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J Biol Chem, Vol. 273, Issue 10, 5771-5779, March 6, 1998
Engineering of Cyclodextrin Product Specificity and pH Optima
of the Thermostable Cyclodextrin Glycosyltransferase from
Thermoanaerobacterium thermosulfurigenes EM1*
Richèle D.
Wind §,
Joost C. M.
Uitdehaag¶,
Reinetta M.
Buitelaar ,
Bauke W.
Dijkstra¶, and
Lubbert
Dijkhuizen
From the Agrotechnological Research Institute
(ATO-DLO), P. O. Box 17, 6700 AA Wageningen, ¶ BIOSON Research
Institute and Laboratory of Biophysical Chemistry, Groningen
Biomolecular Sciences and Biotechnology Institute (GBB), University of
Groningen, Nijenborgh 4, 9747 AG Groningen, and Department of
Microbiology, Groningen Biomolecular Sciences and Biotechnology
Institute (GBB), University of Groningen, Kerklaan 30, 9751 NN
Haren, The Netherlands
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ABSTRACT |
The product specificity and pH optimum of the
thermostable cyclodextrin glycosyltransferase (CGTase) from
Thermoanaerobacterium thermosulfurigenes EM1 was engineered
using a combination of x-ray crystallography and site-directed
mutagenesis. Previously, a crystal soaking experiment with the
Bacillus circulans strain 251 -CGTase had revealed a
maltononaose inhibitor bound to the enzyme in an extended conformation.
An identical experiment with the CGTase from T. thermosulfurigenes EM1 resulted in a 2.6-Å resolution x-ray
structure of a complex with a maltohexaose inhibitor, bound in a
different conformation. We hypothesize that the new maltohexaose conformation is related to the enhanced -cyclodextrin production of
the CGTase.
The detailed structural information subsequently allowed engineering of
the cyclodextrin product specificity of the CGTase from T. thermosulfurigenes EM1 by site-directed mutagenesis. Mutation D371R was aimed at hindering the maltohexaose conformation and resulted
in enhanced production of larger size cyclodextrins ( - and -CD).
Mutation D197H was aimed at stabilization of the new maltohexaose
conformation and resulted in increased production of -CD.
Glu258 is involved in catalysis in CGTases as well as
-amylases, and is the proton donor in the first step of the
cyclization reaction. Amino acids close to Glu258 in the
CGTase from T. thermosulfurigenes EM1 were changed.
Phe284 was replaced by Lys and Asn327 by Asp.
The mutants showed changes in both the high and low pH slopes of the
optimum curve for cyclization and hydrolysis when compared with the
wild-type enzyme. This suggests that the pH optimum curve of CGTase is
determined only by residue Glu258.
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INTRODUCTION |
Cyclodextrins (CDs)1 are
cyclic molecules composed of 6, 7, or 8 glucose units linked via
(1,4)-glycosidic bonds ( -, -, and -CD, respectively). The
ability of cyclodextrins to form inclusion complexes with small
hydrophobic molecules has provided a number of practical uses in the
food, pharmaceutical, and agrochemical industries (1-3). Cyclodextrins
are produced from starch by the action of the enzyme cyclodextrin
glycosyltransferase (CGTase; EC 2.4.1.19). However, apart from the
cyclization reaction, the enzyme can also catalyze disproportionation,
coupling, and hydrolysis reactions. All known CGTases produce a mixture
of -, -, and -cyclodextrins. For the industrial production of
pure cyclodextrins, -CD is selectively crystallized and - and
-CD are complexed with organic solvents. The industrial production of cyclodextrins might be improved by the construction of mutant CGTases with improved product specificity (2, 3).
In the conventional commercial production of cyclodextrins, starch is
first liquefied by the action of a thermostable -amylase, whereafter
cyclodextrins are produced using the mesophilic CGTase from
Bacillus macerans. Two highly thermostable CGTases have been characterized that can directly be used for starch liquefaction, eliminating the need for -amylase pretreatment (2, 3). These enzymes
are produced by thermophilic anaerobic bacteria belonging to the genus
Thermoanaerobacter (9, 10) and Thermoanaerobacterium thermosulfurigenes EM1 (11). The overall amino acid compositions of both enzymes show relatively minor differences, and also the biochemical characteristics of both enzymes are very similar (11). The
T. thermosulfurigenes EM1 CGTase displays maximum
cyclization activity at 80-85 °C and maximum starch hydrolyzing
activity at 90-95 °C. The pH optimum for cyclization is broad, in
the range of pH 4.5-7.0.
The three-dimensional structures of several CGTases have been solved
(4, 5, 7). CGTase belongs to family 13 of the glycosyl hydrolases, a
group of homologous ( / )8-barrel proteins, to which
also the -amylases belong (8). Recently, the three-dimensional structure of the CGTase from T. thermosulfurigenes EM1
(Tabium CGTase) was solved at 2.3-Å resolution (6). In the
present study we describe the three-dimensional structure of an
enzyme-substrate complex of Tabium CGTase. The x-ray
structure of a maltohexaose inhibitor complexed with Tabium
CGTase was solved at 2.6-Å resolution. The detailed information thus
obtained allowed rational engineering of the cyclodextrin product
specificity of Tabium CGTase.
