Ecole Nationale Supérieure Agronomique
de Montpellier-Institut National de la Recherche Agronomique, UFR
de Microbiologie Industrielle et Génétique des
Microorganismes, 34060 Montpellier cedex 01, France
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INTRODUCTION |
Many bacterial amidases (EC 3.5.1.4)
have been described previously because of their amide hydrolysis
activities. Wide-spectrum amidases from Rhodococcus sp.
strain R312 (26) and Pseudomonas aeruginosa
(1), which are very similar, hydrolyze only short-chain amides. These enzymes are made up of four and six identical subunits having molecular weights of about 45,000 and 35,000, respectively. Based on the results of experiments performed with inhibitors, they
have been classified as belonging to a branch of sulfhydryl enzymes
(1, 26). The other amidases, the enantioselective amidases
from Pseudomonas chlororaphis B23 (5),
Rhodococcus erythropolis MP50 (12, 27),
Rhodococcus sp. strain R312 (20), Rhodococcus sp. strain N-774 (10),
Rhodococcus sp. (21), and Rhodococcus
rhodochrous J1 (14), belong to a group of amidases containing a GGSS signature in the amino acid sequence
(4) and are made up of two (or eight) identical subunits.
The corresponding genes are located in clusters containing genes
encoding the two subunits of a nitrile hydratase (EC 4.2.1.84). These
amidases were also previously classified as sulfhydryl enzymes (5,
15), but no active amino acid residue was identified in any of
them. Recently, Kobayashi et al. (15) showed that the real
active site residues of the amidase from R. rhodochrous J1 were Asp-191 and Ser-195 rather than the
generally accepted Cys-203 residue. These authors showed that aspartic
acid and serine residues of this enzyme were also present in the active
site sequences of aspartic proteinases and suggested that there is an
evolutionary relationship between amidases and aspartic proteinases.
All of the different amidases also exhibit an acyl transfer
activity in the presence of hydroxylamine: RCONH2 + NH2OH
RCONHOH + NH3. This kind of
reaction was previously described for the wide-spectrum amidase from
Rhodococcus sp. strain R312 (6), but there has
been no detailed study examining the acyl transfer reaction of amidases
belonging to the GGSS signature-containing group. The final reaction
products (hydroxamic acids) are known to possess high chelating
properties. Some of them (particularly
-aminohydroxamic acid
derivatives) are potent inhibitors of matrix metalloproteases, a family
of zinc endopeptidases involved in tissue remodelling
(3). Some other hydroxamic acids (
-aminohydroxamic acids,
synthetic siderophores, acetohydroxamic acid, etc.) have also been
investigated as anti-human immunodeficiency virus agents or
antimalarial agents or have been recommended for treatment of
ureaplasma infections and anemia (2, 8, 13, 28). Moreover, some fatty hydroxamic acids have been studied as inhibitors of cylooxygenase and 5-lipooxygenase with potent antiinflammatory activity (9).
Apart from these medical applications, some hydroxamic acids
(particularly polymerizable unsaturated hydroxamic acids and mid-chain
or long-chain hydroxamic acids) have also been extensively investigated
in wastewater treatment and nuclear technology studies as a way to
eliminate contaminating metal ions (11, 16, 18).
In this paper we describe the formation of a wide range of hydroxamic
acids with the enantioselective amidase (a 120,000-dalton homodimer)
from Rhodococcus sp. strain R312, and we provide some additional information which enhanced our comprehension of the reaction
mechanism of this amidase.
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MATERIALS AND METHODS |
Bacterial strain and growth medium.
To produce large amounts
of amidase, a construction was made in which the amdA gene
was inserted under the control of the bacteriophage T7 promoter into
the pET3c expression plasmid (24). First, NdeI
and BglII sites were created at the ATG initiation and TGA
stop codons of amdA by PCR amplification. The PCR was performed with Promega Taq polymerase, as described in the
manufacturer's recommendations, 1.5 mM MgCl2, and
deoxynucleoside triphosphates at a concentration of 0.2 mM. For
amplification of the 1,583-bp fragment, the following program was used:
5 min of denaturation at 95°C, 30 cycles consisting of 45 s at
95°C, 30 s at 55°C, and 60 s at 72°C, and a final step
consisting of 5 min at 72°C. The following primers were used: forward
primer
5'-AGCACACTTCATATGGCGACAATCCGACCTGAC-3' and reverse primer
5'-GAAGATCTCAGGCGGGGCTGAGTTGTGGTGC-3' (the start and stop codons are indicated by boldface type, and NdeI and BglII restriction sites are underlined).
The 1,583-bp amplified fragment obtained was then digested by
NdeI and BglII and ligated to pET3c which had
been digested with NdeI and BamHI. The resulting
plasmid (pETADI) was introduced into E. coli BL21(DE3) in
which the bacteriophage T7 RNA polymerase gene, under lacUV5 promoter control, was incorporated into the chromosome (25).
Plasmid isolation from E. coli, DNA manipulations, and
plasmid transformation into E. coli cells were performed as
described by Sambrook et al. (22).
