An important lysine residue in copper
⁄
quinone-containing
amine oxidases
Anna Mura
1
, Roberto Anedda
2
, Francesca Pintus
1
, Mariano Casu
2
, Alessandra Padiglia
1
,
Giovanni Floris
1
and Rosaria Medda
1
1 Department of Applied Sciences in Biosystems, University of Cagliari, Italy
2 Department of Chemical Science, University of Cagliari, Italy
Copper ⁄ quinone-containing amine oxidases [(deami-
nating) (copper-containing) amine:oxygen oxidoreduc-
tase; EC 1.4.3.6] (Cu ⁄ TPQ AOs) found in bacteria,
yeasts, fungi, plants and mammals catalyze the oxida-
tive deamination of primary amines to the correspond-
ing aldehydes while reducing molecular oxygen to
hydrogen peroxide [1]. The ping-pong catalytic mech-
anism of Cu ⁄ TPQ AOs can basically be divided into
two half-reactions.
One, referred to as a ‘reductive half-reaction’,

phenethylamine) quinone (TPQ) amine oxidases from the plant pulses lentil
(Lens esculenta) and pea (Pisum sativum) (seedlings), the perennial Mediter-
ranean shrub Euphorbia characias (latex), and the mammals cattle (serum)
and pigs (kidney), were investigated by NMR and optical spectroscopy of
the aqueous solutions of the enzymes.
129
Xe chemical shift provided evi-
dence of xenon binding to one or more cavities of all these enzymes, and
optical spectroscopy showed that under 10 atm of xenon gas, and in the
absence of a substrate, the plant enzyme cofactor (TPQ), is converted into
its reduced semiquinolamine radical. The kinetic parameters of the ana-
lyzed plant amine oxidases showed that the k
c
value of the xenon-treated
enzymes was reduced by 40%. Moreover, whereas the measured K
m
value
for oxygen and for the aromatic monoamine benzylamine was shown to be
unchanged, the K
m
value for the diamine putrescine increased remarkably
after the addition of xenon. Under the same experimental conditions, the
TPQ of bovine serum amine oxidase maintained its oxidized form, whereas
in pig kidney, the reduced aminoquinol species was formed without the
radical species. Moreover the k
c
value of the xenon-treated pig enzyme in
the presence of both benzylamine and cadaverine was shown to be dramat-
ically reduced. It is proposed that the lysine residue at the active site of
amine oxidase could be involved both in the formation of the reduced TPQ

AOs are homodimers; each subunit (molecular
mass @70–90 kDa) contains an active site composed of
a tightly bound Cu
2+
and a quinone of 2,4,5-tri-
hydroxyphenylalanine (TPQ or TOPA) [2]. Six AOs
[3–8] (including a lysyl oxidase, from Pichia pastoris)
have been crystallized previously, and characterized by
single-crystal X-ray diffraction (XRD). The well-
defined active site within these enzymes presents the
following peculiar structural and functional features
(Table 1): (a) TPQ is derived from the copper-cata-
lyzed oxidation of a post-translationally modified
tyrosine residue in the consensus sequence Asn-Tyr-
Asp ⁄ Glu of the polypeptide chain [9]; (b) the copper
ion is coordinated with the imidazole groups of three
conserved histidine residues and with two water mole-
cules (equatorial We and axial Wa) ) TPQ is close but
not bound to the Cu
2+
, and appears to have high
rotational mobility; (c) after the amine nucleophilic
attack, the proton abstraction requires the presence of
a base, which has been identified in a conserved aspar-
tate residue; (d) a tyrosine residue seems to play an
important role in the active site as a result of its
hydrogen bond to O-4 of TPQ.
Moreover, several amino acid residues have been
shown to be critical in the proper positioning of TPQ
during catalysis [10]. One amino acid implicated in the