Residues Glu258, Asp329, and Asp230
are directly involved in catalysis in CGTase (20). Glu258,
together with Asp230, is believed to cleave the
substrate's (1,4)-glycosidic bonds and to form the product's
(1,4)-glycosidic bonds by a double displacement mechanism (15). In
the first step of the reaction the general acid Glu258
protonates the oxygen of the glycosidic bond to be cleaved. After cleavage of this scissile bond, an oxocarbonium transition state is
formed, which is believed to collapse into a covalently linked intermediate by nucleophilic attack of Asp230 on the
anomeric C1. Subsequently, the reducing end diffuses out of the active
site and an acceptor comes in, which can be a water molecule (in case
of hydrolysis) or a carbohydrate C4-hydroxyl group (in case of
transglycosylation). In the second step of the reaction, the acceptor
hydroxyl group is activated through deprotonation by
Glu258, after which the acceptor performs a nucleophilic
attack on the covalent intermediate. Through another oxocarbonium
transition state, the product ( (1,4)-linked) is then formed (16,
17).
It appears from the double displacement mechanism that for optimal
catalysis the nucleophile Asp230 must be deprotonated in
the first step of the reaction, whereas the general acid
Glu258 must be protonated in the first step, but
deprotonated in the second step of the reaction. A third catalytic
residue, Asp329, has been found to be hydrogen bonded to
Glu258 in the unliganded CGTase, thereby elevating the
pKa of Glu258 and assuring its
protonation. After substrate binding, this hydrogen bond is lost,
making deprotonation of Glu258 possible. It was suggested
that this Glu258-Asp329 interaction is
responsible for the broad pH optimum exhibited by CGTases (16). The
importance of the pKa of Glu258 in the
different reactions catalyzed by Tabium CGTase was further studied. By changing the electrostatic environment of
Glu258 by site-directed mutagenesis, we could drastically
shift the Tabium CGTase pH optimum.
The biochemical characteristics of the various mutant CGTases are
presented with emphasis on the effects of these mutations on the CGTase
cyclization and hydrolytic activities, pH optima, and product formation
from starch.
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EXPERIMENTAL PROCEDURES |
Structure Determination--
Crystals of the Tabium
CGTase were grown from 21% saturated ammonium sulfate in 100 mM Tris buffer, pH 7.6. The crystals were stable in the
presence of carbohydrates.
A double soaking experiment was started identical to that described
earlier for the Bacillus circulans strain 251 CGTase (13). A
Tabium CGTase crystal was soaked for 20 min in a solution of 0.25% w/v acarbose in 21% saturated ammonium sulfate and 100 mM CAPS buffer, pH 9.8, followed by 7 days of soaking in a
solution of 0.5% maltohexaose in 21% saturated ammonium sulfate in
100 mM CAPS buffer, pH 9.8.
Data were collected to a resolution of 2.6 Å on a MacScience Dip2000K
Image Plate system and processed with XDS (23). Refinement of the
structure was done with the TNT package (24), using the 2.3-Å
structure of unliganded Tabium CGTase as a starting model (6). Rigid body refinement was followed by coordinate and all parameter
(coordinates and individual atomic temperature factors) refinement. A
test set for calculating a free R factor (25) comprised 8%
(1956) of the unique reflections. Ideal protein bond lengths and angles
were taken from Engh and Huber (26), ideal bond lengths and angles for
glucose were taken from the crystal structure of maltose (27).
Planarity, van der Waals contacts, and B factor correlations were
restrained, whereas torsion angles were not. Chiral centers were
watched. The model was manually adjusted using O (28), running on a
Silicon Graphics workstation, in combination with the program OOPS
(29). Electron density was displayed using A weighted
Fo Fc, 2Fo Fc maps, and omit difference maps (30, 31).
In the course of the refinement, density appeared for 6 glucose units
in the active site, at subsites 3, 2, 1, 1, 2, and 3. In this
naming convention, the glycosidic bond between 1 and 1 is the
scissile bond, and the substrate reducing end is at position 3. In
previous structures with acarbose and the acarbose derived maltononaose
inhibitor (13, 16), the valienamine moiety of acarbose was located at
subsite 2 and the 6-deoxyglucose group at subsite 1. This time, clear
omit Fo Fc density showed up
at the 6-hydroxyl position at subsite 1, even after thorough refinement
with a hexakis 6-deoxymaltohexaose as a carbohydrate model in the
active site. Refining with maltohexaose as a model removed the
difference density at position 1 completely. We decided to model a
valienamine group, which has a 6-OH group, at subsite 1, and according
to the acarbose structure, 6-deoxyglucose at subsite 1. This resulted
in the N-glycosidic linkage of acarbose being positioned at
the site of hydrolytic cleavage. This binding mode of acarbose in the
active site is also observed in related -amylases (32). At subsites
2 and +2 electron density indicated the presence of 6-OH groups, so
glucoses were modeled in. Furthermore, also at subsites 3 and +3
glucoses were placed, resulting finally in an acarbose derived
maltohexaose in the active site of CGTase.
