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J. Biol. Chem., Vol. 277, Issue 23, 20146-20150, June 7, 2002
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From the Centre for Metalloprotein Spectroscopy and Biology,
Schools of
Received for publication, December 20, 2001, and in revised form, February 27, 2002
Bacterial nitric-oxide reductase catalyzes the
two electron reduction of nitric oxide to nitrous oxide. In the
oxidized form the active site non-heme FeB and high
spin heme b3 are µ-oxo bridged. The heme
b3 has a ligand-to-metal charge transfer band
centered at 595 nm, which is insensitive to pH over the range of
6.0-8.5. Partial reduction of nitric-oxide reductase yields a three
electron-reduced state where only the heme
b3 remains oxidized. This results in a shift of
the heme b3 charge transfer band
Bacterial nitric-oxide reductases
(NOR)1 catalyze shown in the
following Reaction 1.
Primary structure analysis, in combination with spectroscopic studies,
has clearly established NORs as divergent members of the family of
respiratory heme-copper oxidases. Characterization of P. denitrificans NorBC has established that the catalytic NorB subunit binds a bis-histidine-coordinated heme b that is
functionally equivalent to heme a in cytochrome-c
oxidase. It also binds a high spin heme b (termed
b3) that is equivalent to heme
a3 in cytochrome-c oxidase and heme
o3 of Escherichia coli
cytochrome-bo3 quinol oxidase. In
cytochrome-c oxidase and quinol oxidases this heme is
magnetically coupled to a copper ion (CuB) to form a
dinuclear center, which is the site of oxygen binding and reduction. By contrast, in NOR this CuB is replaced with a non-heme iron,
FeB (6-8), which is probably ligated by the three
conserved histidine residues that serve as ligands to CuB
in cytochrome-c oxidase. A fourth metal center, a covalently
bound low spin heme c with histidine and methionine axial
ligands, is bound by the NorC subunit. This site has no structural
counterpart in cytochrome-c oxidase but is functionally
equivalent to CuA in that it serves as a site of electron
input for the respiratory complex.
Recent NOR studies have addressed the nature of the
catalytic site through site-directed mutagenesis (9), redox
potentiometry (8), and ligand binding studies (6). The redox
potentiometry revealed that the high spin heme
b3 of the dinuclear center had a surprisingly
low midpoint redox potential (Em(pH 7.6) = +60 mV) (8),
which imposes a large thermodynamic barrier to reduction by the low
spin electron transferring heme c (Em(pH 7.6) = +310 mV) and heme b (Em(pH 7.6) = +345
mV). This may be a means by which reduction of the heme
b3 is avoided to prevent forming a potentially
dead-end ferrous heme-nitrosyl species with NO (8). It has also been
noted that reduction of the FeB in the dinuclear center,
which occurs when three electrons are introduced to the enzyme, results
in a shift in the absorption maximum of the ligand to metal
charge-transfer (CT) band associated with the high spin ferric heme
b3 from ~595 to 605 nm (8). Taken together
with recent resonance Raman studies of NOR (10), this observation can
be accounted for by a change in the ligation from a µ-oxo bridged
dinuclear center in which there is no proximal ligand to the ferric
heme b3, to a form of the ferric heme
b3 with a proximal histidine ligand and an
anionic distal ligand (8).
There is currently no agreement on a model for the catalytic cycle of
NOR. However, it must involve the transfer of two protons and two
electrons to the active site as these are required for the reduction of
two NO molecules to N2O and H2O (Reaction 1). It is now generally agreed that these protons are moved to the active
site from the periplasm (3). In membranes this overall process is
non-electrogenic because the electrons are also derived from donors
located in the periplasm. A possible proton-conducting pathway that
involves one or more conserved glutamate residues has emerged from
site-specific mutagenesis of NOR (9).
Two recent NOR studies have reported that the spectroscopic properties
of the fully oxidized enzyme are not significantly affected by pH (10,
11). These observations are perhaps surprising given the requirement of
proton uptake to the dinuclear center for NO reduction. This work
reports an electronic absorption and magnetic circular dichroism (MCD)
spectroscopic study of NorCB from P. denitrificans at a
range of pH and redox states. This has led to the identification of
three spectrally distinct forms of the ferric heme
b3, which may reflect µ-oxo bridged,
hydroxide-bound, and water-bound species. The latter two species are
only observed in the three electron-reduced enzyme and are
pH-dependent. The results may help us to elucidate the
catalytic cycle of NOR.
