The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile

Article abstract of DOI:10.1021/ja410462j

Nitrile hydratase (NHase) catalyzes the hydration of nitriles to their corresponding commercially valuable amides at ambient temperatures and physiological pH. Several reaction mechanisms have been proposed for NHase enzymes; however, the source of the nucleophile remains a mystery. Boronic acids have been shown to be potent inhibitors of numerous hydrolytic enzymes due to the open shell of boron, which allows it to expand from a trigonal planar (sp²) form to a tetrahedral form (sp³). Therefore, we examined the inhibition of the Co-type NHase from Pseudonocardia thermophila JCM 3095 (PtNHase) by boronic acids via kinetics and X-ray crystallography. Both 1-butaneboronic acid (BuBA) and phenylboronic acid (PBA) function as potent competitive inhibitors of PtNHase. X-ray crystal structures for BuBA and PBA complexed to PtNHase were solved and refined at 1.5, 1.6, and 1.2 A resolution. The resulting PtNHase-boronic acid complexes represent a "snapshot" of reaction intermediates and implicate the cysteine-sulfenic acid ligand as the catalytic nucleophile, a heretofore unknown role for the αCys¹¹³-OH sulfenic acid ligand. Based on these data, a new mechanism of action for the hydration of nitriles by NHase is presented.

Full text of DOI:10.1021/ja410462j

Communication
pubs.acs.org/JACS
Open Access on 01/02/2015
The Active Site Sulfenic Acid Ligand in Nitrile Hydratases Can
Function as a Nucleophile
Salette Martinez,†,‡,⊥ Rui Wu, Ruslan Sanishvili, Dali Liu, and Richard Holz*
‡,⊥
§
‡
,†
†
Department of Chemistry, Marquette University, Milwaukee, Wisconsin 53201, United States
‡
Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
§
X-ray Science Division, Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439,
United States
*
S Supporting Information
hydrolyzing potential of NHases is becoming increasingly
recognized as a new type of “green” chemistry for the
degradation of environmentally harmful nitriles such as
ABSTRACT: Nitrile hydratase (NHase) catalyzes the
hydration of nitriles to their corresponding commercially
valuable amides at ambient temperatures and physiological
pH. Several reaction mechanisms have been proposed for
NHase enzymes; however, the source of the nucleophile
remains a mystery. Boronic acids have been shown to be
potent inhibitors of numerous hydrolytic enzymes due to
the open shell of boron, which allows it to expand from a
10
bromoxynil, a nitrile-based pesticide.
Several reaction mechanisms have been proposed for NHase
enzymes; however, the precise catalytic pathway remains
elusive. Based on single turnover stopped-flow data, the nitrile
substrate nitrogen was shown to bind directly to the active site
11
metal ion displacing the axial water molecule. Once bound,
2
3
trigonal planar (sp ) form to a tetrahedral form (sp ).
Therefore, we examined the inhibition of the Co-type
NHase from Pseudonocardia thermophila JCM 3095
imidate is likely formed as the result of nucleophilic attack,
which then isomerizes to the corresponding amide. However,
the source of the nucleophile for this transformation is still
under debate. To gain insight into the identity of the active site
nucleophile, we examined the inhibition of the Co-type NHase
from Pseudonocardia thermophila JCM 3095 (PtNHase) by
boronic acids. The resulting X-ray crystal structures of
PtNHase-boronic acid complexes are a “snapshot” of potential
reaction intermediates and implicate the cysteine-sulfenic acid
ligand as the catalytic nucleophile. The combination of these
data with previously reported spectroscopic and X-ray
crystallographic data have allowed a novel mechanism of action
to be proposed for the metal-mediated nitrile hydration
reaction catalyzed by NHase enzymes.
(
PtNHase) by boronic acids via kinetics and X-ray
crystallography. Both 1-butaneboronic acid (BuBA) and
phenylboronic acid (PBA) function as potent competitive
inhibitors of PtNHase. X-ray crystal structures for BuBA
and PBA complexed to PtNHase were solved and refined
at 1.5, 1.6, and 1.2 Å resolution. The resulting PtNHase−
boronic acid complexes represent a “snapshot” of reaction
intermediates and implicate the cysteine-sulfenic acid
ligand as the catalytic nucleophile, a heretofore unknown
1
13
role for the αCys −OH sulfenic acid ligand. Based on
these data, a new mechanism of action for the hydration of
nitriles by NHase is presented.