Recombinant cells were cultured at 29°C in shaking flasks in
Luria-Bertani growth medium containing 0.5% (wt/vol) yeast extract, 1% (wt/vol) tryptone, and 1% (wt/vol) NaCl. Ampicillin (200 µg/ml) was added to maintain selection pressure. Cultures were grown without
induction of enzyme biosynthesis because no increase in acyl transfer
activity was observed in the presence of
isopropyl-
-D-thiogalactopyranoside (IPTG), an inducer of
the lacUV5 promoter.
Preparation of amidase.
One liter of recombinant E. coli cells grown under the conditions described above was
harvested during the stationary phase by centrifugation for 15 min at
10,000 × g, and the cells were resuspended in 20 mM
phosphate buffer (pH 7) (NaH2PO4,
Na2HPO4) in a 10-fold-smaller volume.
Ten-milliliter portions of the cell suspension (150 to 200 mg, dry
weight), cooled with sodium chloride-saturated ice, were subjected to 6 min of ultrasonic treatment with a Branson model 250 Sonifier (output,
50 W; duty cycle, 30%). The cell debris was removed by centrifugation
for 15 min at 10,000 × g. The supernatant of the first
centrifugation (S1 supernatant) was then subjected to
ultracentrifugation for 90 min at 180,000 × g. The
S2 supernatant was designated the crude soluble enzyme
preparation.
Enzyme purification was performed with an anion-exchange carrier
(Q-Sepharose Fast Flow chromatography; Pharmacia). The column (26 by
400 mm) was equilibrated with 50 mM Tris-HCl buffer (pH 7.3). Proteins
were eluted with a linear 0.2 to 0.5 M sodium chloride gradient at a
flow rate of 250 ml/h and were collected in 10-ml fractions. The
amidase eluted as a single peak at an NaCl concentration of about 0.4 M. The active fractions were pooled, and the preparation obtained was
the amidase preparation used for the kinetic studies.
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis.
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis was
performed by the method of Laemmli (17).
Acyl transfer activity.
Acyl transfer activity was
determined spectrophotometrically by a modified version of the method
of Brammar and Clarke (1). Each reaction was performed at
30°C in a glass reaction tube. Unless otherwise specified, the
reaction medium contained 1 ml of a solution of amide (or amide
hydrochloride adjusted to the pH required with 10 N NaOH) at a
concentration that was four times the final amide concentration in the
reaction medium (CA), 1 ml of a solution of
hydroxylamine hydrochloride at a concentration that was four times the
final hydroxylamine concentration in the reaction medium
(CB) adjusted to the pH required with 10 N NaOH, 1 ml of 100 mM monosodium-disodium phosphate buffer at the pH required,
and 1 ml of amidase preparation diluted in the same buffer. The
hydroxylamine stock solution (whose concentration was four times the
CB) was freshly prepared before the start of the
assay. Aliquots (500 µl) of reaction medium were removed at regular
intervals (e.g., after 1.5, 3, 4.5, and 6 min), and each aliquot was
mixed with 1 ml of an acidic FeCl3 solution (356 mM FeCl3 in 0.65 M HCl). The formation of hydroxamic acids was
assayed spectrophotometrically at 500 nm. The molar extinction
coefficients (
M) of the different hydroxamic
acid-Fe(III) complexes were determined previously (7). As
suggested previously, for a new hydroxamic acid-Fe(III) complex the
mean
M obtained with the corresponding class of
hydroxamic acids was used. For example, the
M used for the butyrohydroxamic acid assay was 1,016 liters/mol/cm. This was the
mean of the
M values for the Fe(III) complexes of
acetohydroxamic acid (996 liters/mol/cm), propionohydroxamic acid
(1,029 liters/mol/cm), and valerohydroxamic acid (1,023 liters/mol/cm).
Amide hydrolysis activity.
Amide hydrolysis activity was
determined in the presence or absence of hydroxylamine. Each reaction
was performed at 30°C in a glass reaction tube, and the reaction
medium was the same as the medium used for the acyl transfer activity
assay. In the absence of hydroxylamine, 1 ml of hydroxylamine
hydrochloride was replaced by 1 ml of H2O. Aliquots (500 µl) of reaction medium were removed at regular intervals, and each
aliquot was mixed with 500 µl of 1 M H3PO4 to
stop the reaction. Formation of the corresponding carboxylic acids was
determined by high-performance liquid chromatography (HPLC).
HPLC analysis.
Amides and carboxylic acids were analyzed by
HPLC. The chromatographic column used was a C18
reverse-phase Spherisorb ODS-2 column (diameter of particles, 5 µm;
length, 250 mm; inside diameter, 4.6 mm; Alltech Associates,
Deerfield, Ill.). The aqueous solvent systems contained 25 mM
H3PO4, plus 1 or 25% (vol/vol) methanol depending on the hydrophobicity of the amide, as well as the
corresponding carboxylic acid assayed. Each 5-µl sample injected was
eluted at a flow rate of 1.0 ml/min and was detected at 210 nm.
Protein determination.
The protein concentrations were
determined spectrophotometrically by the method of Lowry et al.
