional analysis of key residues in activation and
stabilization by calcium. J Biol Chem 281, 5885–5894.

47 Harris MN & Ming L (1999) Different phosphate bind-
ing modes of Streptomyces griseus aminopeptidase
between crystal and solution states and the status of
zinc-bound water. FEBS Lett 455, 321–324.
48 Benett B & Holz RC (1997) EPR studies on the mono-
and dicobalt (II)-substituted forms of the aminopepti-
dase from Aeromonas proteolytica. Insight into the cata-
lytic mechanism of dinuclear hydrolases. J Am Chem
Soc 119, 1923–1933.
49 Gilboa R (2004) The relationship between structure and
function of the enzyme Streptomyces griseus aminopept-
idase (SGAP). PhD Thesis, The Hebrew University,
Jerusalem.
50 Leskovac V (2003) The pH dependence of enzyme cata-
lysis. In Comprehensive Enzyme Kinetics (Leskovac V,
ed.), pp. 300–302. Kluwer Academic Press ⁄ Plenum
Publishers, New York, NY.
51 Fersht A (1999) The pH dependence of enzyme cata-
lysis. In Structure and Mechanism in Protein Science
(Fersht A, ed.). WH Freeman, New York, NY.
52 Greene D, Das B & Fricker LD (1992) Regulation of
carboxypeptidase E. Effect of pH, temperature and
Co
2+
on kinetic parameters of substrate hydrolysis.
Biochem J 285, 613–618.
53 Dixon NE, Blakeley RL & Zerner B (1980) Jack bean
urease (EC 3.5.1.5). III. The involvement of active-site
nickel ion in inhibition by beta-mercaptoethanol, phos-
phoramidate, and fluoride. Can J Biochem 58 , 481–488.

54 Vallee BL & Galdes A (1984) The metallobiochemistry
of zinc enzymes. Adv Enzymol Relat Areas Mol Biol 56,
283–430.
55 Vincent JB, Crowder MW & Averill BA (1991) Spectro-
scopic and kinetics studies of a high-salt-stabilized form
of the purple acid phosphatase from bovine spleen.
Biochemistry 30, 3025–3034.
56 Williams AC & Auld DS (1986) Kinetic analysis by
stopped-flow radiationless energy transfer studies: effect
of anions on the activity of carboxypeptidase A.
Biochemistry 25, 94–100.
57 Yang JJ, Artis DR & Van Wart HE (1994) Differential
effect of halide anions on the hydrolysis of different
dansyl substrates by thermolysin. Biochemistry 33,
6516–6523.
58 Yang JJ & Van Wart HE (1994) Kinetics of hydrolysis
of dansyl peptide substrates by thermolysin: analysis of
fluorescence changes and determination of steady-state
kinetic parameters. Biochemistry 33, 6508–6515.
59 Leatherbarrow RJ (2001). GraFit, Version 5.0. Erithacus
Software Ltd, Horley.
60 Segel IH (1975) Effects of pH and temperature.
Enzymes Kinetics: Behavior and Analysis of Rapid Equi-
librium and Steady-State Enzyme Systems (Segel IH,
ed.). John Wiley & Sons, New York, NY.
61 Segel IH (1975) Simple inhibition systems. In Enzymes
Kinetics: Behavior and Analysis of Rapid Equolobrium
and Steady-State Enzyme Systems (Segel IH, ed.). John
Wiley & Sons, New York, NY.
62 Martell AE & Hancock RD (1996) Metal Complexes in

Aqueous Solutions, pp. 199–202. Plenum Press, New
York, NY.
63 Dunn BM (2001) Determination of protease mechanism.
In Proteolytic Enzymes: A Practical Approach (Beynon
B & Bond JS, eds), pp. 83–86. Oxford University Press,
New York, NY.
64 Cleland WW (1982) Use of isotope effects to elucidate
enzyme mechanisms. CRC Crit Rev Biochem 13, 385–
428.
65 Albery WJ (1975) Proton Transfer Reactions. Chapman
& Hall, London.
66 Segel IH (1975) Kinetics of unireactant enzymes. In
Enzymes Kinetics: Behavior and Analysis of Rapid Equol-
obrium and Steady-State Enzyme Systems (Segel IH,
ed.). John Wiley & Sons, New York, NY.
67 Makinen MW, Wells GB & Kang SO (1984) Structure
and mechanism of carboxypeptidase A. Adv Inorg
Biochem 6, 1–69.
68 Mustafi D & Makinen MW (1994) Catalytic conforma-
tion of carboxypeptidase A. Structure of a true enzyme
reaction intermediate determined by electron nuclear
double resonance. J Biol Chem 269, 4587–4595.
69 Bienvenue DL, Mathew RS, Ringe D & Holz RC (2002)
The aminopeptidase from Aeromonas proteolytica can
function as an esterase. J Biol Inorg Chem 7, 129–135.
70 De Paola CC, Bennett B, Holz RC, Ringe D & Petsko
GA (1999) 1-Butaneboronic acid binding to Aeromonas
proteolytica aminopeptidase: a case of arrested develop-
ment. Biochemistry 38
, 9048–9053.

71 Harris MN, Bertolucci CM & Ming LJ (2002) Paramag-
netic cobalt (II) as a probe for kinetic and NMR relaxa-
tion studies of phosphate binding and the catalytic
mechanism of Streptomyces dinuclear aminopeptidase.
Inorg Chem 41, 5582–5588.
Mechanism of an aminopeptidase from S. griseus Y. F. Hershcovitz et al.
3876 FEBS Journal 274 (2007) 3864–3876 ª 2007 The Authors Journal compilation ª 2007 FEBS