The ability of both 1-butaneboronic acid (BuBA) and
phenylboronic acid (PBA) to inhibit PtNHase was examined by
monitoring the hydration of acrylonitrile to acrylamide
itrile hydratase (NHase, E.C. 4.2.1.84) is a metal-
spectrophotometrically at 225 nm (ε = 2.9 mM− cm ). In
1
−1
N
loenzyme within the nitrile degradation pathway that
catalyzes the hydration of nitriles to their corresponding amides
under mild conditions (room temperature and physiological
the absence of inhibitors, PtNHase catalyzed the hydration of
acrylonitrile at pH 7.5 and 25 °C with a k value of 1310 ±
cat
1
1
,2
110 s and a Km value of 0.8 ± 0.1 mM. Inspection of the
pH). NHases consist of two nonhomologous subunits, α and
3
−6
reaction time course for the hydration of acrylonitrile at pH 7.5
and 25 °C by PtNHase in the presence of BuBA or PBA
indicates that both boronic acids function as potent competitive
inhibitors of PtNHase. For BuBA, linear reaction progress
β, that form α β heterotetramers.
Several NHases have
2
2
been structurally characterized and shown to contain either a
low-spin nonheme Fe(III) ion (Fe-type) or a low-spin
noncorrin Co(III) ion (Co-type) in their active site. The
metal ion is coordinated by three cysteine sulfur atoms, two
curves were observed providing an inhibition constant (K ) of
i
7
0.5 ± 0.1 μM. On the other hand, PBA displayed biphasic
amide nitrogens, and a water molecule. Two of the active site
progress curves, which is characteristic of slow-binding
cysteine residues are post-translationally modified to cysteine-
12
inhibition (Figure S1).
sulfinic acid (Cys−SO H) and cysteine-sulfenic acid (Cys−
2
The slow-binding inhibition properties of PBA were analyzed
SOH) yielding an unusual metal coordination geometry,
7
based on the equilibrium shown in Scheme 1, where K (K =
termed a “claw setting”. NHases have attracted substantial
i
i
k /k ) is the equilibrium inhibition constant for the formation
interest as biocatalysts in preparative organic chemistry and are
1
2
used in several industrial applications such as the large scale
8
,9
production of acrylamide and nicotinamide. In addition,
Received: October 11, 2013
Published: January 2, 2014
because of their exquisite reaction specificity, the nitrile-
©
2014 American Chemical Society
1186
dx.doi.org/10.1021/ja410462j | J. Am. Chem. Soc. 2014, 136, 1186−1189

Journal of the American Chemical Society
Communication
Scheme 1
of the initial complex, EI, and k and k are the forward and
3
4
reverse rate constants for the equilibrium between the EI and
12
the EI* complex. By measuring the reaction time course at
different concentrations of PBA and substrate, the initial K was
i
found to be 5.0 ± 0.9 μM. The overall K * of 0.04 ± 0.01 nM,
i
Figure 1. Stereoview of PtNHase bound by BuBA after soaking a
crystal of WT PtNHase in cryo-protectant containing 10 mM BuBA
for 20 s followed by flash freezing in liquid nitrogen. The 2f − f map
where K * = K k /(k + k ), was determined by preincubating
i
i
4
3
4
PtNHase with PBA for 1 h at pH 7.5 and 25 °C followed by
reaction with various concentrations of acrylonitrile.
o
c
is shown as a transparent gray surface at the 1.1 σ level around BuBA
and αCys1 . The simulated-annealing omit map (f − f ) is shown
13
Since both BuBA and PBA function as competitive inhibitors
of PtNHase, they must bind to the enzyme active site. In
solution, BuBA was reported to be >99% in the boronic acid
o
c
around BuBA as a green mesh at 2.7 σ.
2
13
the sulfenic acid O-atom on the empty p orbital of the B-atom
form (sp hybridized) at pH 8.0, with a reported pK of 10.6.
z
a
14
and the subsequent loss of a boronic acid O-atom. Even though
Similarly, the pK of PBA is 8.9, so it too will be in the
a
113
the O-atom of αCys -OH is covalently bound to boron,
αCys1 remains ligated to the low-spin Co(III) ion with a bond
distance of 2.2 Å identical to that observed in the WT enzyme.
boronic acid form at pH 7.5. Therefore, both BuBA and PBA
13
2
likely bind to PtNHase in their sp hybridized forms resulting in
the displacement of the axial water molecule. This initial
Co(III) binding step was hypothesized to be followed by attack
of an active site nucleophile, such as the sulfenic acid ligand, on
2
The resulting B-atom is essentially trigonal planar (sp ) with a
dihedral angle of ∼170°.