(19), using bovine serum albumin as the standard.
Substrate specificity for acyl transfer activity.
The
experiments to determine substrate specificity for acyl transfer
activity (see Table 2) were performed at room temperature. Each
reaction mixture was composed of 125 µl of a solution of amide at a
concentration that was four times the CA,
125 µl of 2 M hydroxylamine hydrochloride adjusted to pH 7 with 10 N
NaOH, 125 µl of 100 mM phosphate buffer (pH 7), and 125 µl of
amidase preparation diluted in the same buffer (6.6 µg/ml). The final amide and hydroxylamine concentrations were CA
and 500 mM, respectively. The CA depended on the
solubility of the amide tested. When possible, CA was 100 mM. After 30 min, 1 ml of an acidic
FeCl3 solution was added to stop the reaction. The
resulting stained complex was visually quantified. Reaction media
lacking amidase were also included to take into account possible
spontaneous chemical synthesis of hydroxamic acids.
Chemicals.
All chemicals were purchased from Sigma, Aldrich,
or Fluka. Valeramide was purchased from Interchim (Montluçon,
France). Benzamide was purchased from Merck (Nogent-sur-Marne,
France). DL-Lactic acid, benzoic acid, and urea were
purchased from Prolabo (Vaulx-en-Velin, France).
L-Alaninamide, D-alaninamide,
-alaninamide, DL-methioninamide,
DL-phenylalaninamide,
DL-phenylglycinamide, DL-isoleucinamide, and
DL-
-aminobutyramide were provided by the Laboratoire de l'Alimentation Equilibrée of Rhône-Poulenc
(Commentry, France).
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RESULTS |
Amidase preparation.
The recombinant amidase was prepared as
described in Materials and Methods. After the cell extract was
prepared, amidase was purified by an anion-exchange chromatographic
step. As shown in Table 1, the level of
purification was only threefold, but the amidase preparation obtained
was almost homogeneous. In fact, the high level of expression of the
amdA gene in E. coli BL21(pETADI) (amidase
accounted for about 30% of the endocellular soluble proteins) facilitated amidase purification considerably.
Enzyme stability during storage.
Purified amidase was
stored at 4°C for several months at a concentration of 4.7 mg/ml in 50 mM Tris-HCl buffer (pH 7.3) containing 0.4 M NaCl.
The activity at pH 7 was regularly tested by using valeramide and
hydroxylamine as substrates (CA = 50 mM and
CB = 500 mM), as described in Materials and
Methods. Amidase was diluted 200-fold in 100 mM phosphate buffer (pH 7)
before the start of the assay. The purified enzyme was extremely stable
since no loss of activity was observed for 5 months.
Substrate specificity for acyl transfer activity.
The purified
amidase catalyzed the acyl transfer reaction on hydroxylamine from a
broad spectrum of amides. As shown in Table 2, the best results were obtained with
linear aliphatic monoamides. Only formamide gave a negative result,
since no difference was observed between the level of response in the
amidase-containing tube and the level of response in the very rapid
spontaneous chemical reaction.
Urea and diamides were not substrates. Only the very short-chain
diamides (diacetamide and malonamide) were slightly
transformed enzymatically, despite of a rapid spontaneous
chemical reaction.
Unsaturated aliphatic monoamides, arylamides, and
heterocycle-containing amides were quite good substrates. Only
acrylamide reacted spontaneously with hydroxylamine.
Of the different
-hydroxyamides and
-,
-, and
-aminoamides tested, only polar side-chain-containing
-,
-, and
-aminoamides (glycinamide, L-serinamide,
L-asparagine, and L-glutamine) and bulky
side-chain-containing
-aminoamides (L-tryptophanamide
and DL-phenylglycinamide) were not amidase
substrates. All of the other amides tested were quite good substrates
and did not react (or reacted only very slightly) spontaneously with
hydroxylamine.
Optimum working pH.
As some of the amidase substrates were
ionized at pH 7, the acyl transfer reaction was performed with all
amides at the following pH values: pH 4 to 9 for neutral amides and pH
6 to 10 for
-aminoamides. As shown in Fig.
1, the optimum working pH obtained with
aliphatic amides, arylamides, and heterocycle-containing amides (i.e.,
neutral amides) was 7, whereas the optimum working pH obtained with
-aminoamides was 8. At pH 6, the acyl transfer activities obtained
with
-aminoamides and neutral amides represented 10 and 80%,
respectively, of the acyl transfer activities obtained at the optimum
working pH. Amide electroneutrality thus seemed to be required for
amidase-catalyzed formation of the corresponding hydroxamic acids. This
explains the higher optimum working pH obtained with
-aminoamides,
since the pKa values of such molecules were around 8 to 9.

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FIG. 1.