The source of the NOR used in this study was P. denitrificans strain 93.11 ( Electronic absorbance spectra were recorded either on an Aminco DW2000
spectrophotometer or a Hitachi U3000 spectrophotometer. Room
temperature magnetic circular dichroism (RT-MCD) spectra were recorded
on a Jasco J-500D circular dichrograph. An Oxford Instruments
super-conducting solenoid with a 25-mm room temperature bore was used
to generate magnetic fields of up to 6 tesla. MCD spectral intensities
depend linearly on the magnetic field at room temperature and are
expressed per unit magnetic field as Mediated equilibrium redox titrations of NOR were done at 20 °C in
20 mM bis-Tris propane (BTP) supplemented with 0.05% (w/v) dodecyl maltoside, 0.5 mM EDTA, and 340 mM NaCl
and adjusted to the required pH. The methodology was essentially as
that described by Dutton (13). Dithionite was used as the reductant and
potassium ferricyanide as the oxidant. The redox mediators, each at a
final concentration of 10 µM, were phenazine methosulfate
(PMS), phenazine ethosulfate (PES), 5-anthraquinone 2-sulfonate,
6-anthraquinone 2,6-disulfonate, and benzylviologen. A solution of
saturated quinhydrone at pH 7 was used as a redox standard (E = +295 mV). All potentials quoted are with respect to the standard
hydrogen electrode.
Preparation of three electron-reduced NOR under the control of a
potentiostat was achieved using a three-electrode cell configuration with a closed sample compartment thermostated at 4 °C. All
manipulations were performed in an anaerobic chamber (N2
atmosphere with O2 at less than 2 ppm). A 200-µl sample
of 25 µM NOR in 20 mM BTP, 0.05% (w/v)
dodecyl maltoside, 0.34 M NaCl, and 0.5 mM EDTA
at the desired pH and supplemented with a mixture of redox mediators, which included ferricyanide, PES, PMS, and 2,6-dimethylbenzaquinone, was placed in a glassy carbon pot that provided the working
electrode. A Ag/AgCl reference electrode and a platinum foil counter
electrode contacted the solution through a Luggin tip and Vycor frit,
respectively. The potential of the carbon pot was held at +150 mV with
respect to the standard hydrogen electrode for 1 h, during which
time the sample was stirred, and the current flowing from the cell fell
to a negligible level. After this time the sample was withdrawn from
the electrochemical cell and transferred to an anaerobic cell for MCD spectroscopy.
Samples of P. denitrificans NOR were equilibrated at pH
6.5, 7.0, 7.5, 8.0, and 8.5 in BTP buffer. Samples were poised at a
range of potentials between +400 and 0 mV and absorbance spectra were
collected in the range of 500 to 700 nm. At each pH value the oxidized
(~+400 mV) spectrum showed the characteristic
Spectral Properties of Bacterial Nitric-oxide Reductase
RESOLUTION OF pH-DEPENDENT FORMS OF THE ACTIVE SITE HEME
b3*
,
¶,
,
, and
**
Biological Sciences and § Chemical
Sciences, University of East Anglia,
Norwich NR4 7TJ, United Kingdom
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ABSTRACT
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEEDURES
RESULTS AND DISCUSSION
REFERENCES
max to longer wavelengths. At pH 6.0 the charge transfer
band
max is 605 nm, whereas at pH 8.5 it is 635 nm. At
pH 6.5 and 7.5 the nitric-oxide reductase ferric heme
b3 population is a mixture of both 605- and
635-nm forms. Magnetic circular dichroism spectroscopy suggests
that at all pH values examined the proximal ligand to the ferric heme b3 in the three electron-reduced form is
histidine. At pH 8.5 the distal ligand is hydroxide, whereas at pH 6.0, when the enzyme is most active, it is water.
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INTRODUCTION
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEEDURES
RESULTS AND DISCUSSION
REFERENCES
This reaction serves either as a key step in the pathway of
denitrification that uses N-oxyanions and
N-oxides as respiratory electron acceptors or as a way of
removing cytotoxic NO (1). The capacity for NO reduction is now
recognized in a phylogenetically diverse range of bacteria, which
includes soil denitrifying bacteria such as Paracoccus
denitrificans and pathogenic bacteria such as Neiserria
meningitidis (2-4). Three classes of NOR have been identified.