On the other hand, the PtNHase-BuBA structure obtained
via cocrystallization of WT PtNHase and 10 mM BuBA reveals
that the S−O boronic acid oxygen interaction is significantly
diminished (Figure 2). BuBA binding displaces the axial water
the electron deficient p orbital of the boron atom, since it was
z
recently suggested that boronic acids might inhibit NHases by
15
interacting with the sulfenic acid ligand. Nucleophilic attack
of the electron-deficient p orbital of the boron atom is also
z
consistent with previous studies of boronic acid inhibitors
bound to hydrolytic enzymes, as hydrolytic reactions typically
proceed through a transition state resulting from nucleophilic
16,17
attack of the substrate.
To confirm that BuBA binds directly to the low-spin Co(III)
ion in the active site of PtNHase and to determine if BuBA has
undergone nucleophilic attack, X-ray crystal structures of wild-
type (WT) PtNHase and two PtNHase−BuBA complexes
formed by either soaking or cocrystallization were solved and
refined to 1.9, 1.5, and 1.6 Å resolution, respectively. Details of
the data collection and refinement statistics are given in Table
S1 of the Supporting Information (SI). The overall structure of
WT PtNHase is identical to the previously reported structure
Figure 2. Stereoview of PtNHase bound by BuBA obtained via
cocrystallization of WT PtNHase and 10 mM BuBA. The 2f − f map
o
c
is shown as a transparent gray surface at the 1.1 σ level around BuBA
18
(
PDB code: 1IRE). The active site is the typical “claw setting”
113
and αCys . The simulated-annealing omit map (f − f ) is shown
o
c
observed in all nitrile hydratases with an axial water molecule
around BuBA as a green mesh at 2.8 σ.
1
12
that forms hydrogen bonds with αSer , the sulfinic acid ligand
11
113
(
αCys1 −O H), and the sulfenic acid ligand (αCys −OH).
2
The protonation states of the sulfenic and sulfinic acid ligands
have previously been assigned based on sulfur K-edge XAS
data, which indicated the presence of three types of Cys ligands
molecule resulting in a Co(III)−O bond distance of 2.2 Å;
however, the second O-atom of BuBA is 2.9 Å away from the S-
19
113
in a WT Fe-type NHase. These XAS data combined with
geometry-optimized DFT calculations suggested the presence
atom of Cys . While this distance is still within the van der
Waals radii of S and O, which is ∼3.3 Å, it is clear that the
−
−
113
of CysS , CysSOH, and CysSO at pH 7.5.
αCys −OH interaction is considerably weakened compared
2
Upon soaking a crystal of WT PtNHase in cryo-protectant
containing 10 mM BuBA for 20 s followed by flash freezing in
liquid nitrogen, electron density corresponding to the boronic
acid inhibitor was present at the active site replacing the axial
water molecule (Figure 1). This observation is consistent with
the fact that BuBA is a competitive inhibitor of PtNHase. In the
to that observed in the PtNHase-BuBA structure obtained via
soaking. This weak S−O interaction is likely due to the initial
dissociation of boronic acid from the active site and not the
initial binding step. If it were the initial binding step of a
113
boronic acid, αCys would need to be in its fully reduced form
which is not the case, as αCys1 is clearly oxidized to its
sulfenic acid form in the WT PtNHase structure. Therefore, the
observed S−O elongation is assigned to boronic acid
dissociation. The αCys1 sulfur remains bound to the Co(III)
ion with a bond length of 2.3 Å. The B-atom of BuBA also
13
WT structure (not shown) the Co(III)−O
bond distance is
.3 Å compared to a Co(III)−O boronic acid oxygen bond
water
2
13
distance of 2.2 Å. Interestingly, the O-atom of the sulfenic acid
ligand (αCys1 −OH) is covalently bound to the boron atom of
BuBA (1.5 Å) (Figure 1). This covalent bond, which has not
been observed previously, is the result of nucleophilic attack of
13
2
remains nearly trigonal planner (sp ) with a dihedral angle of
∼160°.