Solvent molecules were taken from the 2.3-Å Tabium
structure (6), and runs of the program ARP (33) were used to add and remove water molecules with bad electron density. Finally, water molecules with bad density, B factors larger than 50 Å2, or no hydrogen bonds were removed by hand.
Furthermore, at a binding site distant from the active site, equivalent
to maltose binding site 3 (MBS3) in BC251 CGTase (5),
density for a maltotriose was found, which was subsequently modeled in.
MBS1 and MBS2 of BC251 CGTase (5) were not occupied in
Tabium CGTase.
The final model was analyzed with the PROCHECK package (34). It
contained all 683 amino acids, 2 Ca2+, an acarbose-based
maltohexaose inhibitor in the active site, a maltotriose at MBS3, and
185 solvent oxygens. Refinement details and statistics can be found in
Table I.
Bacterial Strains, Plasmids, and Growth
Conditions--
Escherichia coli JM109 (35) was used for
recombinant DNA manipulations. E. coli PC1990 (36), known to
leak periplasmic proteins into the supernatant because of a mutation in
its tolB locus, was used for (extracellular) production of
CGTase (mutant) proteins. Plasmid pCT2, a derivative of pUC18
containing the amyA (cgt) gene of T. thermosulfurigenes EM1 (37), was used for site-directed mutagenesis, sequencing, and expression of the CGTase (mutant) proteins
(Fig. 1). Plasmid-carrying bacterial
strains were grown on LB medium with 100 µg/ml ampicillin. When
appropriate, isopropyl- -D-thiogalactopyranoside was
added at a concentration of 0.1 mM for induction of protein expression.
DNA Manipulations--
DNA manipulations and transformation of
E. coli were essentially as described by Sambrook et
al. (38). Electrotransformation of E. coli was
performed using the Bio-Rad gene pulser apparatus (Bio-Rad, Veenendaal,
The Netherlands). The selected conditions were 2.5 kV, 25 µF, and 200 .
Site-directed Mutagenesis--
Mutant CGTase genes were
constructed via a double PCR method using Pfu DNA polymerase
(Stratagene, Westburg, Leusden, The Netherlands). A first PCR reaction
was carried out with the mutagenesis primer for the coding strand plus
a primer 195-715 base pairs downstream on the template strand. The
reaction product was subsequently used as primer in a second PCR
reaction together with a primer 295-815 base pairs upstream on the
coding strand. The product of the last reaction was cut with
NcoI and MunI and exchanged with the
corresponding fragment (900 base pairs) from the vector pCT2 (Fig. 1).
The resulting (mutant) plasmid was transformed to E. coli
JM109 for sequencing and to E. coli PC1990 for production of
the (mutant) proteins. The following oligonucleotides were used to
produce the mutations: D197H,
5'-CGTAACTTATTTCATTTAGCAGATCTAAATCAACAG-3'; F284K, 5'-GTCTTTTGGACAAGAGGTTTTCTC-3'; N327D,
5'-GGTTACTTTTATTGATGATCATGATATGG-3'; D371R,
5'-GACAGGCAATGGACGTCCTTATAATAGAGC-3'.
The bold codons indicate the changed amino acids. Successful
mutagenesis resulted in appearance of the underlined restriction sites
(BglII for D197H, BclI for N327D and
AatII for D371R), which allowed rapid screening of potential
mutants. It was not possible to find a convenient restriction site for
mutant F284K. Mutations were verified by DNA sequencing (39). All 900 base pairs on the MunI-NcoI fragment obtained by
PCR were checked by DNA sequencing.
Production and Purification of CGTase Proteins--
For
production of CGTase proteins, E. coli PC1990 (pCT2) was
grown in a 2-liter fermentor at pH 7.0 and 30 °C. The medium contained 2% (w/w) trypton (Oxoid, Boom BV, Meppel, The Netherlands), 1% (w/w) yeast extract (Oxoid), 1% (w/w) sodium chloride, 1% (w/w) casein hydrolysate (Merck, Darmstadt, Germany), 100 µg/liter
ampicillin, and 0.1 mM
isopropyl- -D-thiogalactopyranoside. Growth was monitored by measuring the absorbance (A) at 450 nm. At an
A450 nm of 2-3, an extra amount of 50 g
of trypton was added to the fermentor. Cells were harvested after
20-24 h of growth (8000 × g, 30 min, 4 °C), at
absorbance values of 8-12. The supernatant was directly applied to an
-CD-Sepharose-6FF affinity column (40) for further purification of
the CGTase proteins. After washing the column with 10 mM
sodium acetate, pH 5.5, the CGTase was eluted with the same buffer
supplemented with 1% (w/w) -CD. Purity and molecular weight of the
CGTase (mutant) proteins were checked on SDS-polyacrylamide gel
electrophoresis (11). Protein concentrations were determined by the
method of Bradford (42), using the Coomassie protein assay reagent of
Pierce (Pierce Europe bv, Oud-Beijerland, The Netherlands).