The two-subunit (NorCB)-dependent class from P. denitrificans, Pseudomonas stutzeri, and
Rhodobacter sphaeroides, which use cytochromes c
or cupredoxins as an electron donor, the single subunit (NorB) quinol-oxidizing class from Ralstonia eutropha and N. meningitidis, and the CuA containing quinol and
cytochrome c oxidizing enzyme of Bacillus
azotoformans (2, 3, 5).
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EXPERIMENTAL PROCEEDURES
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ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEEDURES
RESULTS AND DISCUSSION
REFERENCES
ctaDI,
ctaDII
qoxB::kanR) (12) grown in
batch culture in minimal medium under anaerobic denitrifying
conditions. The two-subunit form of the enzyme was purified essentially
as described by Grönberg et al. (8).

/H
(M
1 cm
1
tesla
1).
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RESULTS AND DISCUSSION
TOP
ABSTRACT
INTRODUCTION
EXPERIMENTAL PROCEEDURES
RESULTS AND DISCUSSION
REFERENCES
/
band absorption
features of low spin ferric hemes in the region 520-570 nm (Fig.
1). These features have previously been
assigned to the histidine/methionine-ligated c-heme of the
NorC subunit and the bis-histidine-ligated b heme of the
NorB subunit (14). Each sample also exhibited a clearly resolved
absorption shoulder at ~595 nm. The
max and intensity
of this band was not significantly affected by the pH of the bulk
phase. This 595-nm feature arises from a CT band associated with ferric
high spin heme b3, which has no proximal ligand
but has a distal µ-oxo bridge to the FeB (10, 14).
Complete reduction (E = ~0 mV) of NOR at each pH led to the
appearance of the intense absorption peaks at 550 and 560 nm that arise
from reduction of the low spin heme c (550 nm) and heme
b (560 nm) (Fig. 1). The heme b3 595 nm CT band disappears on reduction. Again, analysis of the reduced
spectrum at each pH value revealed no substantial differences in the
max and intensity of the absorption peaks.

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Fig. 1.
Effects of pH and redox state on visible
absorption spectra of NOR. Spectra were recorded during mediated
potentiometric titrations. Panels A-D, dashed
line, fully oxidized sample; dotted line, three
electron-reduced sample; solid line, fully reduced sample.
Panel A, recorded at pH 6.5. Panel B, recorded at
pH 7. Panel C, recorded at pH 7.5. Panel D,
recorded at pH 8.5. Spectra were recorded on samples of NOR at
concentrations of between 10 and 30 µM, buffered in BTP
supplemented with 0.34 M NaCl, 0.5 mM EDTA, and
0.05% dodecyl maltoside.
In an earlier study of NOR (8) carried out in Tris-HCl buffer at pH
7.6, it was demonstrated that lowering the potential of the NOR sample
buffer from approximately +400 to +150 mV results in the reduction of
the low spin hemes (heme b and heme c) and the
non-heme iron (FeB). In the resulting three
electron-reduced species the
max of the heme
b3 CT band shifts from 595 to ~605 nm, and the
extinction coefficient decreases. Thus, reduction of the
FeB in the dinuclear center resulted in a change in the coordination environment of the heme b3. On the
basis of MCD analysis and taking into account recent resonance Raman
studies (10), this coordination change is likely to be a rebinding of
the proximal histidine and the breaking of the µ-oxo bridge to form a
His/anion species.
In the present study the three electron-reduced state of the enzyme has
been investigated at a range of pH values in BTP buffer, which allows
examination over a broad range of pH values and temperatures. Chemical
poising of samples at +150 mV led to the reduction of the two low spin
hemes and the FeB, whereas the high spin heme b3 remained oxidized. Analysis of these samples
revealed that the absorption intensity of the red-shifted CT band is
strongly affected by pH. The CT band is least intense at pH 6.5 and
most intense at pH 8.5 (Fig. 1, A and D). This
suggests that the form of the heme b3 present at
pH 8.5 is different from that present at pH 6.5. Examination of (three
electron-reduced)
(fully reduced) difference spectra (Fig.
2) shows that at pH 8.5 the CT band is positioned at 605 nm. At pH 7.5 the heme b3
appears to in a mixed form, with one population exhibiting a 605-nm CT
band and a second population exhibiting a 635-nm CT band. At pH 6.5 the
635-nm form dominates the spectrum. From these data, molar extinction
coefficients of
605-700 or
700-635 as
3.66 mM
1 cm
1 and 1.18 mM
1 cm
1 were calculated for the
605 and 635-nm bands, respectively. These data suggest that at
different pH values the ferric heme b3 in the
three electron-reduced enzyme has a different distal ligand.