AO inhibitors [17]. Although the involvement of a
lysine has been postulated [14,17], compelling evidence
has not been presented.
Finally, an important lysine has been suggested in
the crystal structure of pea AO at the active site
(Lys296), forming a hydrogen bond with the phe-
nolic group of TPQ [4], although Duff et al. [18]
later demonstrated that the published crystal showed
TPQ in a nonproductive ‘on-copper conformation’.
The role of Lys296 in the ‘off-copper conformation’
is therefore still unclear. The ‘on-copper and off-cop-
per conformations’ refer to the orientation of TPQ
and copper, as is clearly described by Dawkes &
Phillips [19].
It is well known that the noble gas xenon specifically
interacts with the hydrophobic interior of proteins,
and an increasing number of papers in the recent lit-
erature confirm that
129
Xe NMR spectroscopy is a
very good technique for the characterization of cavities
and channels in biologically related compounds
[20–27]. Moreover, it is generally believed that xenon
atoms can induce structural changes in some of the
cavities or channels that they are bound to, both in
solution [28] and in the solid state [29]. Xenon has
been used as a probe for dioxygen-binding cavities in
copper AOs by recording XRD data under pressure of
xenon gas [7,18], and in a recent paper [30] we demon-
strated that, under 10 atm of xenon gas, an AO from

seedling AO (LSAO) showed that the chemical shift of
129
Xe changes as a function of protein concentration
(10.4 p.p.m.Æmm
)1
), and that the relaxation time
(T
1
¼ 3.2 s) is significantly reduced as compared to T
1
in the buffer ($ 500 s). These changes are commonly
used as a tool to produce evidence of xenon–protein
interactions [30]. In the present study, three AOs
[pea seedling AO (PSAO), Euphorbia characias AO
(ELAO) and pig kidney AO (PKAO)] were tested
by
129
Xe NMR spectroscopy. Figure 1 shows the
129
Xe NMR spectra of the PKAO and ELAO AOs
compared with the
129
Xe NMR spectra of LSAO and
xenon dissolved in buffer solution. The presence of a
single resonance in the protein solution indicates that
xenon undergoes fast exchange in all available environ-
ments. Under 10 atm of xenon gas, the
129
Xe NMR
signal in AO samples is shifted downfield (ELAO

Xe NMR experiments can-
not provide a more detailed characterization of the
interaction between xenon and the protein, and the
actual location of a possible involved cavity or cavities
remains unknown and would require further studies;
this, however, is beyond the purpose of this work.
Owing to the high enzyme concentrations (0.25–
0.35 mm) and the low ionic strength (1 mm) of the
buffer used in the experiments in the presence of
xenon, we were unable to obtain significant results
with bovine serum AO (BSAO), on account of its
tendency to form an irreversible inactive precipitate
under such experimental conditions.
Xenon-induced spectroscopic features in plant
enzymes
Owing to the presence of the TPQ cofactor, the
oxidized form of AOs has a distinctive pink color and
absorbs in the visible region: BSAO shows an electronic
absorption band at 476 nm (e
476
¼ 3800 m
)1
Æcm
)1
) [31],
PKAO at 490 nm (e
490
¼ 4000 m
)1
Æcm

and the solution immediately turns yellow as a result of
the formation of new absorption bands centered at 464,
434 and 360 nm [36] (Fig. 2). In PKAO, the transfor-
mation of TPQ
aq
to TPQ
sq
was observed only in the
presence of CN
–
[37] (Fig. 2). On the other hand,
BSAO, an enzyme which is not formed in the radical
species during the normal catalytic cycle [38], stayed in
the reduced aminoquinol form.
As previously reported [30], when a solution con-
taining LSAO (10 lm) was equilibrated with 10 atm of
xenon gas without a substrate, after a marked lag per-
iod ($ 6 h), bleaching of the 498 nm band started with
Fig. 1.
129
Xe NMR spectra of AOs.
129
Xe (10 atm) spectra in a solu-
tion (sodium phosphate buffer 1 m
M, pH 7.0, 20% D
2
O) containing
0.35 m
M ELAO, 0.28 mM LSAO and 0.15 mM PKAO. Shifts refer to
the