Enzyme Assays--
Specific assays were used to determine the
activities (initial rates) of the four different reactions catalyzed by
CGTases (14). In the cyclization reaction the reducing end of a sugar is transferred to another sugar residue in the same oligosaccharide chain, resulting in the formation of cyclic compounds. Coupling is the
reverse reaction in which a cyclodextrin molecule is linked to a linear
oligosaccharide chain, producing a longer oligosaccharide chain. In the
disproportionation reaction, part of a linear donor-oligosaccharide is
transferred to a linear acceptor chain. The saccharifying activity is
the hydrolysis of starch into linear oligosaccharides. All assays were
standardly performed at pH 6.0 and 60 °C. Cyclization and
saccharifying assays were performed as described by Penninga et
al. (14). Coupling activity was measured essentially as described by Nakamura et al. (41). -CD (2.5 mM) was
used as donor substrate and methyl -D-glucopyranoside
(100 mM) as acceptor substrate. The linear oligosaccharide
formed in the reaction was converted to single glucose units by the
action of amyloglucosidase (Sigma, Darmstadt, Germany). Glucose was
detected with the glucose/GOD-Perid method of Boehringer Mannheim
(Almere, The Netherlands). Disproportionation activity was measured as
described by Nakamura et al. (18). EPS,
4-nitrophenyl- -D-maltoheptaoside-4-6-O-ethylidene
(3 mM, Boehringer Mannheim), was used as donor substrate
and maltose (10 mM) as acceptor substrate. The reaction
product containing the nitrophenyl group was cleaved by the action of
-glucosidase (Boehringer Mannheim). For each reaction units were
defined as the amount of enzyme producing/converting 1 µmol of
product/substrate at pH 6.0 and 60 °C.
The pH optimum for cyclization was determined by incubating 0.1 units/ml ( -CD forming activity) of the enzyme with 5% Paselli SA2
(partially hydrolyzed potato starch; AVEBE, Foxhol, The Netherlands) in
a 10 mM sodium citrate solution set at a specific pH (range 4.0-8.0). For each pH a new calibration curve was prepared with 0-2
mM -CD. The pH optimum for the saccharifying reaction
was determined in a similar way.
HPLC Product Analysis--
Formation of cyclodextrins was
measured under industrial process conditions by incubation of 0.1 unit/ml CGTase ( -CD forming activity) with 10% Paselli WA4
(pregelatinized drum-dried starch with a high degree of polymerization;
AVEBE) in 10 mM sodium citrate buffer, pH 6.0, at 60 °C
for 45 h. Samples were taken at regular time intervals and boiled
for 10 min. Products formed were analyzed by HPLC, using a 25-cm
Econosil-NH2 10-µm column (Alltech Nederland bv, Breda,
The Netherlands) eluted with acetonitrile/water (65:45) at 1 ml/min.
Products were detected by a refractive index detector (Waters 410, Waters Chromatography Division, Milford, MA). The temperature of the
flow cell and column was set at 50 °C, to avoid possible
precipitation of starch. Formation of linear products was directly
analyzed. Formation of CDs was analyzed after incubation of the samples
with an appropriate amount of -amylase (type I-B from sweet potato,
Sigma, Boom BV, Meppel, The Netherlands), degrading linear sugars (but
not CDs) to glucose. The retention times for -, -, and -CD
were the same as those for G4, G5, and G6 linear oligosaccharides,
respectively.
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RESULTS AND DISCUSSION |
Binding of the Maltohexaose Inhibitor
The maltohexaose inhibitor complexed with the CGTase from T. thermosulfurigenes EM1 was bound at subsites 3 to +3 (Fig.
2). In complexes with BC251
CGTase (13) or other CGTases, binding at subsite 3 has never been
observed. The present study thus reveals the nature of subsite 3 for
the first time. The glucose at subsite 3 (overall B
factor: 58 Å2) has long distance interactions with
Glu264 O- 1 and Thr262 N, both at 3.6 Å. A
better contact is formed at 3.4 Å with the Asn591 O 1
from a symmetry related molecule. This stabilization by a crystal
contact may explain why in BC251 CGTase crystals a glucose at subsite 3 has never been observed. The interactions that do not
result from a crystal contact are very weak, indicating that subsite
3 is not of large relevance.

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Fig. 2.
Conformation of the maltohexaose inhibitor in
the active site of the CGTase from T. thermosulfurigenes
EM1. The inhibitor is occupying subsites 3 to +3 in domains A
and B of the CGTase.