Influence of pH on the acyl transfer activity of
purified amidase with neutral amides ( ) and -aminoamides ( ) as
substrates. The curves are the mean plots obtained with 13 neutral
amides (acetamide, propionamide, butyramide, isobutyramide,
valeramide, pivalamide, hexanoamide, acrylamide,
methylacrylamide, benzamide, nicotinamide,
isonicotinamide, and DL-lactamide) and eight
-aminoamides (L-alaninamide,
DL- -aminobutyramide, L-leucinamide,
DL-isoleucinamide, DL-methioninamide,
L-prolinamide, L-threoninamide, and
DL-phenylalaninamide). Reactions were performed
as described in Materials and Methods. The different amide
concentrations (CA) used are shown in Table 2,
and the CB was 500 mM. The buffers used were 100 mM citrate-phosphate buffer for pH 4, 5, and 6, 100 mM
monosodium-disodium phosphate buffer for pH 6, 7, and 8, 100 mM
Tris-HCl buffer for pH 8 and 9, and 100 mM
carbonate-bicarbonate buffer for pH 9 and 10.
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Reaction mechanism and kinetic constants.
Nineteen acyl
transfer reactions were investigated. For each of them, all
combinations possible with five amide concentrations and five
hydroxylamine concentrations were tested in the presence of amidase.
The reaction conditions and hydroxamic acid assay used are described in
Materials and Methods. The reaction pH depended on the type of amide;
pH 8 was used for
-aminoamides, and pH 7 was used for the other
compounds. Reciprocal plots of 1/v (where v is
the initial velocity of the acyl transfer reaction) versus 1/CA with different hydroxylamine concentrations
(CB) gave parallel lines for all amides. A
typical graph is shown in Fig. 2A. As expected for most acyl transfer reactions or substituted enzyme reactions, the mechanism involved in the acyl transfer reactions to
hydroxylamine catalyzed by the amidase from Rhodococcus sp. strain R312 was determined to be a Ping Pong Bi Bi mechanism
(23). If we show the individual steps by using the Cleland
notation, the reaction can be written
as:
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In the absence of NH3 and RCONHOH, the initial
velocity, in reciprocal form, is given by (23):
As shown in Fig. 2A, reciprocal plots drawn with amide as
the varied substrate gave five 1/Vmaxapp
values. Vmax and
KmNH2OH values were then determined from the 1/v-axis intercept
replot (Fig. 2B). The plots and replot obtained when hydroxylamine was the varied substrate were symmetrical with the plots and replot obtained for the various amide concentrations and led to determination of Kmamide.

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FIG. 2.
Reciprocal plots obtained with propionamide as the
substrate. (A) 1/v versus 1/CA at
different hydroxylamine concentrations. Symbols: , 40 mM; , 50 mM; , 66.6 mM; , 100 mM; , 200 mM. (B) 1/v-axis
intercept replot.
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All of the kinetic constants determined are described in Table
3. The Vmax values
are expressed as turnover numbers (kcat) corresponding to the numbers of hydroxamic acid molecules produced per
active site and per second (the amidase is made up of two identical
subunits). Several types of substrates can be clearly distinguished.
With respect to the Kmamide values, the substrates for which the amidase exhibited the highest affinity were
the substrates containing a hydrophobic moiety lacking a polar group
(e.g., all aliphatic amides with more than three carbon atoms,
arylamides, heterocycle-containing amides, and hydrophobic
-aminoamides, such as L-leucinamide and
L-phenylalaninamide). Substitution of an
H
atom in propionamide with an OH or NH2 group, thus giving lactamide or alaninamide, considerably increased the Kmamide value.
On the other hand, the acyl-enzyme complex exhibited the highest
affinity for hydroxylamine when the acyl group was short, polar, or
unsaturated. By comparing the different
KmNH2OH values obtained with acetamide, propionamide, butyramide,
valeramide, and hexanoamide as substrates, we found that
KmNH2OH increased considerably when the carbon chain length increased, indicating that a long acyl side chain hindered nucleophilic attack by
hydroxylamine.
Finally, the highest kcat values were
obtained with linear hydrophobic aliphatic amides (e.g.,
kcat = 333 s
1 with hexanoamide as
the substrate), thus suggesting that branched-side-chain-, aryl
group-, or heterocycle-containing amides were sterically hindered. By
comparing the results obtained when propionamide, isobutyramide,
and pivalamide were the substrates, we found that addition of one or
two methyl groups at the
position considerably decreased the
kcat values (192, 109, and 15 s
1,
respectively), whereas addition of methyl groups at the
position, which resulted in the linear compounds butyramide and valeramide, increased the kcat values (229 and 313 s
1, respectively). This is also why
L-methioninamide turned out to be the most rapidly
transformed
-aminoamide.
Undesirable reactions.
Several undesirable reactions could
occur when hydroxamic acids were produced from amides (Fig.
3). At the start of the bioconversion, water and hydroxylamine were in competition with each other as acyl
acceptors after enzyme acylation by amides, and carboxylate could be
produced at the same time as the corresponding hydroxamic acid. As
shown below, carboxylates were not amidase substrates for acyl transfer
activity at pH 7 to 8. Their formation at the start of the
bioconversion, due to amide hydrolysis, was thus irreversible.