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High spin ferric hemes give two characteristic CT bands that produce
derivative-shaped features in the MCD spectrum (15, 16). The higher
energy band is seen in the 600-700-nm region, and its precise
wavelength is sensitive to the nature of the axial ligands (Table
I). RT-MCD studies have been successfully
used to assign the exogenous-bound distal ligand of histidine-ligated high spin ferric heme of E. coli cytochrome
bo3 (30). Thus, this approach was exploited to
determine the likely nature of the distal ligand to NOR heme
b3 samples buffered at pH 6.0 and 8.5. Samples
were poised electrochemically at +150 mV and examined by electronic
absorption and RT-MCD spectroscopy. Electrochemical poising allowed the
preparation in a small volume of the concentrated samples required for
MCD analysis. The electronic absorption spectra clearly show that at pH
6.0 the heme b3 is in a pure 635-nm form and at
pH 8.5 in a pure 605-nm form (Fig.
3A, inset). The
RT-MCD spectra show peaks in the
,
, and Soret regions dominated
by signals from low spin ferrous heme. CT bands associated with the high spin ferric heme b3 are seen in the
600-650-nm region of the RT-MCD spectrum. Analysis of this region
shows a band at 620 nm in the pH 8.5 sample, which is characteristic of
high spin heme with a proximal histidine and a distal hydroxide
(His/OH
). In the pH 6.0 sample this band is red-shifted
to 640 nm, a position characteristic of His/H2O-ligated
high spin ferric heme (Table I). This analysis is in good agreement
with the UV-visible spectroscopic analysis of the three
electron-reduced NOR generated by chemical reduction and confirms that
the ligand change is not an artifact of reduction with sodium
dithionite. Moreover, these data suggest that direct ligation of the
heme b3 is dependent on both the redox state of
the dinuclear center and on pH. In the oxidized form the heme
b3 and non-heme FeB are bridged by a
µ-oxo group. As the non-heme FeB is reduced, the heme
b3 becomes ligated by hydroxide at high pH
levels (~8.5) and by water at low pH levels (~6). Recent evidence
from a study of carbon monoxide binding to the fully reduced (four
electron-reduced) NOR suggests that these coordination states are
retained by ferrous heme b3 (31).
|
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Quantitative analysis of the dependence of the 605- and 635-nm bands on
the potential at pH 7 to obtain E°' for each redox species is made
difficult by the low intensities and overlapping nature of these bands.
In the fully oxidized enzyme (Fig. 4,
) the CT band is clearly positioned at 595 nm. As the dinuclear center
starts to become reduced, the 595-nm band begins to decrease in
intensity. At +250 mV (Fig. 4, ---) it has decreased to approximately half its original intensity, and a new band has appeared centered at
635 nm. This movement in the CT band represents a change from a µ-oxo
bridged species to one where the heme b3 is
ligated by His/H2O. The next phase of reduction from +250
mV to +140 mV (Fig. 4, ····) causes the 595-nm band to further
decrease in intensity. However, this further decrease does not
correspond to a further increase in the 635-nm band but to the
appearance of another new band at 605 nm. This represents the formation
of a His/OH
-ligated heme b3 from
the µ-oxo bridged species. During the remainder of the reduction of
the dinuclear center the 605 and 635-nm bands titrate at similar
potentials and have completely disappeared by +22 mV with the full
reduction of the heme b3 (Fig. 4, ·
·
). This three-phase reduction of the dinuclear center can be clearly seen
when fitting the change in absorbance of the 595-nm band against
potential (Fig. 5A). The data
can be fitted to three n = 1 Nernst components. The
first phase corresponds to the breaking of the µ-oxo bridge, between
the FeB and the heme b3 and the
associated shift of the 595-nm band to 635 nm, to form the
His/H2O-ligated heme b3. This
rearrangement of ligation within the dinuclear center has an E°' of
+325 mV. The second phase represents a change in the dinuclear center
from the µ-oxo bridged species to one where the heme
b3 is His/OH
-ligated and is
associated with the shift in the 595-nm band to 605 nm. This phase has
an E°' of +240 mV. The final phase corresponds to the full reduction
of both species from a ferric heme b3 to a
ferrous heme b3 where the shoulder of the 605 and 635 bands detected at 595 nm disappear. Both processes occur at
isopotentials where the E°' is +50 mV (Fig
6). By contrast, at pH 8.5, where only a
single species is present (His/OH
) in the three
electron-reduced form, a simple two-phase titer is seen (Fig.