1
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Journal of the American Chemical Society
Communication
These two structures represent a “snapshot” of two potential
intermediate states in nitrile hydration by depicting nucleo-
philic attack by the sulfenic acid ligand and the initial stage of
the product-release step. Product loss may occur as the result of
a concomitant nucleophilic attack on the αCys ligand by a
water molecule. This is consistent with the observation that a
nitrile substrate that are consistent with the sulfenic acid ligand
functioning as a nucleophile. Kinetic and X-ray crystallographic
1
13
data indicate that proper oxidation of the αCys ligand to a
cysteine-sulfenic acid is essential for NHase enzymes to be
active catalysts suggesting that the S−OH bond is polarized and
1
13
2
0−22
poised for nucleophilic attack.
The catalytic function of the
αCys1 −OH is also consistent with the rate constants provided
by single-turnover stopped-flow studies that indicate a fast
pseudo-first-order step that involves substrate binding to the
trivalent metal ion in the enzyme active site, while product
release is the rate-limiting step consistent with a sulfenic acid
covalent intermediate complex. Additional evidence for
metal-ligated sulfenic acids that can function as nucleophiles
can be gleaned from NHase model complex studies.
13
water molecule that is H-bound (2.9 Å) to the NH group of
2
βArg1 is only 3.3 Å from the αCys113 ligand. This water
57
molecule may represent the incoming O-atom required to
1
13
reestablish the αCys −OH ligand. Interestingly, no water
molecule is observed within 4 Å of the B-atom in either BuBA
structure (Figure 2), suggesting that a water molecule is not
poised for nucleophilic attack on the B-atom facilitating boronic
acid formation and product release.
1
1
23−25
A
18
Since PtNHase can hydrate both alkyl and aromatic nitriles,
coordinatively saturated bis(sulfenato-S)Co(III) complex was
shown to slowly hydrate acetonitrile to acetamide under acidic
conditions while the bis(sulfinato)Co(III) complex was unable
to hydrate nitriles. As neither of these compounds have an open
coordination site to allow nitrile or water binding, these data
implicated the Co(III) sulfenic acid ligand as the nucleophile.
In conclusion, it has long been assumed that a water
molecule or a hydroxide ion in the NHase active site functions
in the initial nucleophilic attack on an activated nitrile C-atom.
the X-ray crystal structure of the PtNHase−PBA complex also
was obtained via cocrystallization of WT PtNHase and 10 mM
PBA and refined to 1.2 Å resolution (Figures 3 and S2). Details
1
13
However, in this work we present evidence that the αCys
−
OH ligand can function as a nucleophile. The combination of
these data with previously reported stopped-flow, kinetic, and
X-ray crystallographic data allows a novel catalytic mechanism
to be proposed for NHase enzymes with a heretofore unknown
role for the αCys1 −OH sulfenic acid ligand (Figure 4).
13
11,26−28
Figure 3. Stereoview of PtNHase bound by PBA at 1.2 Å resolution
obtained via cocrystallization of WT PtNHase and 10 mM PBA. The
2
f − f map of the structural model representing 80% occupancy is
o
c
shown as a transparent gray surface at the 1.4 σ level around PBA and
αCys1 . The simulated-annealing omit map (f − f ) is shown around
13
o
c
PBA as a green mesh at 2.8 σ.
of data collection and refinement statistics are given in Table S1
of the SI. Interestingly, electron density corresponding to the
active site cobalt ion and the PBA suggests ∼80% occupancy.
These data are consistent with inductively coupled atomic
emission spectroscopy (ICP-AES), which typically indicates
that only 0.8 to 0.9 cobalt ions are present per αβ dimer.
Similar to the PtNHase-BuBA structure obtained via soaking,
the structural model representing 80% occupancy contains a
boronic acid O-atom that displaces the axial water molecule and
binds directly to the active site Co(III) ion with a bond distance
of 2.2 Å (Figures 3 and S2). Similar to the PtNHase-BuBA
structure (Figure 1), the B-atom of PBA has undergone
Figure 4. Proposed catalytic mechanism for NHase.
Stopped-flow data indicate that the first step in catalysis
1
13
nucleophilic attack by the αCys −OH O-atom forming a
involves the direct ligation of the nitrile to the active site low-
11
covalent bond with a B−O distance of 1.5 Å and a S−O bond
spin, trivalent metal ion. Displacement of the metal-bound
water molecule by a nitrile and coordination to the active site
metal center activates the CN bond toward nucleophilic attack
by the αCys1 −OH sulfenic acid ligand. Once nucleophilic
attack of the nitrile carbon occurs, two protons are transferred
in the rate-limiting step for both Fe- and Co-type NHase
1
13
distance of 1.8 Å. The S-atom of αCys −OH remains a
Co(III) ligand with a bond distance of 2.2 Å. The resulting B-
atom is nearly trigonal planar with a dihedral angle of ∼160°,
and the unbound O-atom of the original boronic acid moiety is
lost. The structural model representing the remaining ∼20% of
the observed density is similar to the previously reported apo-
13
2
8,29
enzymes.