Moreover, we found that the amidase exhibited very high affinities for
hydroxamic acids (e.g., Kmvalerohydroxamic
acid = 0.2 mM and
KmL-leucine hydroxamic acid = 4.9 mM). This means that the hydroxamic acids
produced could also be enzymatically hydrolyzed to the
corresponding carboxylates. Once again, as carboxylates were not
substrates for the acyl transfer activity, their formation at the
end of the bioconversion was irreversible.
The importance of these undesirable amide and hydroxamic acid
hydrolysis reactions compared to the importance of the acyl transfer
reaction was a function of the nature of the molecules. Linear
molecules, such as valeramide and its corresponding hydroxamic acid, were slightly hydrolyzed (kcat
hydrolysis = 35 and 18 s
1,
respectively) compared to results of the acyl transfer
reaction (kcat acyl transfer = 313 s
1). On the other hand, the kcat
hydrolysis values obtained with bulky
side-chain-containing amides, such as benzamide and its corresponding hydroxamic acid (kcat
hydrolysis =6.2 and 4.3 s
1,
respectively), were very close to the kcat acyl
transfer value (kcat acyl transfer = 5.9 s
1 with benzamide). The results
obtained with bulky side-chain-containing substrates could
be explained by the dimensions of the molecules, which were an
important limiting factor for the acyl transfer reaction.
However, as shown in Fig. 4 with
benzamide as the substrate, we demonstrated that increasing the
hydroxylamine concentration permitted us to considerably reduce both of
the undesirable hydrolysis reactions (initial amide hydrolysis and
final hydroxamic acid hydrolysis).

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FIG. 4.
Influence of hydroxylamine concentration on hydrolysis
of both benzamide and benzohydroxamic acid. The initial
benzamide concentration and the amidase concentration in the
reaction media were 5 mM and 44 µg/ml, respectively. The following
four initial hydroxylamine concentrations were tested: 0 mM (A), 10 mM
(B), 50 mM (C), and 500 mM (D). Symbols: , amount of benzoate
formed; , amount of benzohydroxamic acid.
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Enantioselectivity of the purified amidase for the acyl transfer
activity.
As we could not purchase all of the
D-enantiomers of amides containing an asymmetrical carbon,
enantioselectivity was investigated by comparing the kinetic constants
obtained with the L- and D-enantiomers of
lactamide and alaninamide only. Enantioselectivity towards other amides
(methioninamide, leucinamide, and phenylalaninamide) was
investigated by comparing the kinetic constants obtained with the
L-enantiomers and the racemic mixtures. The results are
shown in Table 4. With methioninamide,
leucinamide, and phenylalaninamide, the amidase was
found to be L-enantioselective. The
kcat values obtained with the racemic mixtures
were lower and the Kmamide and
KmNH2OH
values were higher than the values obtained with the
L-enantiomers. Greater enantioselectivity was observed with leucinamide; the kcat obtained with the
racemic mixture was 2.6-fold lower than that obtained with the
L-enantiomer (24 versus 63 s
1), the
Kmamide value was 1.8-fold higher (2.4 versus 1.3 mM), and the
KmNH2OH
value was 4.8-fold higher (187 versus 39 mM). We also observed that the
rate of bioconversion of the racemic leucinamide mixture did not exceed
50%, whereas the rates obtained with the racemic
methioninamide and phenylalaninamide mixtures did (data not shown). Finally, we showed that for leucinamide, the D-enantiomer acted as a mixed-type inhibitor after
transformation of the L-enantiomer (Fig.
5), whereas this was not the case for methioninamide and phenylalaninamide.
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TABLE 4.
Kinetic constants for amidase-catalyzed acyl transfer
reactions with L-enantiomers, D-enantiomers,
and racemic mixtures of several -substituted amides
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FIG. 5.
Reciprocal plot showing the influence of
D-leucinamide on the acyl transfer reaction from
L-leucinamide to hydroxylamine. As we could not purchase
D-leucinamide, different mixtures of
L-leucinamide and DL-leucinamide allowed us to
prepare solutions with different concentrations of the two enantiomers.
The following five D-leucinamide concentrations were
tested: 0 mM ( ), 2 mM ( ), 2.5 mM ( ), 3.33 mM ( ), and 5 mM
( ). The amidase concentration in the reaction medium was 24 µg/ml.
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Unexpected results were obtained with lactamide and
alaninamide. The amidase was also
L-enantioselective since the
Kmamide values obtained with the racemic
mixtures or with the D-enantiomers were higher than
the values obtained with the L-enantiomers.
However, the kcat values obtained with the
D-enantiomers, together with the
KmNH2OH
values, were surprisingly very high. A possible explanation
for this is discussed below.
Search for other acyl donors.