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In the vicinity of the scissile bond the active site architecture is
identical in Tabium and BC251 CGTase. It is
therefore not surprising that at subsites 2 to +2, the maltohexaose
inhibitor is bound in the same fashion to Tabium CGTase as
the maltononaose inhibitor to BC251 CGTase (13). Even though
the acarbose binding mode has been modeled differently, the same amino
acids are providing similar interactions from subsites 2 to +2,
suggesting that acarbose can adapt its conformation easily to that
required by the active site. It is clear that differences in
characteristics between Tabium and BC251 CGTase
must originate from interactions at more distant subsites.
In contrast to subsites 2 to +2, at subsite +3 the binding mode of
the maltohexaose inhibitor is radically different from the maltononaose
binding mode, the former being more bent. In Fig.
3, an overlay of the two inhibitor
conformations can be seen. All enzyme-substrate interactions are given
in Table II. The glucose at subsite 3 of
the maltohexaose inhibitor occupies a position more bent toward
Phe196. This conformation at subsite 3 is stabilized by
Lys47. In BC251 CGTase this residue is
Arg47, which so far has never been found to be involved in
substrate binding. Furthermore, in the BC251 enzyme
Tyr89 has strong interactions at subsite 3, but in the
Tabium CGTase this residue is an Asp. The conformation of
Asp89 does not allow any interactions with substrate. Apart
from these two differences at subsite 3, residues in Tabium
CGTase at subsites 4-7 might be unfavorable to the maltononaose
binding mode (straight), although we could not find evidence for that
from the structure of Tabium CGTase. The maltohexaose
conformation observed is only stabilized by the protein through the
contact with Lys47. The maltohexaose conformation, however,
might have less internal strain because it allows the O2-O3
interglucoside hydrogen bond between subsites 2 and 3 to be formed at
2.7 Å, whereas in the straight conformation the O2-O3 distance is 4.0 Å (13) prohibiting hydrogen bond formation. In addition, the lack of
interactions with the enzyme might allow for more flexibility of the
maltohexaose chain, which would thus be entropically stabilized. On the
basis of these data, we thought it possible to favor one binding mode over the other by site-directed mutagenesis, thereby investigating whether it could be related to one of the Tabium CGTase
characteristics.

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Fig. 3.
Superposition of the maltohexaose
(sticks) and maltononaose (lines) inhibitor
structures. At subsite +3 the conformation of the maltohexaose
inhibitor is more bent toward Phe196 and is stabilized by
Lys47, which is Arg47 in the CGTase from
B. circulans strain 251. Moreover, the replacement of
Tyr89 (B. circulans CGTase) by Asp89
(T. thermosulfurigenes EM1 CGTase) makes that the
"straight" maltononaose conformation at subsite +3 is not as stably
bound in T. thermosulfurigenes EM1 CGTase than as in
B. circulans CGTase.
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Table II
Interactions of a maltohexaose inhibitor with T. thermosulfurigenes
CGTase
Stack indicates an aryl-carbohydrate stacking interaction; w.m.,
water-mediated contact; distances are specified for putative hydrogen
bonds or other electrostatic interactions.
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The Tabium and BC251 CGTases are different in
many respects. The molecular basis for thermostability of the
Tabium CGTase has been extensively discussed (6).
Furthermore, Tabium CGTase displays a relatively high
hydrolytic activity (24 units/mg), compared with BC251
CGTase (3.5 units/mg), which results in formation of substantial
amounts of linear sugars besides cyclodextrins from starch (11).
Tabium CGTase produces a mixture of -, -, and -CD
at a ratio of 28:58:14, respectively, whereas BC251 CGTase has a product ratio of 13:64:23 (14). A mutant BC251 CGTase with a substantially higher -cyclodextrin production also showed preference for a bent maltohexaose inhibitor over a straightly bound
maltononaose inhibitor (43). This suggests a relation between the bent
conformation and -cyclodextrin production. The maltohexaose and
maltononaose binding modes thus may reflect (part of) specific
intermediates for -CD and -CD production by Tabium CGTase and BC251 CGTase, respectively. Further experimental
evidence for this was sought by modifying relevant residues in
Tabium CGTase, using site-directed mutagenesis. Since the
maltohexaose and maltononaose inhibitors are synthesized by CGTase
in situ in the crystal, no sufficient quantities were
available to determine their binding or inhibitor constants. Therefore
we designed our mutants only by qualitative arguments.
Our first approach was to design a mutation that would hinder the
maltononaose binding mode and possibly bind a substrate in the
maltohexaose conformation. We found that the replacement of
Asp197 by His fulfilled these requirements, since modeling
of the mutation D197H (Fig. 4) shows that
the His ring cannot assume a conformation in which all the atoms are
more than 2.0 Å away from the atoms in the maltononaose inhibitor. So
His197 is likely to block the straight conformation.