after readmission of oxygen, and 1 mol of ammonia
and 1 mol of hydrogen peroxide per mole of active site
were detected.
In BSAO, no changes in the spectral features were
observed under 10 atm of xenon gas, indicating that
the TPQ cofactor remained in its oxidized form.
Characteristics of xenon-treated AOs
After exhaustive dialysis, the xenon-treated LSAO
was allowed to react with a substrate under anaer-
obic conditions, and behavior similar to that of the
native enzyme was observed. Nevertheless, the cata-
lytic activity of xenon-treated LSAO towards putres-
cine was shown to be about 40% of that of the
native LSAO (Table 2), whereas the k
c
for benzylam-
ine did not change (Table 2). Also, whereas the K
m
values for oxygen and benzylamine were similar with
native and xenon-treated LSAO, the K
m
for the
amine putrescine was considerably higher (Table 2).
The k
c
⁄ K
m
ratio, a more useful measure of substrate
specificity, was shown to be dramatically reduced,
and a comparison with those obtained for other

(pH 7.0). The spectra of the reduced forms (–––) were recorded
after 48 h.
600500400300
0.2
0.15
0.1
0.05
0
Wavelength (nm)
AbsorbanceAbsorbance
A
600500400300
0.2
0.1
0
Wavelen
g
th (nm)
B
Fig. 2. Absorption spectra of AOs. (A) Native LSAO, 16 lM,in
1m
M sodium phosphate buffer (pH 7.0), under anaerobic condi-
tions before (- - -) and after (–––) addition of 10 m
M putrescine. (B)
PKAO, 19 l
M,in1mM sodium phosphate buffer (pH 7.0), before
(- - -) and after (–––) addition of 10 m
M cadaverine in anaerobic con-
ditions and in the presence of 100 l
M CN

inhibitor has been found to be a suicide substrate for
plant copper AO (Cu-AO) from pea seedlings [14] and
grass pea [15], and for mammalian AOs from pig kid-
ney [40] and from beef serum [17]; and (b) it has been
postulated that the irreversible inhibition of all
enzymes involves an intermediate aminoallenic com-
pound that forms covalently bound pyrrole in the reac-
tion with a nucleophile at the active site.
The exact mechanism of inhibition was elusive, and
it was only in grass pea AO that the involved nucleo-
phile was identified as Glu113, a residue corresponding
to a Lys113 in PSAO [14]. DABY was also shown to
be a mechanism-based inactivator for native LSAO
and ELAO, with a k
inh
of 0.1 min
)1
and a half-max-
imal inactivation of 4 · 10
)5
m for ELAO (Fig. 4),
and a k
inh
of 5 min
)1
and a half-maximal inactivation
of 4 · 10
)4
m for LSAO. Moreover, all the xenon-trea-
ted AOs were inactivated by the reaction with DABY,

0.24 646
1
b
0.45 2.2
Xenon-treated 62
a
1.4 44.2
LSAO 0.9
b
0.46 1.95
ELAO 38
b
0.2 190
0.18
b
0.4 0.45
Xenon-treated 13.3
a
1.9 7
ELAO 0.17
b
0.4 0.43
PSAO 140
a
0.2 700
0.5
b
0.45 1.1
Xenon-treated 53.2
a

before and after xenon treatment (not shown).
d
Using spermine as
substrate.
e
Using cadaverine as substrate.
SDs are not reported.
3020100
100
10
Time (min)
Residual activity (%)
0.090.060.030
40
20
0
1/[DABY] (µ
M
-1
)
k/1
p
pa
Fig. 4. Inactivation of ELAO by DABY. The enzyme (6 nM) was pre-
incubated with the indicated concentrations of DABY at 25 °Cin
1m
M sodium phosphate buffer (pH 7.0). The concentrations of
DABY were: d,10l
M; s,20lM; .,30lM; w,40lM. Inset. Dou-
ble reciprocal plot of apparent first-order rate constants of inactiva-