Five carboxylic acids and two
methyl esters were tested as amidase substrates and compared with the
corresponding amides as a function of pH. Acyl transfer activities were
assayed as described in Materials and Methods. Each solution
(concentration, four times the CA) was adjusted
to the pH required before the start of the reaction. Standards lacking
amidase were also included to take into account possible spontaneous
chemical formation of hydroxamic acid. As shown in Table
5, rapid spontaneous reactions occurred with lactate and methyl esters at very basic pH values. As far as
enzymatic activities are concerned, amides were undeniably the best
acyl donors. Amino acids were logically not amidase substrates since
they are amphoteric molecules that are electrically hindered. Similarly, carboxylic acids were very poor acyl donors. Only butyric acid and lactic acid reacted with amidase, but they reacted at pH
values between the optimum working pH of the enzyme and the pKa values of the acids, as if only protonated forms of the
acids could be transformed. This has also been observed for the
wide-spectrum amidase from Rhodococcus sp. strain R312
(6). Both methyl esters (methyl butyrate and
L-methionine methyl ester) were very slightly transformed (at pH 7 for neutral methyl butyrate and at pH 8 for L-methionine methyl ester). Under the experimental
conditions used, the specific activities obtained with methyl esters
represented less than 0.2% of the specific activities obtained with
the corresponding amides.
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TABLE 5.
Acyl transfer activities and spontaneous chemical
reactions obtained with different amides, carboxylic acids, and
methyl esters as acyl donorsa
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Search for other acyl acceptors.
The following five potential
acyl acceptors were tested because of their polarity and were compared
with water and hydroxylamine: N-methylhydroxylamine
(CH3-NHOH), ethanolamine
(NH2-CH2-CH2-OH), hydrazine
(NH2NH2), N-methylhydrazine
(CH3-NHNH2), and methanol (CH3-OH). The initial concentration of each of these
compounds in the reaction medium was 500 mM. Reactions were performed
at pH 7 with 100 mM butyramide as the acyl donor and with 44 µg
of amidase per ml. After 40 min, 0.5 ml of 1 M
H3PO4 was added to 0.5 ml of reaction medium to
stop the reaction, and the mixture was analyzed by HPLC as described in
Materials and Methods. Whereas 500 mM hydroxylamine totally inhibited
residual butyramide hydrolysis and led to the formation of
butyrohydroxamic acid with a bioconversion rate of up to 90%, the
different molecules tested did not affect the hydrolysis reaction, and
none of them turned out to be an acyl acceptor (data not shown). A
previous study (6) showed that the wide-spectrum amidase
from Rhodococcus sp. strain R312 catalyzed the acyl transfer
reaction from amides to water and hydroxylamine and also to hydrazine.
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DISCUSSION |
The enantioselective amidase from Rhodococcus sp.
strain R312 was shown to catalyze the acyl transfer reaction to
hydroxylamine from a broad spectrum of amides. The reaction mechanism
was determined to be a Ping Pong Bi Bi system; i.e., amides react with
the enzyme to give acyl-enzyme complexes, which then transfer acyl
groups to the second substrate (hydroxylamine).
Acylation was facilitated when amides contained a marked hydrophobic
moiety which contrasted with the polar amide group. Diamides and amides
lacking a hydrophobic area were not amidase substrates. On the
other hand, the affinities of the different acyl-enzyme complexes for
hydroxylamine were highest when the acyl side chain was short,
polar, or unsaturated. Very low levels of affinity were obtained when
long-chain aliphatic amides were the acyl donors. In these cases,
attack of the carbonyl group of the acylated enzyme by hydroxylamine
seemed to be hindered. With respect to the kcat values, the best results were obtained with linear molecules. Very high
kcat values (up to 300 s
1) were
obtained with valeramide and hexanoamide. We suppose that heptanamide, octanamide, and other linear fatty amides should be very good substrates if solubility is not a limiting factor.
The above-mentioned results suggested that amides are geometrically
oriented before they enter the amidase by their polar amide groups and
that the active site is located at the end of a narrow funnel. Such
steric constraints could be responsible for the restricted velocities
observed with amides containing branched side chains
(isobutyramide, pivalamide), aryl groups (benzamide,
phenylalaninamide), or heterocycles (nicotinamide, isonicotinamide). This finding differs markedly from the data obtained
with the enantioselective amidase from P. chlororaphis B23,
which, despite a high level of sequence homology (level of strict
identity, 46%) with the enantioselective amidase from
Rhodococcus sp. strain R312, exhibited the highest levels of
hydrolysis activity with isobutyramide, nicotinamide, and
DL-phenylalaninamide (5).
Carboxylic acids, electrically charged at pH 7, could be very slightly
transformed into the corresponding hydroxamic acids when the reaction
pH was between pH 7 (the optimum working pH) and the pKa of
the acyl donor, but amino acids, which are amphoteric molecules, could
not be transformed at all. The different kcat values obtained with
-aminoamides as substrates, also electrically charged at pH 7, were quite high at pH 8 because this optimum pH value
was close both to the pKa values (about pH 8 to 9) and to
pH 7.
Although methyl esters were not charged, they were found to be very bad
acyl donors. The specific activities obtained with methyl butyrate and
L-methionine methyl ester were less than 0.2% of the
specific activities obtained with the corresponding amides, suggesting
that in addition to the electrical constraints, there was an amide bond
recognition site in the active site area. This would explain the
importance of the hydrolysis of hydroxamic acids (which also contain
amide bonds) observed at the end of the bioconversions.