Moreover, the His197 N- 2 atom could potentially
stabilize the bent conformation by forming a hydrogen bond with the
glucoside O6 at subsite +3. The D197H mutation changes the
electrostatic field of the active site, which could have long distance
effects by changing charge-charge interactions. However, since the
substrate is uncharged, effects on the substrate binding mode will have
to be indirect, in contrast to the van der Waals and hydrogen bonding
interactions.

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Fig. 4.
Model of the mutations D371R and D197H in the
CGTase from T. thermosulfurigenes EM1 (green
and yellow) together with the maltohexaose structure.
The mutations (red) have been given the most frequently
occurring side chain conformation (with O; Ref. 28) that doesn't
involve steric clashes with the enzyme. The maltohexaose chain is
depicted in light blue; the modeled maltononaose chain in
the B. circulans 251 CGTase structure is colored dark
blue.
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Our second approach was to construct a mutant that would stimulate the
maltononaose conformation over the maltohexaose conformation, which is
easiest achieved, not by constructing a specific interaction with the
straight conformation, but by destabilizing the bent conformation. With
the mutation Asp371 to Arg we aimed at introducing a bulky
residue that would clash with the maltohexaose conformation, but be
less hindering to the straight maltononaose conformation (Fig. 4). The
long and flexible side chain of Arg371 could probably
extend its effect to subsite +3, where the bent and straight
conformations differ most. The mutation D371R changes again the
electrostatics of the active site, with possible indirect consequences
for substrate binding. However, the mutation conserves the polarity of
residue 371.
Of the two mutants D197H, designed to relatively stabilize the
maltohexaose conformation, is expected to produce more
-cyclodextrin. Mutant D371R, designed to prefer the maltononaose
conformation, is expected to produce less -cyclodextrin. The
experimental data show that these mutants display altered cyclodextrin
product specificity according to expectation (Table
III).
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Table III
Starch conversion of T. thermosulfurigenes wild-type and mutant CGTase
proteins
Proteins (0.1 unit/ml -CD forming activity) were incubated for
45 h at pH 6.0 and 60 °C with 10% Paselli WA4.
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Production and Purification of CGTase (Mutant) Proteins
Mutants of Tabium CGTase were successfully constructed
by site-directed mutagenesis via PCR; all mutations were verified by restriction site analysis (except for mutant F284K) and DNA sequencing. Amounts of 0.4-1.2 mg of pure protein were obtained in a single fermentor run depending on the construct used (Table
IV). Purification yields varied between
11% for mutant D371R and 58% for mutant D197H. Purity and molecular
weight of the (mutant) CGTases were checked on SDS-polyacrylamide gel
electrophoresis. All proteins were purified to apparent homogeneity and
displayed a molecular mass of 68 kDa.
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Table IV
Purification of T. thermosulfurigenes wild-type and mutant CGTase
proteins from E. coli PC1990 culture supernatants
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Characterization of CGTase Mutant Proteins
Cyclodextrin Product Specificity--
Mutant D197H has a
cyclodextrin production profile different from wild-type CGTase (Fig.
5). At the initial stages of the reaction, the mutant has an increased preference for -cyclodextrin production, mostly due to a collapse of the production of
-cyclodextrin. At later stages of the reaction, the production of
-cyclodextrin increases, but the product ratio is then a result of a
subtle equilibrium between cyclization and cyclodextrin breakdown
specificities, as well as the solubilities of the diverse
cyclodextrins. However, the cyclodextrin production ratio after 45 h still shows a small preference for -cyclodextrin (Table III),
proving that the total product ratio can be modified by changing the
initial reaction rates. The initial reaction's preference for
-cyclodextrin is according to the expectations we had upon designing
the mutant (see above). An additional effect of the mutation D197H is
that coupling activity is reduced by a factor 4 when compared with the
activity of the wild-type enzyme (Table
V), possibly because coupling activity
was measured with -cyclodextrin whereby a maltononaose was formed as
an intermediate. The mutation was, however, designed to make binding of
maltononaose less favorable.

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Fig. 5.
Cyclodextrins formed during incubation of
(mutant) CGTase proteins from T. thermosulfurigenes EM1
(0.1 unit/ml -CD forming activity) with 10% (w/v) Paselli WA4
starch for 50 h at pH 6.0 and 60 °C. , -CD; ,
-CD; , -CD. A, wild-type CGTase; B,
mutant D197H; C, mutant D371R; D, mutant F284K;
E, mutant N327D.
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Table V
Specific enzyme activities and pH optima for activity of T. thermosulfurigenes EM1 wild-type and mutant CGTase proteins
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Mutant D371R displayed drastically decreased cyclization, coupling,
disproportionation and saccharifying activities when compared with the
wild-type enzyme (Table V). Asp371 has a very important
role in substrate binding at subsite +2, both in the BC251
and Tabium CGTase (Table II; Ref. 13). When Asp371 is replaced by Arg, the bulk of the residue could
hamper efficient substrate binding at subsite +2 and the charge
difference could interfere with the catalytic process in site +1,
resulting in having an overall activity of only 9% of the wild-type
CGTase (Table V). However, not the efficiency of the catalytic process is determining product specificity, but the preference for forming a
specific intermediate leading to a specific product at an initial stage
in the CGTase reaction. The product specificity changed from 28:58:14
for the wild-type enzyme to 6:68:26 for mutant D371R (Table III, Fig.
