Functional significance of Glu-77 and Tyr-137 within the active site of isoaspartyl dipeptidase

Article abstract of DOI:10.1016/j.bioorg.2005.10.002

Isoaspartyl dipeptidase (IAD) is a binuclear metalloenzyme and a member of the amidohydrolase superfamily. This enzyme catalyzes the hydrolytic cleavage of β-aspartyl dipeptides. The pH-rate profiles for the hydrolysis of β-Asp-Leu indicates that catalysis is dependent on the ionization of two groups; one that ionizes at a pH ～6 and the other ～9. The group that must be ionized for catalysis is directly dependent on the identity of the metal ion bound to the active site. This result is consistent with the ionization of the hydroxide that bridges the two divalent cations. In addition to the residues that interact directly with the divalent cations there are two other residues that are highly conserved and found within the active site: Glu-77 and Tyr-137. Mutation of Tyr-137 to phenylalanine reduced the rate of catalysis by three orders of magnitude. The three dimensional X-ray structure of the Y137F mutant did not show any significant conformation changes relative to the three dimensional structure of the wild-type enzyme. The positioning of the side-chain phenolic group of Tyr-137 in the active site of IAD is consistent with the stabilization of the tetrahedral adduct concomitant with nucleophilic attack by the hydroxide that bridges the two divalent cations. Mutation of Glu-77 resulted in the reduction of catalytic activity by five orders of magnitude. The three dimensional structure of the E77Q mutant did not show any significant conformational changes in the mutant relative to the three dimensional structure of the wild-type enzyme. The positioning of the side-chain carboxylate of Glu-77 is consistent with the formation of an ion pair interaction with the free α-amino group of the substrate.

Full text of DOI:10.1016/j.bioorg.2005.10.002

Bioorganic Chemistry 33 (2005) 448–458
www.elsevier.com/locate/bioorg
Functional significance of Glu-77 and Tyr-137
within the active site of isoaspartyl dipeptidase
b
a
´
Ricardo Martı-Arbona , James B. Thoden ,
Hazel M. Holden a, Frank M. Raushel b,*
a
Department of Biochemistry, University of Wisconsin, Madison, WI 53706, USA
Department of Chemistry, PO Box 30012, Texas A&M University, College Station, TX 77842-3012, USA
b
Received 19 August 2005
Available online 11 November 2005
Abstract
Isoaspartyl dipeptidase (IAD) is a binuclear metalloenzyme and a member of the amidohydrolase
superfamily. This enzyme catalyzes the hydrolytic cleavage of b-aspartyl dipeptides. The pH-rate pro-
files for the hydrolysis of b-Asp-Leu indicates that catalysis is dependent on the ionization of two
groups; one that ionizes at a pH ꢀ6 and the other ꢀ9. The group that must be ionized for catalysis
is directly dependent on the identity of the metal ion bound to the active site. This result is consistent
with the ionization of the hydroxide that bridges the two divalent cations. In addition to the residues
that interact directly with the divalent cations there are two other residues that are highly conserved
and found within the active site: Glu-77 and Tyr-137. Mutation of Tyr-137 to phenylalanine reduced
the rate of catalysis by three orders of magnitude. The three dimensional X-ray structure of the Y137F
mutant did not show any significant conformation changes relative to the three dimensional structure
of the wild-type enzyme. The positioning of the side-chain phenolic group of Tyr-137 in the active site
of IAD is consistent with the stabilization of the tetrahedral adduct concomitant with nucleophilic
attack by the hydroxide that bridges the two divalent cations. Mutation of Glu-77 resulted in the reduc-
tion of catalytic activity by five orders of magnitude. The three dimensional structure of the E77Q
mutant did not show any significant conformational changes in the mutant relative to the three dimen-
sional structure of the wild-type enzyme. The positioning of the side-chain carboxylate of Glu-77 is
consistent with the formation of an ion pair interaction with the free a-amino group of the substrate.
ꢀ 2005 Elsevier Inc. All rights reserved.
Keywords: Isoaspartyl dipeptidase
*
Corresponding author. Fax: +1 979 845 9452.
E-mail address: raushel@tamu.edu (F.M. Raushel).
0045-2068/$ - see front matter ꢀ 2005 Elsevier Inc. All rights reserved.
doi:10.1016/j.bioorg.2005.10.002