So far, only water and hydroxylamine have been found to be efficient
acyl acceptors. In addition to the substrate spectrum, this was an
important difference from the wide-spectrum amidase family since the
wide-spectrum amidase from Rhodococcus sp. strain R312 was
shown to catalyze the formation of acid hydrazides from amides and
hydrazine (6).
Amidases from P. chlororaphis B23, R. erythropolis MP50, Rhodococcus sp. strain R312,
Rhodococcus sp., and R. rhodochrous J1 were shown
to exhibit an (S)-enantioselective hydrolysis activity towards several 2-arylpropionamides (5, 12, 14, 20, 21). The
amidase from Rhodococcus sp. strain R312 was also determined to be L-enantioselective [or
(S)-enantioselective] towards
-substituted amides
(
-hydroxyamides and
-aminoamides). This suggested that there is
an additional recognition site for groups located at the
position.
Surprisingly, very high kcat and
KmNH2OH values were determined with the D-enantiomers of
lactamide and alaninamide. A possible explanation for this is shown in
Fig. 6. Because of the small size of the
CH3 group at the
position, rotation of CH3,
H, and OH (or NH2) around the C---CO axis of the D-enantiomer might be possible, so that the CH3
group would be positioned at the same place as the OH (or
NH2) group of the L-enantiomer. In this case,
the OH (or NH2) group would be positioned at a site which
might hinder nucleophilic attack by hydroxylamine but which also might
facilitate release of the hydroxamic acid formed. Further studies of
the amidase from Rhodococcus sp. strain R312 and
particularly its three-dimensional structure could provide information
about the mechanism and thus confirm the geometrical organization of the active site proposed above.

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|
FIG. 6.
Possible rearrangement of the D-enantiomer
of lactamide in the active site. (A) L-Lactamide. (B)
D-Lactamide.
|
|
The results described here, particularly the high
kcat values obtained with aliphatic amides,
-hydroxyamides, and
-aminoamides, highlighted the interest in
amidases for use in the production of a wide range of hydroxamic acids
and showed that enzymatic synthesis of such molecules is an interesting
alternative to chemical synthesis methods. Reactions occurred in medium
lacking organic solvents and led to production of both
-aminohydroxamic acids, which are interesting because of their
medical applications as enzyme inhibitors, and mid-chain or unsaturated
hydroxamic acids, which are interesting because of their environmental
applications as chelating agents for wastewater treatment.
| 1.
|
Brammar, W. J., and P. H. Clarke.
1964.
Induction and repression of Pseudomonas aeruginosa amidase.
J. Gen. Microbiol.
37:307-319.
|
| 2.
|
Brown, D. A.,
M. V. Chidambaram,
J. J. Clarke, and D. M. McAleese.
1978.
Design of iron(III) chelates in oral treatment of anemia: solution properties and absorption of iron(III) acetohydroxamate in anemic rats.
Bioinorg. Chem.
9:255-275[Medline].
|
| 3.
|
Cawston, T. E.
1996.
Metalloproteinase inhibitors and the prevention of connective tissue breakdown.
Pharmacol. Ther.
70:163-182[Medline].
|
| 4.
|
Chebrou, H.,
F. Bigey,
A. Arnaud, and P. Galzy.
1996.
Study of the amidase signature group.
Biochim. Biophys. Acta
1298:285-293[Medline].
|
| 5.
|
Ciskanik, L. M.,
J. M. Wilczek, and R. D. Fallon.
1995.
Purification and characterization of an enantioselective amidase from Pseudomonas chlororaphis B23.
Appl. Environ. Microbiol.
61:998-1003[Abstract].
|
| 6.
|
Fournand, D.,
A. Arnaud, and P. Galzy.
1998.
Study of the acyl transfer activity of a recombinant amidase overproduced in an E. coli strain. Application for short-chain hydroxamic acid and acid hydrazide synthesis.
J. Mol. Catal. B
4:77-90.
|
| 7.
|
Fournand, D.,
J. L. Pirat,
F. Bigey,
A. Arnaud, and P. Galzy.
1997.
Spectrophotometric assay of aliphatic monohydroxamic acids and -, -, and -aminohydroxamic acids in aqueous medium.
Anal. Chim. Acta
353:359-366.
|
| 8.
|
Gao, W. Y.,
H. Mitsuya,
J. S. Driscoll, and D. G. Johns.
1995.
Enhancement by hydroxyurea of the anti-human immunodeficiency virus type 1 potency of 2'- -fluoro-2',3'-dideoxyadenosine in peripheral blood mononuclear cells.
Biochem. Pharmacol.
50:274-276[Medline].
|
| 9.
|
Hamer, R. R. L.,
J. J. Tegeler,
E. S. Kurtz,
R. C. Allen,
S. C. Bailey,
M. E. Elliott,
L. Hellyer,
G. C. Hessley,
P. Przekop,
B. S. Freed,
J. White, and L. L. Martin.
1996.
Dibenzoxepinone hydroxylamines and hydroxamic acids: dual inhibitors of cyclooxygenase and 5-lipoxygenase with potent topical antiinflammatory activity.