5B). The first phase represents the reduction of the
FeB and breaking of the µ-oxo bridge and the second phase represents the full reduction of the high spin
His/OH
-ligated heme b3.
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Having identified three spectral forms of the ferric heme
b3, it is possible to forward tentative
suggestions as to both their origin and their role in possible
catalytic cycles of the enzyme. At present there is no agreement on the
mechanism of NO reduction by NOR. Arguments have been put forward for
the two substrate NO molecules binding to FeB in the
so-called cis model (2). An alternative trans mechanism where one NO
molecule binding to each of FeB and heme
b3 has also been forwarded (2). However, in both
cases it is likely that at some point in the catalytic cycle a ferric
heme b3 bound by a water molecule is formed. The identification of the 635-nm spectral form of heme
b3 is the first time such a species has been
identified. It can be supposed that this can be derived from the
reduction of a µ-oxo bridged Fe(III)-Fe(III) dinuclear center, which
would correlate to the 595-nm form of oxidized NOR. It then seems
plausible that on reduction of the FeB of the dinuclear
center with one electron a proton will also enter the catalytic site
leading to a hydroxide-bound ferric heme b3
(Fig. 6). MCD studies of this spectral form of the heme
b3 are consistent with this assertion. There are
many examples of high spin hemes that exhibit CT bands at ~630 nm,
and these characteristically arise from ferric hemes with
His-H2O coordination (e.g. in E. coli
cytochrome-bo3 oxidase (16)). Thus it seems most
likely that the low pH 635-nm form of heme b3
arises from a simple protonation of the putative hydroxide-bound high
pH 605-nm form (Fig. 6). It is also important to note that experiments
in our laboratory have shown that NOR activity in BTP buffer at pH 6.0 is 8-fold higher (~70 s
1) than at pH 8.5 (~8
s
1) (data not shown). The acidic nature of this optimal
activity is in agreement with previously published data obtained in
various buffers (32, 33). At this pH the His-H2O form of
the enzyme dominates. The higher midpoint redox potential of this
species than that of the His-hydroxide form may allow more rapid
electron transfer from physiological electron donors such as cytochrome c and pseudoazurin.
Having identified spectral signals that might correspond to distinct
intermediates in the catalytic cycle of NOR, it is now necessary to try
to trap these spectral forms in rapid-reaction experiments. Such
experiments may in turn provide further insight into the
N2O-generating half of the catalytic cycle.
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ACKNOWLEDGEMENTS |
|---|
We thank Ann Reilly, Jeremy Thornton, and David Clark for expert technical contributions and Gareth Butland for helpful discussions. We also thank the EU SENORA groups of Simon de Vries, Matti Saraste, Rob van Spanning, and Costos Varotsis for useful discussions.
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FOOTNOTES |
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* This work was supported by European Union SENORA Grant B104-CT98-0507 (to M. D. R), a Biotechnology and Biological Sciences Research Council Grant 83/C13457, and an Engineering and Physical Sciences Research Council studentship (to L. P.).The costs of publication of this article were defrayed in part by the payment of page charges. The article must therefore be hereby marked "advertisement" in accordance with 18 U.S.C. Section 1734 solely to indicate this fact.
¶ Present address: Dept. Bioquímica y Biologia Molecular, Campus de Rabanales, Edificio C6, 1a planta, Universidad de Córdoba, 14071, Córdoba, Spain.
A Wellcome Trust University Award lecturer
(054798/Z/98/Z).
** To whom correspondence should be addressed. Tel.: 44-1603-593250; Fax: 44-1603-592250; E-mail: d.richardson@uea.ac.uk.
Published, JBC Papers in Press, March 18, 2002, DOI 10.1074/jbc.M112202200
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ABBREVIATIONS |
|---|
The abbreviations used are: NOR, nitric-oxide reductase; CT, charge transfer; RT-MCD, room temperature magnetic circular dichroism; BTP, bis-Tris propane; PMS, phenazine methosulfate; PES, phenazine ethosulfate..
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