R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
449
1. Introduction
Isoaspartyl dipeptidase (IAD)1 catalyzes the hydrolytic cleavage of b-aspartyl dipep-
tides [1–3]. These unusual peptide bonds are formed via the spontaneous, but slow, isom-
erization of the protein backbone at amide bonds to asparagine and aspartate residues.
The best substrate found to date for this enzyme is b-Asp-Leu with a Km of 1.0 mM
and a kcat of 104 sꢁ1 [4]. However, IAD exhibits no activity toward the hydrolysis of trip-
eptides or c-glutamyl dipeptides [1,2]. Amino acid sequence identity and three dimensional
structure comparisons demonstrate that this enzyme is a member of the amidohydrolase
superfamily and most closely resembles dihydroorotase and D-hydantoinase [5,6]. The gen-
eral reaction catalyzed by IAD is presented in Scheme 1.
Three dimensional crystal structures of IAD have been solved to high resolution [4,7,8].
These structures include the apo-enzyme and complexes with the substrate (b-Asp-His),
product (aspartate), and a phosphonate inhibitor [4,6]. The individual subunits of the
octameric protein are folded into two domains. The N-terminal domain is composed of
eight mixed b-strands while the C-terminal domain folds as a conventional (b/a)8-barrel.
A binuclear metal center is located within the active site at the C-terminal end of the (b/
a)8-barrel motif. The two metal ions are ligated by four histidines, an aspartic acid and a
carboxylated lysine residue. The a-metal ion is coordinated by His-68, His-70, and Asp-
285 while the b-metal is coordinated by His-201 and His-230. The two metal ions are
bridged by the carboxylated Lys-162 and a molecule from solvent that is presumed to
be hydroxide.
Kinetic and structural investigations of IAD have indicated that the binuclear metal cen-
ter is critical for the enhancement of the nucleophilic character of the hydrolytic water mol-
ecule and the activation of the peptide bond prior to substrate turnover. The b-metal ion is
thought to polarize the carbonyl oxygen bond while the a-metal ion has been proposed to
stabilize the binding of hydroxide [4,8]. The side-chain carboxylate group of Asp-285 has
been postulated to shuttle the proton from the bridging hydroxide to the a-amino group
of the departing amino acid during cleavage of the peptide bond [4,8]. Support for this
chemical mechanism is derived from the X-ray crystal structures of the wild-type and
D285N mutant enzymes and the pH-rate profiles of the wild-type enzyme substituted with
a variety of divalent cations [4]. The proposed reaction mechanism is presented in Scheme 2.
The pH-rate profile of wild-type IAD displays a bell-shaped dependence for the hydro-
lysis of b-Asp-Leu [4]. The decrease in catalytic activity at low pH indicates that the pro-
tonation of a single group results in the loss of catalytic activity. The systematic variation
in the kinetic pKa, obtained from the pH-rate profiles with different metal substituted vari-
ants of IAD, demonstrated that the pKa for the ionization at low pH is dependent on the
identity of metal ions in the binuclear metal center [4]. This result is consistent with the
protonation of the bridging hydroxide. The pKa of the group that needs to be protonated
for catalytic activity is independent of changes to the specific metal ion bound within the
binuclear metal center. This ionization has been proposed to be due to deprotonation of
the a-amino group of the aspartate moiety of the substrate [4].
1
Abbreviations used: DHO, dihydroorotase; IAD, isoaspartyl dipeptidase; Hepes, N-2-hydroxyethylpiperazine-
N0-2-ethanesulfonic acid; Ches, 2-(cyclohexylamino)ethanesulfonic acid; Mes, 2-morpholinoethanesulfonic acid;
Pipes, piperazine-N,N00-bis(2-ethanesulfonic acid); Taps, N-[Tris-(hydroxymethyl)methyl]-3-aminopropanesulf-
onic acid.