J. Med. Chem.
39:246-252[Medline].
|
| 10.
|
Hashimoto, Y.,
M. Nishiyama,
O. Ikehata,
S. Horinouchi, and T. Beppu.
1991.
Cloning and characterization of an amidase gene from Rhodococcus species N-774 and its expression in Escherichia coli.
Biochim. Biophys. Acta
1088:225-233[Medline].
|
| 11.
| Heitner, H. I., and R. G. Ryles. November
1992. European patent 0 514 648 B1.
|
| 12.
|
Hirrlinger, B.,
A. Stolz, and H.-J. Knackmuss.
1996.
Purification and properties of an amidase from Rhodococcus erythropolis MP50 which enantioselectively hydrolyzes 2-arylpropionamides.
J. Bacteriol.
178:3501-3507[Abstract/Free Full Text].
|
| 13.
|
Holmes, L. B.
1996.
Hydroxamic acid: a potential human teratogen that could be recommended to treat ureaplasma.
Teratology
53:227-229[Medline].
|
| 14.
|
Kobayashi, M.,
H. Komeda,
T. Nagasawa,
M. Nishiyama,
S. Horinouchi,
T. Beppu,
H. Yamada, and S. Shimizu.
1993.
Amidase coupled with low-molecular-mass nitrile hydratase from Rhodococcus rhodochrous J1.
Eur. J. Biochem.
217:327-336[Medline].
|
| 15.
|
Kobayashi, M.,
Y. Fujiwara,
M. Goda,
H. Komeda, and S. Shimizu.
1997.
Identification of active sites in amidase: evolutionary relationship between amide bond- and peptide bond-cleaving enzymes.
Proc. Natl. Acad. Sci. USA
94:11986-11991[Abstract/Free Full Text].
|
| 16.
|
Koide, Y.,
M. Uchino, and K. Yamada.
1987.
Studies of collectors. IX. The flotation of a trace amount of uranium by using 2-(alkylamino)propionohydroxamic acid and cotelomer-type surfactants bearing hydroxyaminocarbonyl and pyridyl groups.
Bull. Chem. Soc. Jpn.
60:3477-3483.
|
| 17.
|
Laemmli, U. K.
1970.
Cleavage of structural proteins during the assembly of the head of bacteriophage T4.
Nature (London)
227:680-685[Medline].
|
| 18.
| Lewellyn, M. E. May 1996. World patent WO
96/14271.
|
| 19.
|
Lowry, O. H.,
N. J. Rosebrough,
A. L. Farr, and R. J. Randall.
1951.
Protein measurement with the Folin phenol reagent.
J. Biol. Chem.
193:265-275[Free Full Text].
|
| 20.
|
Mayaux, J.-F.,
E. Cerbelaud,
F. Soubrier,
D. Faucher, and D. Pétré.
1990.
Purification, cloning, and primary structure of an enantiomer-selective amidase from Brevibacterium sp. strain R312: structural evidence for genetic coupling with nitrile hydratase.
J. Bacteriol.
172:6764-6773[Abstract/Free Full Text].
|
| 21.
|
Mayaux, J.-F.,
E. Cerbelaud,
F. Soubrier,
P. Yeh,
F. Blanche, and D. Pétré.
1991.
Purification, cloning, and primary structure of a new enantiomer-selective amidase from Rhodococcus strain: structural evidence for a conserved genetic coupling with nitrile hydratase.
J. Bacteriol.
173:6694-6704[Abstract/Free Full Text].
|
| 22.
|
Sambrook, J.,
E. F. Fritsch, and T. Maniatis.
1989.
Molecular cloning: a laboratory manual, 2nd ed.
Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y.
|
| 23.
|
Segel, I. H.
1975.
Enzyme kinetics, p. 602-625.
John Wiley & Sons, New York, N.Y.
|
| 24.
|
Studier, F. W.,
A. H. Rosenberg,
J. J. Dunn, and J. W. Dubendorff.
1990.
Use of T7 polymerase to direct expression of cloned genes.
Methods Enzymol.
185:60-89[Medline].
|
| 25.
|
Studier, F. W., and B. A. Moffatt.
1986.
Use of bacteriophage T7 RNA polymerase to direct selective high-level expression of cloned genes.
J. Mol. Biol.
189:113-130[Medline].
|
| 26.
|
Thiéry, A.,
M. Maestracci,
A. Arnaud,
P. Galzy, and M. Nicolas.
1986.
Purification and properties of an acylamide amidohydrolase (E.C. 3.5.1.4) with a wide activity spectrum from Brevibacterium sp. R312.
J. Basic Microbiol.
26:299-311.
|
| 27.
| Trott, S. Personal communication.
|
| 28.
|
Tsafack, A.,
J. Golenser,
J. Libman,
A. Shanzer, and Z. I. Cabantchik.
1995.
Mode of action of iron(III) chelators as antimalarials. III. Overadditive effects in the combined action of hydroxamate-based agents on in vitro growth of Plasmodium falciparum.
Mol. Pharmacol.
47:403-409[Abstract].
|