We propose that one proton transfer occurs
18
113
PtNHase (Figure S2). These data indicate that the PtNHase−
PBA complex represents a covalently bound intermediate state
for nitrile hydration, similar to the PtNHase−BuBA complexes,
where the αCys1 −OH ligand functions as the nucleophile.
Based on the three structures reported herein, parallels can
be drawn between boronic acid binding to PtNHase and a
between the αCys −CH ligand and the nitrile N-atom, while
the second transfer occurs between the water molecule that
reforms αCys1 −OH and the newly forming imidate N-atom,
13
13
28,29
consistent with the observed normal isotope effect.
That
the αCys-OH ligand is protonated was suggested by S K-edge
19
XAS and DFT studies. Once proton transfer occurs, the
1
188
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Journal of the American Chemical Society
Communication
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(
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C-atom of the imidate intermediate could occur (pathway B),
such that the O-atom of the amide product would be derived
2
(
from H O, not the sulfenic group. In this alternative, the
2
Co(III) ion and sulfenic acid group work together to form and
stabilize the imidate intermediate, which can then be hydrated
with sulfenic acid functioning as the leaving group. Finally, the
amide product can be displaced by a water molecule and thus
provide the regenerated catalyst.
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ASSOCIATED CONTENT
Supporting Information
■
*
S
(
A detailed description of the materials, methods, kinetic
analysis, and X-ray data collection and refinement, along with
supplementary figures. This material is available free of charge
via the Internet at http://pubs.acs.org. The reported
coordinates and structure factors have been deposited in the
PDB bank as Native PtNHase (PDB code: 4OB3), PtNHase-
BuBA Co-crystal (PDB code: 4OB1), PtNHase-BuBA soaking
(
PDB code: 4OB2), and PtNHase-PBA Co-crystal (PDB code:
OB0).
(22) Arakawa, T.; Kawano, Y.; Katayama, Y.; Nakayama, H.;
4
Dohmae, N.; Yohda, M.; Odaka, M. J. Am. Chem. Soc. 2009, 131,
1
4838.
AUTHOR INFORMATION
Corresponding Author
richard.holz@marquette.edu
Author Contributions
S.M. and R.W. contributed equally.
Notes
The authors declare no competing financial interest.
■
(23) Heinrich, L.; Mary-Verla, A.; Li, Y.; Vaissermann, J.; Chottard,
J.-C. Eur. J. Inorg. Chem. 2001, 2203.
(24) Heinrich, L.; Li, Y.; Vaissermann, J.; Chottard, J.-C. Eur. J. Inorg.
Chem. 2001, 1407.
(25) Yano, T.; Wasada-Tsutsui, Y.; Arii, H.; Yamaguchi, S.;
Funahashi, Y.; Ozawa, T.; Masuda, H. Inorg. Chem. 2007, 46, 10345.
⊥
(
26) Hashimoto, K.; Suzuki, H.; Taniguchi, K.; Noguchi, T.; Yohda,
M.; Odaka, M. J. Biol. Chem. 2008, 105, 15334.
27) Yamanaka, Y.; Hashimoto, K.; Ohtaki, A.; Noguchi, K.; Yohda,
M.; Odaka, M. J. Biol. Inorg. Chem. 2010, 15, 655.
(
ACKNOWLEDGMENTS
■
(
(
28) Mitra, S.; Holz, R. C. J. Biol. Chem. 2007, 282, 7397.
29) Rao, S. N.; Holz, R. C. Biochemistry 2008, 47, 12057.
The authors thank Dr. Miguel Ballicora for helpful discussions
on enzyme kinetics. This work was supported by the National
Science Foundation (CHE-1058357, RCH). GM/CA @ APS
has been funded in whole or in part with Federal funds from
the National Cancer Institute (Y1-CO-1020) and the National
Institute of General Medical Sciences (Y1-GM-1104). Use of
the Advanced Photon Source was supported by the U.S.
Department of Energy, Basic Energy Sciences, Office of
Science, under Contract No. DE-AC02-06CH11357.
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