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R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
NH3+ O
R
NH3+ O
R
IAD
O-
-O
O-
-O
+H3N
O-
+
N
H
H2O
O
O
O
O
Scheme 1.
O
O
β
α
C
α
β
α
C
O
β
O
O
O
O
O
O
O
O
C
H
C
H
O
HN
R
HN
Asp-285
O
H3N
R
H3N
O
H3N
C
O
C
C
O
O
O
Scheme 2.
In addition to the residues that make direct interactions with the binuclear metal center
in the active site of IAD, there are two other highly conserved residues within the active
site that may contribute to the overall rate enhancement for this enzyme. In the X-ray
crystal structure of IAD, the side-chain phenolic group of Tyr-137 is orientated in a posi-
tion where it may function as a 5th metal ligand to the b-metal ion and/or serve as a Lewis
acid catalyst for the polarization of the carbonyl oxygen of the scissile amide bond. The
side chain carboxylate of Glu-77 likely functions in an ion pair arrangement with the free
a-amino group of the substrate or, alternatively, as part of a proton shuttle mechanism.
Y137
α
β
R233
R169
T106
S289
G75
E77
Fig. 1. A close-up view of the active site of the D285N mutant with bound b-Asp-His, highlighted in gold bonds.
Potential hydrogen bonding interactions between b-Asp-His and the D285N mutant are represented by the blue
˚
dashed lines. The side-chain phenolic oxygen of Y137 is 2.4 A away from the carbonyl oxygen of the scissile bond
˚
of the bound substrate. The side-chain carboxylate of E77 is 2.9 A away from the free a-amino group of the
bound b-Asp-His. The image was drawn with the program WebLab Viewer Pro using the coordinates from PDB
file 1YBQ (4).

R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
451
The relative orientations of these two residues within the active site of IAD are presented
in Fig. 1. In this article, we have probed the contribution of these two residues in the cat-
alytic activity of IAD by measuring the kinetic constants for site directed mutants of IAD
and have determined the alterations in the three dimensional structure by electron diffrac-
tion for E77Q and Y137F.
2. Materials and methods
2.1. Materials
All chemicals, substrates, and coupling enzymes were obtained from Sigma or Aldrich.
The iadA gene was cloned from the Escherichia coli XL1Blue strain into a pET30 plasmid
obtained from Stratagene [8]. Site directed mutagenesis of IAD at residues Glu-77 and
Tyr-137 was accomplished using the Quick Change site-directed mutagenesis kit from
Stratagene.
2.2. Protein purification
The pET30 plasmids encoding wild-type and mutant IAD were transformed in JDG
1000 (kDE3). IAD was purified according to published procedures [4]. Cultures were
grown in Luria–Bertani medium at 37 ꢁC until the absorbance at 600 nm reached 0.6
OD. The expression of IAD was induced by the addition of 1.0 mM isopropyl-b-thioga-
lactoside and incubated for 12 h at 37 ꢁC. Cells were harvested by centrifugation and
resuspended in 50 mM Hepes buffer at pH 8.1 (buffer A) containing 5 lg/mL RNAse
and 0.1 mg/mL phenylmethylsulfonyl fluoride. The cells were lysed by sonication and
the soluble protein was isolated by centrifugation and then fractioned between 20 and
50% saturation of ammonium sulfate in buffer A. The precipitated protein was resuspend-
ed and loaded onto a Superdex 200 gel filtration column (Amersham Pharmacia). The
active fractions were pooled and loaded onto a Resource Q ionic exchange column (Amer-
sham Pharmacia) and eluted with a gradient of NaCl in buffer A. The purification was
finalized by pooling and precipitating the fractions that contained IAD with ammonium
sulfate. The pellet was resuspended and reloaded onto the Superdex 200 gel filtration col-
umn and eluted with buffer A. The presence and purity of IAD in the fractions was con-
firmed by SDS–PAGE. The chromatographic profiles for wild-type and mutant IAD were
identical. The purified enzyme was stored at ꢁ20 ꢁC.
2.3. Kinetic measurements and data analysis
The specific activity of IAD was assayed by the coupling the formation of aspartate to
the oxidation of NADH [9]. The oxidation of NADH at 30 ꢁC was followed spectropho-
tometrically at 340 nm with a SPECTRAmax-340 microplate reader (Molecular Devices
Inc.). The assay solutions contained 100 mM Hepes, 100 mM KCl, 3.7 mM a-ketoglutar-
ate, 0.4 mM NADH, and 0.64 U of malate dehydrogenase, 6 U of aspartate aminotrans-
ferase, and variable amounts of b-Asp-Leu and IAD in a final volume of 250 lL. The
kinetic constants were determined by fitting the initial velocity data to the Eq. (1) [10].
In Eq. (1), v is the initial velocity, Et is the enzyme concentration, kcat is the turnover num-
ber, A is the substrate concentration, and Km is the Michaelis constant.