5). This suggests that the intermediate specific for -cyclodextrin
production in the cyclization reaction of the mutant D371R is less
frequently formed. As pointed out above, we think that this
intermediate has a conformation resembling the maltohexaose "bent"
conformation, formation of which could be sterically hindered by the
bulky Arg371 residue.
These results lend more credence to the theory that the bent
conformation is correlated with -cyclodextrin production and show
that it can be used to rationally engineer a CGTase with desired
cyclodextrin product specificity (12). The results show that the
Tabium CGTase can be changed from an / -cyclodextrin producer to a / -cyclodextrin producer by just one mutation. We
currently are working on a wider range of mutations and a more detailed
thermodynamical and structural characterization of them to further
investigate the significance of the bent conformation and other
structure-function relationships in CGTase.
Site-directed Mutations Close to the Proton Donor
Glu258: Implications for pH Optima of CGTases--
To
further investigate the role of the environment of Glu258
on the pKa of Glu258 in the different
reactions catalyzed by CGTases we replaced Phe284 by Lys
(F284K) in Tabium CGTase. Residue Phe284 is
located in a hydrophobic cavity immediately above the active site,
close to Glu258 (Fig. 6). At
most physiological pH values Lys can be expected to bear a positive
charge. Positioning of a positive charge near Glu258
stabilizes its deprotonated form, so decreasing its
pKa. This would predict a shift of the pH optimum
for this mutant toward acidity. Fig. 7, A and
B, show that this indeed
happens for both the cyclization and hydrolysis activity. Apart from
this effect, the optimum curves also become more narrow, an observation
that was also made for a F184L mutant in Bacillus sp. 1011 CGTase (18). The mutation F184L does not introduce any charges;
therefore, the narrowing effect can be best explained by a reduction of
the hydrophobicity of the environment of Glu258 (see
below).

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Fig. 6.
Model of the mutations near
Glu258. Residues in the CGTase from T. thermosulfurigenes EM1 are shown in green and
yellow. The maltohexaose structure is given in
blue. The mutations N327D and F284K are modeled in
red, as described in the legend to Fig. 4. The red
sphere is the water as mentioned in the text.
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Fig. 7.
A, effect of pH on the cyclization
activity of CGTase (mutant) proteins from T. thermosulfurigenes EM1. B, effect of pH on the
saccharifying activity of the CGTase (mutant) proteins from T. thermosulfurigenes EM1.
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Residue Asn327 is also situated above the active site,
close to Glu258 (Fig. 6). Mutation N327D in T. thermosulfurigenes CGTase introduced a group that can bear a
negative charge at high pH next to Glu258. This would
increase the pKa of Glu258 by
destabilizing its deprotonated form. A shift of the pH optimum toward
alkaline regions is expected. However, we observe that both cyclization
and hydrolysis optima shift to lower pH (Fig. 7, A and
B). A similar loss of activity at high pH has been observed in a N327D mutant of Bacillus stearothermophilus
-amylase, an enzyme homologous to CGTase (21). A N327V mutant of the
same enzyme remained active at high pH, suggesting that the effects of
mutations N327D are due specifically to introduction of an acidic
group.
A possible explanation for the observed shift of activity to acidic
regions for mutant N327D of T. thermosulfurigenes CGTase can
be found by observing that Asn327 binds Glu258
via a water molecule (Fig. 6) and is secluded from the bulk solvent by
hydrophobic residues such as Phe284, Phe324,
Phe260, Met330, and Leu282. In such
an environment, the Asp327 and the water molecule would
form a very stable salt bridge between the negatively charged
carboxylate group and a H3O+ ion. Because the
H3O+ ion is closest to Glu258, the
net effect of the mutation would be to bring a positive charge close to
Glu258, resulting in an overall decrease of its
pKa. This would explain why the behavior of the
N327D and F284K mutations are so alike.
Cyclodextrin product ratios of mutants F284K and N327D were not
significantly changed compared with the wild-type enzyme, which might
be expected, since both residues are not involved in substrate binding
(Table V). All specific enzyme activities were decreased for mutants
F284K and N327D compared with the wild-type activities, except for the
disproportionation activity of F284K (Table III). Mutations near the
proton donor thus have an overall negative effect on catalysis
rates.
pH Optimum Curve for Cyclization and Hydrolysis--
In
Tabium CGTase residue Glu258 is the proton donor
in the first step of catalysis, so a protonated state of
Glu258 is essential. In the second step of catalysis,
Glu258 is suggested to activate the acceptor by
deprotonation, in this case a deprotonated state of Glu258
would be essential. Furthermore, for optimal activity the catalytic nucleophile, Asp230, must remain deprotonated in the first
step of catalysis. The Tabium CGTase displays a broad pH
optimum for cyclization in the range of pH 4-7 (Fig. 7A).