ciently flexible to accommodate such a change.
Although TPQ has been found to be characterized by
considerable conformational flexibility, it has also been
pointed out that when an amine substrate attacks the
TPQ at C-5, H
+
abstraction of the active site base
Asp300 would require it to rotate by 180° [4]. This sig-
nificant displacement would contrast with the previous
observation that the TPQ cofactor could remain fixed
during the catalytic cycle [41–43]. Currently, new forms
of PSAO native protein crystal are available [18] in the
so-called ‘off-copper conformation’. In this structure,
the O-4 of TPQ is hydrogen bonded to the hydroxyl
group of conserved tyrosinyl residue Tyr286, and the
TPQ orientation is in the active form, with the aspartic
active site base residue (Asp300) in an excellent posi-
tion for abstraction of the Ca proton from the sub-
strate, so that TPQ does not rotate during the catalytic
mechanism. Duff et al. have recently reported a new
crystal form of the P. pastoris lysyl oxidase that has a
covalent crosslink between two lysine residues, Lys778
and Lys66 [44]. Whereas Lys778 can readily reach the
TPQ cofactor in the active site of the enzyme without
any other conformational changes, Lys66 is in a well-
ordered region and cannot do so. The authors pro-
posed that the lysyl oxidase oxidized Lys778 to the
corresponding aldehyde allysine, which can react spon-
taneously with Lys66, which is is nearby and appropri-
ately oriented.

involved in the formation of the radical in
plant AOs, is in green; the nucleophilic
residue probably involved in the mechanism-
based inhibition by DABY is in red. The
Gene Bank accession numbers of each
sequence are: PSAO, AB026253; LSAO,
X64201; ELAO, AF171698; and BSAO,
S69583. HKAO (human kidney AO) is from
Novotny et al. [45].
Lysine residue and copper–quinoproteins A. Mura et al.
2590 FEBS Journal 274 (2007) 2585–2595 ª 2007 The Authors Journal compilation ª 2007 FEBS
Another interesting result is that xenon-treated
LSAO shows lower activity and a higher K
m
value for
diamine putrescine as substrate, but not for aromatic
monoamine benzylamine. However, xenon treatment
of PKAO was accompanied by loss of activity for both
cadaverine and benzylamine. These results are most
compatible with two different mechanisms being
involved in the interaction between enzyme and sub-
strate. It is possible, only in the plant enzyme, that the
e-amino group of Lys296 may interact with the posit-
ive charge of the amino group of putrescine, as shown
in Fig. 6. This residue could have an important role
in conferring substrate specificity, with consequences
for catalytic efficiency when lysine is transformed into
allysine.
Thanks to DABY, a mechanism-based inhibitor,
we can confirm that an amino acid residue is impli-

129
Xe NMR spectros-
copy in the characterization of biological compounds
in solution, it must be pointed out that these systems
are generally characterized by complex structures and
often by the presence of more than one specific site for
ligands and ⁄ or substrates. The nearest neighbor resi-
dues of the bound xenon atoms in the cavities are pre-
dominantly nonpolar side chains, but they include
polar side chains and backbone peptide groups. This,
together with the fact that the observed
129
Xe chemical
shift is dynamically averaged among different binding
sites and at the same time interacts with the protein
surface, makes it difficult to separate the individual
contributions so as to show whether a particular
xenon-binding site is responsible for the different com-
ponents observed in the studied AOs in solution.
Hyperfine interactions with unpaired electrons in
radical species and ⁄ or paramagnetic metal ions could
be a further source of information, as long as they can
be distinguished from other structural or dynamic fac-
tors affecting NMR parameters.
These
129
Xe NMR outputs cannot provide local
information on the host–guest interaction involved.
Experimental evidence of the fast diffusion of xenon
within AOs clearly opposes the static and average pic-