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R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
The pH dependence of the kinetic parameters was determined for the Zn/Zn-substitut-
ed forms of the wild-type and the Y135F mutant using b-Asp-Leu as the variable sub-
strate. The pH range was assayed between 5.0 and 10.0 in 0.2 pH unit increments. The
buffers Mes (5.0–6.6), Pipes (6.6–7.2), Hepes (7.2–8.2), Taps (8.2–8.8), and Ches (8.8–
10.0) were used at a concentration of 100 mM and the pH of each solution was measured
after the reaction was completed. Eq. (2) was utilized to fit the data when the activity
diminished at both low and high pH [10]. In Eq. (2), y is the value of kcat or kcat/Km, c
is the pH-independent value of y, Ka and Kb are the dissociation constants of the groups
that ionize and H is the hydrogen-ion concentration.
v=Et ¼ kcatA=ðKm þ AÞ
log y ¼ logðc=ð1 þ ðH=KaÞ þ ðKb=HÞÞÞ
ð1Þ
ð2Þ
2.4. Structural analysis
Large single crystals of the E77Q and Y137F mutant proteins were grown by the hang-
ing drop method of vapor diffusion against precipitant solutions containing 6–8%
Table 1
X-ray data collection statistics
a
˚
Data set
Resolution (A)
Independent
reflections
Completeness (%)
Redundancy
Avg I/Avg r (I)
Rsym
E77Q
30.0–1.95
2.04–1.95b
30.0–1.95
2.04–1.95
68348
6900
71537
7448
93.4
75.7
97.9
81.8
3.7
1.5
3.3
1.8
8.2
1.7
11.6
2.5
7.0
28.0
6.5
Y137F
26.4
P
P
a
ꢀ
Rsym
¼
jI ꢁ Ij= IÞ ꢂ 100.
b
Statistics for the highest resolution bin.
Table 2
Relevant refinement statistics
Complex
E77Q
Y149F
˚
Resolution limits (A)
30.0–1.95
30.0–1.95
18.5/71537
18.3/64418
21.3/7119
5559c
a
R-factor (overall)%/# rflns
18.0/68348
17.9/61482
21.9/6866
5579b
426d
0.013
R-factor (working)%/# rflns
R-factor (free)%/# rflns
No. Protein atoms
No. Hetero-atoms
375e
˚
Bond lengths (A)
0.013
Bond angles (ꢁ)
Trigonal planes (A)
General planes (A)
Torsional angles (ꢁ)f
2.29
0.008
0.016
16.9
2.33
0.009
0.014
16.3
˚
˚
P
P
a
R ꢁ factor ¼ ð jF o ꢁ F cjÞ= jF oj ꢂ 100 where Fo is the observed structure-factor amplitude and Fc is the
calculated structure-factor amplitude.
b
These include multiple conformations for V100 and N341 in chain A and K150 and N341 in chain B.
These include multiple conformations for V100, R330, and N341 in chain A and V100 and N341 in chain B.
These include 4 zinc ions and 422 waters.
These include 4 zinc ions and 371 waters.
c
d
e
f
The torsional angles were not restrained during the refinement.