Other CGTases have an efficient cyclization reaction from pH 5 to 7 (16, 18, 21, 22). It might be expected that the drop in enzyme activity
at high pH is caused by deprotonation of Glu258 in the
first step of the reaction and that the activity drop at low pH is
caused by protonation of Asp230. The combination of these
two effects would result in a pH optimum curve. In Fig. 7A,
however, it can be seen that the mutations near Glu258
shift both the slopes at high and low pH, while we had expected only to
see effects on the high pH slope of the optimum curve, which is
affected by Glu258. Similar observations have been
described before in literature. The mutation F284L in
Bacillus sp. 1011 CGTase shifts the pH optimum both over
acidic and alkaline pH ranges (18). This mutation is close to the
proton donor and is unlikely to have long distance effects. Mutation of
Asp329 in BC251 CGTase to Asn had a most
pronounced effect on the low pH slope of the optimum curve (20).
Furthermore, mutation of Asp230 to Asn in the
BC251 CGTase did not result in any shift of the pH optimum,
whereas a shift was observed with the Glu258 to Gln
mutation (20). Therefore, it is likely that the protonation state of
Glu258 determines both slopes of the pH optimum curve. At
high pH, the first step of the double displacement mechanism is
hindered by lack of a proton donor, at low pH the second step is
inhibited by incomplete substrate activation. If the protonation state
of Glu258 determines both slopes of the pH profile, it is
unexpected that the pH optimum is so broad. This broad pH range of
activity must be explained by a different environment for
Glu258 in the first and second step of catalysis. Indeed,
in Tabium CGTase (6) the third catalytic residue
Asp329 probably forms a hydrogen bond with
Glu258 initially, increasing the pKa of
Glu258 and ensuring its protonation. This bond is broken
after substrate binding, facilitating again deprotonation of
Glu258 in the ensuing second catalytic step. The impact of
changes near Glu258 during catalysis is enhanced by its
hydrophobic environment, in which electrostatic interactions are much
stronger. Changes in the environment of Glu258 before and
after substrate binding have also been observed in the structure of
BC251 CGTase (13, 16).
The pH optimum for hydrolysis is much sharper and lies about 1 pH unit
lower than the pH optimum for cyclization in the Tabium CGTase (Fig. 7B). The only difference between these two
reactions is the acceptor molecule, water in the hydrolysis reaction,
and a C4-hydroxyl group in the cyclization reaction. The fact that the
pH optimum for hydrolysis is less broad could result from a decreased
hydrophobicity of the Glu258 environment with water as an
acceptor. The shift toward lower pH might be explained from the fact
that water as an acceptor is much easier activated, making the
requirement for an unprotonated Glu258 in the second
reaction step less stringent, thus increasing activity at low pH.
 |
CONCLUSIONS |
At subsite 3 the binding mode of the maltohexaose inhibitor in
Tabium CGTase is radically different from the maltononaose binding mode in the BC251 CGTase. The bent conformation of
the maltohexaose inhibitor, in contrast to the straight conformation of
the maltononaose inhibitor, was found to be correlated to enhanced -cyclodextrin production. Mutations stabilizing the bent
conformation but hindering the straight conformation resulted in
enhanced production of -CD, whereas mutations hindering the bent
conformation but stabilizing the straight conformation resulted in
decreased production of -CD. The Tabium CGTase can hence
be changed from an / -cyclodextrin producer to a
/ -cyclodextrin producer by a single mutation, illustrating the
feasibility of CGTase protein engineering.
Mutations near the proton donor Glu258 suggest that the pH
optimum curve of CGTase may be determined only by the protonation state
of residue Glu258. Both the high and low slopes of the pH
optimum curve could be manipulated by site-directed mutations close to
Glu258. Changes in the environment of Glu258
before and after substrate binding can account for its broad pH
optimum.
 |
ACKNOWLEDGEMENTS |
The assistance of Dirk Penninga, Jan
Springer, and Gerard Rouwendaal with construction of the mutants and
the assistance of Gert-Jan van Alebeek with the enzyme assays is
gratefully acknowledged.
 |
FOOTNOTES |
*
This work was supported by European Community Grants
AIR-CT-93-1023 (to R. D. W. and R. M. B.) and
ERBIO2-CT-94-3071 (to J. U., B. W. D., and L. D.).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.
§
To whom correspondence should be addressed: ATO-DLO, P. O. Box 17, 6700 AA Wageningen, The Netherlands. Tel.: 31-317-475321; Fax:
31-317-475347; E-mail: r.d.wind{at}ato.dlo.nl.
1
The abbreviations used are: CD(s),
cyclodextrin(s); CGTase, cyclodextrin glycosyltransferase; CAPS,
3-(cyclohexylamino)propanesulfonic acid; MBS, maltose binding site;
PCR, polymerase chain reaction; HPLC, high performance liquid
chromatography.
 |
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