enzymes show a high affinity for putrescine and a
lower activity for benzylamine. In contrast, xenon-trea-
ted plant AOs show a high loss in catalytic activity
towards putrescine, but not towards benzylamine. The
transformation of a lysine residue, probably Lys296,
into allysine, four residues from the active site base
identified in a conserved aspartate residue (Asp300),
could have an important role in the recognition of sub-
strates with a positively charged amino group.
In conclusion, although the data reported in the pre-
sent article may well be valid generally, the exact loca-
tion and nature of the observed interactions between
xenon and the enzymes studied remain somewhat
hypothetical and are not of any functional significance.
Nevertheless, from our results, we conclude that xenon
is capable of forcing a conformational change in AOs,
such that most of them react with one of their own
lysine residues. As reported for other amino acid resi-
dues, changes in active site architecture and charge dis-
tribution seem to be critical during catalysis in AOs.
Thus, further comparative investigation of the active
site in AOs from plants, mammals and bacteria is nee-
ded to understand whether these enzymes, which differ
in structure and action mechanism, follow a similar
metabolic pathway.
Experimental procedures
Materials
All reagents were of the highest purity degree available.
1,4-Diaminobutane dihydrochloride (putrescine), 1,5-dia-
minopentane dihydrochloride (cadaverine), benzylamine

c
¼ 23 s
)1
using
putrescine as substrate) [35] were prepared according to the
described procedures.
The activities of the tested enzymes were measured
according to the procedures reported in the related refer-
ences. Oxygen uptake was determined with a Clark-type
electrode coupled to an OXYG1 Hansatech oxygraph
(Hansatech Instruments Ltd, King’s Lynn, UK). The tem-
perature of the reaction chamber was kept at 37 °Cby
using a circulating water bath. The solution (1 mL) con-
taining the enzyme in a 1 mm sodium phosphate buffer
(pH 7.0) was maintained for 20 min at a constant level of
oxygen, as previously reported [46,47], and the reaction was
started by addition of the related substrate. The K
m
values
for AOs using different substrate concentrations at a satur-
ating concentration of oxygen (219 lm), or varying concen-
trations of oxygen at a saturating concentration of
substrate, were calculated from initial velocity data fitted to
the Michaelis–Menten equation by nonlinear regression and
by double reciprocal plots by Michaelis–Menten analysis in
a1mm sodium phosphate buffer (pH 7.0). Benzylamine
oxidase activity was measured in a 1 mm sodium phosphate
buffer (pH 7.0), by monitoring the increase in absorbance
of UV light at 250 nm using an e
250

diameter 5 mm and internal diameter 2.2 mm; Buena, NJ)
and allowed to equilibrate for 48 h.
129
Xe NMR spectra
were recorded on a Varian VXR-300 spectrometer (Varian,
Palo Alto, CA), and
129
Xe NMR spin lattice relaxation
times (T
1
) of native AOs were measured using the inversion
Lysine residue and copper–quinoproteins A. Mura et al.
2592 FEBS Journal 274 (2007) 2585–2595 ª 2007 The Authors Journal compilation ª 2007 FEBS
recovery method with an acquisition time of 1 s and a
recycling delay of 3T
1
.
Assays of products
Ammonia production was determined from the amount of
NADH consumed in the presence of glutamate dehydroge-
nase, and hydrogen peroxide formation was detected with the
peroxidase ⁄ 4-hydroxy-3-methoxyphenylacetic acid method
[36]. a-Aminoadipic-d-semialdehyde (allysine) residue was
derivatized to a decarboxylated fluoresceinamine (a-amino-
adipic-d-semialdehyde-derivatized fluoresceinamine) and
determined by HPLC as previously reported [30,39].
Acknowledgements
This study was supported partly by MURST 60%, by
FIRB (Fondo per gli investimenti della ricerca di
base), and by Fondazione Banco di Sardegna (Sassari,

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