R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
453
poly(ethylene glycol) 8000, 100 mM homopipes (pH 5.0), and 50–100 mM MgCl2. They
contained two subunits in the asymmetric unit and belonged to space group P4212 with
˚
˚
unit cell dimensions of a = b = 119.2 A and c = 138.6 A. X-ray data sets were collected
˚
to 1.95 A resolution at 4 ꢁC with a Bruker HISTAR area detector system equipped with
Supper ‘‘long’’ mirrors. The X-ray source was Cu Ka radiation from a Rigaku RU200
X-ray generator operated at 50 kV and 90 mA. The X-ray data were processed with
XDS [11,12] and internally scaled with XSCALIBRE (Rayment and Wesenberg, unpub-
lished program). Relevant X-ray data collection statistics are presented in Table 1.
The structure was determined by difference Fourier techniques using as a starting model
the wild-type structure (PDB 1ONW). Iterative cycles of least-squares refinement with
TNT [13] and manual model building reduced the R-factors to 18.0% (for the E77Q)
˚
and 18.5% (for the Y137F) all measured X-ray data from 30.0 to 1.95 A resolution. Rel-
evant least-squares refinement statistics are given in Table 2.
3. Results
3.1. Mutation of residues glutamate-77 and tyrosine-137
The kinetic parameters for the Zn/Zn-substituted forms of the wild-type and mutants
of IAD at pH 8.1 are presented in Table 3. Wild-type IAD exhibits a Km of 1.0 mM and
a kcat/Km of 105 Mꢁ1 sꢁ1 for the catalytic hydrolysis of b-Asp-Leu [4]. The mutation of
Glu-77 to either alanine or aspartate results in a significant decrease in the specific activ-
ity by reducing the kcat by approximately five orders of magnitude. For the mutant
E77D, the Km is increased 7-fold but there is no apparent effect on the Km for the
E77Q mutant. Site directed mutagenesis of Tyr-137 to an alanine resulted in a mutant
with a Km that is elevated by 2.5-fold relative to the wild-type enzyme. The Km for
the phenylalanine mutant at this site is identical to the wild-type enzyme. For both
mutants made at position Y137 the value of kcat is diminished by about three orders
of magnitude.
3.2. pH-rate profiles
The kinetic pKa values were determined from the pH-dependence of the catalytic
parameters for wild-type IAD and the Y137F mutant. The pH-rate profiles for wild-type
IAD and the Y137F mutant are bell-shaped as presented in Fig. 2. These results indicate
that one group must be unprotonated while another group must be protonated for opti-
Table 3
Kinetic parameters for IAD and mutants with b-Asp-Leu as the substratea
IAD
Km (mM)
kcat (sꢁ1
)
kcat/Km (Mꢁ1sꢁ1
)
WT
1.0 0.1
6.9 0.9
0.8 0.1
2.5 0.2
0.97 0.07
(1.04 0.03) · 1ꢁ023
(5.1 0.3) · 10ꢁ3
(5.6 0.1) · 10ꢁ1
(3.2 0.1) · 10
(1.0 0.1) · 105
E77D
E77Q
Y137A
Y137F
a
(7.4 0.1) · 10ꢁ1
7
1
(1.26 0.01) · 101
(3.1 0.1) · 10ꢁ1
(3.16 0.1) · 101
The kinetic constants were determined at pH 8.1 from a fit of the data to Eq. (1).

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R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
2.2
2.2
2.0
1.8
1.6
1.4
1.2
1.0
A
B
2.0
1.8
1.6
1.4
1.2
1.0
5
6
7
8
pH
9
10
5
6
7
8
9
10
pH
0.0
-0.2
-0.4
-0.6
-0.8
-1.0
-1.2
-0.4
-0.6
-0.8
-1.0
-1.2
-1.4
-1.6
C
D
5
6
7
8
9
10
5
6
7
8
9
10
pH
pH
Fig. 2. The pH-rate profiles of kcat and kcat/Km for wild-type (n), and Y137F mutant enzyme (m). The pH-rate
profiles for the wild-type enzyme are presented in (A and B). The pH-rate profiles for the mutant Y137F are
shown in (C and D). The data were fit to Eq. (2) using b-Asp-Leu as the variable substrate. Additional details are
provided in the text and in Table 4.
mum catalytic activity. The pKa values for wild-type IAD and the Y137F mutant,
obtained from fits of the data to Eq. (2), are provided in Table 4. For the mutant
Y137F, the pKa value for the group that must be unprotonated for maximum catalytic
activity, obtained from the variation of kcat with pH, is somewhat lower than the value
observed with the wild-type enzyme (5.6 relative to 6.1 for wild-type IAD). The pKa for
the group that must be protonated for maximum catalytic activity is essentially the same
for the mutant and the wild-type enzyme. A bell-shaped profile was also observed for the
wild-type IAD when kcat/Km was measured as function of pH. For the mutant enzyme, the
kinetic pKa values for the two ionizations from kcat/Km are somewhat lower than that
observed for the wild-type enzyme.
Table 4
pKa values for wild-type and Y137F mutant of IAD from pH-rate profilesa
IAD
log kcat vs. pH
pKa
log kcat/Km vs. pH
pKa
pKb
pKb
WT
Y137F
a
6.1 0.4
5.6 0.1
9.6 0.1
9.6 0.1
5.8 0.4
5.3 0.1
9.6 0.1
9.1 0.1
The kinetic constants were determined with b-Asp-Leu as the substrate from a fit of the data to Eq. (2).

R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
455
H68
K162
H230
D/N285
α
H201
H70
β
E/Q77
Fig. 3. Superposition of the active site region for the apo-form of IAD (PDB: 1ONW), the mutant E77Q (PDB:
2AQO), and the substrate bound complex of the mutant D285N (PDB: 1YBQ). The side chains of the apo-form
of IAD are depicted with blue bonds, the side chains for the E77Q mutant are depicted in green, and the substrate
bound complex of the D285N mutant is displayed in grey. The positions of the zinc ions for all of the structures
are very similar and are presented as yellow spheres. The substrate b-Asp-His is presented with gold bonds. The
image was drawn with the program WebLab viewer Pro.
3.3. X-ray structures of the E77Q and Y137F mutant proteins
The three dimensional X-ray structures of the E77Q and Y137F mutant proteins were
2
˚
determined to a resolution of 1.95 A with R-factors of 18.0 and 18.5%, respectively . The
mutation of these two residues within the active site of IAD did not affect the relative occu-
pancies of the zinc ions in the binuclear metal center. The overall molecular fold of the
mutant proteins is identical to that of the wild-type IAD. The electron density of Lys-
162 in both of the subunits is consistent with the carboxylation of the side-chain e-amino
group to a carbamate functional group. In the previously determined structure of the
D285N mutant complexed with the substrate b-Asp-His, the side-chain carboxylate of
Glu-77 appears to ion pair to the a-amino group of the b-Asp-His substrate [4]. Interest-
ingly, the orientation of Gln-77 in the E77Q mutant is similar to that obtained for the crys-
tal structures of the wild-type IAD complexed with the product aspartate and the D285N
mutant complexed to b-Asp-His (Fig. 3) rather than of the apo-form of IAD. However,
the c-carbonyl oxygen of Gln-77 in the E77Q mutant remains virtually in the same posi-
tion as one of the oxygens of the c-carboxylate of Glu-77.
The superposition of the active site residues for the unliganded form of IAD and the
Y137F mutant is presented in Fig. 4. In the structure of the wild-type enzyme the Og
2
X-ray coordinates have been deposited in the Protein Data Bank (Accession Nos. 2AQO and 2AQV).

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R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
H68
K162
H230
D285
H201
α
β
H70
Y/F137
Fig. 4. Superposition of the wild-type IAD (PDB: 1ONW) and the Y137F mutant (PDB: 2AQV). The side chains
corresponding to the wild-type enzyme are depicted in the dark blue bonds while those of the Y137F mutant
protein are displayed in light blue. The positions of the zinc ions both structures are essentially the same and are
indicated by yellow spheres. The solvent molecule that bridges the binuclear metal center is drawn as a red sphere.
The image was created with the program WebLab Viewer Pro.
˚
˚
for the side-chain of Tyr-137 is situated 3.4 A from the b-metal and 2.4 A from the carbon-
yl oxygen of the scissile peptide bond of the substrate. The removal of the phenolic
hydroxyl from the side-chain of Tyr-137 did not result in any significant perturbation of
the phenyl ring relative to the corresponding side-chain within the active site of the
wild-type enzyme.
4. Discussion
Isoaspartyl dipeptidase is a member of the amidohydrolase superfamily [5,6]. IAD cat-
alyzes the hydrolysis of b-aspartyl dipeptides with a variety of side chains at the C-termi-
nus. These variations include amino acid residues that are hydrophobic, aromatic, or
hydrophilic. The binuclear metal center of IAD is similar to that found for phosphotries-
terase [14], dihydroorotase [15], and urease [16]. The reaction mechanism for IAD pro-
posed in Scheme 2 postulates the activation of the solvent molecule between the two
metals via proton transfer to the carboxylate group of Asp-285. The pH-rate profiles
for the wild-type IAD display a significant decrease in catalytic activity at pH values lower
than 6 and higher than 9. The loss of catalytic activity at low pH suggests the protonation
of a single group with a pKa of ꢀ6. The kinetic pKa, obtained from the pH-rate profiles of
metal-substituted variants of IAD, was found to be dependent on the specific metal ion
bound to the active site [4]. The loss of the catalytic activity at low pH is consistent with
the protonation of the bridging hydroxide [4]. In contrast, the kinetic pKa for the group
that must be protonated for catalytic activity was independent of the specific metal ion
bound to the active site. The decrease in the catalytic activity at high pH was proposed
to be caused by the deprotonation of the a-amino group of the aspartate moiety of the
substrate [4].
Amino acid sequence alignments and the three dimensional X-ray structures of IAD
have identified two highly conserved residues within the active site that are not directly

R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
457
a part of the binuclear metal center. However, the precise functions of Glu-77 and Tyr-137
in the catalytic reaction mechanism are not known. When Tyr-137 is mutated to either ala-
nine or phenylalanine the catalytic activity is reduced by approximately three orders of
magnitude. The pH-rate profiles for the Y137F mutants are similar to the wild-type
enzyme in that activity is lost as the pH is lowered below ꢀ6 or elevated above ꢀ9. These
results suggest that ionization of this residue is unlikely to be responsible for the loss of
catalytic activity observed in the pH-rate profiles of the wild-type enzyme. However, the
significant drop in catalytic activity for the Y137F mutant does suggest a critical role
for the phenolic hydroxyl of Tyr-137. The X-ray structure of the Y137F mutant reported
here shows that the aromatic ring of the phenylalanine is oriented in precisely the same
way as the aromatic ring of the tyrosine found in the structure of the wild-type enzyme.
This observation rules out the possibility of a conformational difference between the
mutant and the wild-type enzyme as the root cause for the diminution of catalytic activity.
In the structure of the inactive D285N mutant bound with the substrate b-Asp-His the
˚
phenolic oxygen of Y137 is 2.4 A away from the carbonyl oxygen of the scissile peptide
bond. This distance is consistent with a hydrogen bond from the tyrosine to the tetrahedral
intermediate during hydrolysis of the peptide bond. This feature within the active site
would serve to augment the stabilization of the tetrahedral intermediate by the b-metal
ion. However, residues with similar function have not been detected within the active sites
of phosphotriesterase [14], dihydroorotase [15], or urease [16].
When the side-chain carboxylate of Glu-77 is mutated to either aspartate or glutamine
the catalytic activity is reduced by about five orders of magnitude. Unfortunately, the dra-
matic loss in catalytic activity precluded an accurate assessment of the overall effects on
the pH-rate profiles for the mutant enzyme. Nevertheless, the three dimensional X-ray
structure of the E77Q mutant demonstrates that the net loss in catalytic activity is not
due to any apparent conformational differences between the wild-type and mutant
enzyme. In the X-ray structure of the D285N protein, determined in the presence of the
bound substrate b-Asp-His, the side-chain carboxylate of Glu-77 is ion paired with the free
a-amino group of the substrate. Therefore, the most likely function of Glu-77 is to help
orient the substrate within the active site. This ion pair is critical for catalytic activity since
the removal of the free amino group in dipeptide substrates results in the loss of catalytic
activity and the ability to function as an inhibitor [4]. The mutation of Glu-77 results in
Tyr-137
O
α
H
β
COO-
NH3
O
C
O
H
O
R
Asp-285
O
O
HN
O
H2N
O
Glu-77
O
HN
Arg-169
NH
Scheme 3.

458
R. Martı´-Arbona et al. / Bioorganic Chemistry 33 (2005) 448–458
relatively minor effects on the Km for the substrate b-Asp-Leu. The substantially larger
effects on kcat must therefore reflect a coupling of ion pair formation with catalytic
turnover.
In this investigation, we have explored the role of two highly conserved residues in the
active site of isoaspartyl dipeptidase. The side-chain carboxylate of Glu-77 is critical for
catalytic activity through an ion pair interaction with the free a-amino group of dipeptide
substrates. The phenolic hydroxyl of Tyr-137 serves as a Lewis acid catalyst via stabiliza-
tion of the tetrahedral adduct formed upon nucleophilic attack by the bridging hydroxide
within the binuclear metal center. The remaining critical residue is the highly conserved
Arg-169 that makes an ion pair with the terminal carboxylate of the substrate. These
molecular interactions are summarized in Scheme 3.
Acknowledgments
This work was supported in part by NIH Grants GM-33894. R.M.-A. was supported as
a trainee of the Chemistry-Biology Interface Training Program (T32GM 008523).
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