![]()
|
|
||||||||
(Received for publication, November 7,
1994; and in revised form, November 30, 1994) From the
In Endo-1,3-1,4- Like other The crystal
structure of the hybrid Bacillus This paper focuses on
the further identification of the catalytic residues in Bacillus
The
structure was solved with the molecular replacement facilities of
X-PLOR (Brünger, 1990) with the structure of the
hybrid
The two molecules in the asymmetric unit are
very similar and have identical secondary structure. After a least
squares superposition, the r.m.s. separation is 0.36 Å for
equivalent C
The
Figure 1:
Stereo drawing of the B. macerans
Figure 2:
Views along the substrate binding channel
of the B. macerans
Figure 3:
Comparison of conformation and
intramolecular hydrogen bonding of the NH
Figure 4:
Active site geometry of B. macerans
At the bottom of the groove mainly polar side chains are
located, especially acidic amino acid residues. They are thought to
interact with the polar groups of the polysaccharide and to position it
for cleavage. In contrast, the upper and lower rims of the crevice are
lined with hydrophobic amino acid residues presumed to contribute to
substrate binding through van der Waals interactions (Fig. 2).
The secondary structure of the wild-type and hybrid
enzymes differs in their NH
Hydrogen
bonds are formed between O
Figure 5:
Mutations within the active site region of B. macerans
Figure 6:
Immunoblot of B. macerans wild-type and mutant
Figure 7:
Circular dichroism spectra of B.
macerans wild-type and mutant
The mutations introduced in
sequence positions 101, 103, 105, and 107 are mostly conservative,
changing Trp to Phe or Tyr, Glu to Asp, Gln or His, and Asp to Asn or
Lys. Nevertheless, all result in a drastic loss in enzymatic activity
by a factor of at least 300 (Table 4). With the exception of
mutant E107D the change of active site residue affects mostly k
The crystal structure of B. macerans Enzyme
variants W101F, W101Y, E103D, E103Q, D105N, D105K, E107D, E107Q, and
E107H resulting from site-directed mutagenesis of the active site
residues Trp In
mutants W101F and W101Y a hydrogen bond to Glu A possible
mechanism for The results of the
structural and mutational analysis of B. macerans The
involvement of two carboxylate functions in glycosylases working under
retention of configuration is rather common. It has been demonstrated,
for instance, for Agrobacterium glycosylase (Whithers et
al., 1990), cellobiohydrolases I and II and endoglucanase III from Trichoderma reesei (Divne et al., 1994; Rouvinen et al., 1990; Macarron et al., 1993), endocellulase
E2 from Thermomonospora fusca (Spezio et al., 1993),
and hen egg white as well as phage T4 lysozyme to which the bacterial
A comparison of the
sequences of bacterial lichenases and laminarinases suggests a set of
amino acids essential for catalysis and supports the previous findings.
Glu
Figure 8:
Conserved region of bacterial
endo-1,3-1,4-
Volume 270,
Number 7,
Issue of February 17, 1995 pp. 3081-3088
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
1,4-
-glucanase (*)
ABSTRACT
INTRODUCTION
MATERIALS AND METHODS
RESULTS
DISCUSSION
FOOTNOTES
ACKNOWLEDGEMENTS
REFERENCES
-glucans those
-1,4 glycosidic bonds which are
adjacent to
-1,3 bonds are cleaved by
endo-1,3-1,4-
-glucanases (
-glucanases). Here, the
relationship between structure and activity of the
-glucanase of Bacillus macerans is studied by x-ray crystallography and
site-directed mutagenesis of active site residues. Crystal structure
analysis at 2.3-Å resolution reveals a jellyroll protein
structure with a deep active site channel harboring the amino acid
residues Trp
, Glu
, Asp
, and
Glu
as in the hybrid Bacillus
-glucanase
H(A16-M) (Keitel, T., Simon, O., Borriss, R., and Heinemann, U.(1993) Proc. Natl. Acad. Sci. U. S. A. 90, 5287-5291).
Different mutant proteins with substitutions in these residues are
generated by site-directed mutagenesis, isolated, and characterized.
Compared with the wild-type enzyme their activity is reduced to less
than 1%. Several mutants with isosteric substitutions in Glu
and Glu
are completely inactive, suggesting a
direct role of these residues in glycosyl bond hydrolysis. The kinetic
properties of mutant
-glucanases and the crystal structure of the
wild-type enzyme are consistent with a mechanism where Glu
and Glu
are the catalytic amino acid residues
responsible for cleavage of the
-1,4 glycosidic bond within the
substrate molecule.
-glucanase (
-glucanase,
1,3-1,4-
-D-glucan 4-glucanohydrolase, EC 3.2.1.73)
hydrolyzes
-1,4-linkages adjacent to
-1,3 linkages in mixed
linked polymeric
-glucans (Anderson and Stone, 1975). Genes
encoding bacterial
-glucanases have been cloned and sequenced from
different Bacillus species (Murphy et al., 1984;
Hofemeister et al., 1986; Tezuka et al., 1989;
Borriss et al., 1990; Lloberas et al., 1991; Gosalbes et al., 1991; Louw and Reid, 1993), Fibrobacter
succinogenes (Teather and Erfle, 1990), Ruminococcus
flavefaciens (Flint et al., 1993), and Clostridium
thermocellum (Schimming et al., 1992). All bacterial
endo-1,3-1,4-
-glucanases (``lichenases'') known to
date share sequence similarities with endo-1,3-
-glucanases
(``laminarinases'') and have been classified into glycosyl
hydrolase family 16 (Henrissat, 1991; Henrissat and Bairoch, 1993).
-glycosidases,
-glucanase acts by a general
acid catalysis in which 2 acidic residues participate in a single or
double replacement reaction, resulting in the inversion, or more
likely, retention of the configuration at the anomeric carbon (Sinnot,
1990). General acid catalysis requires the participation of a proton
donor residue and a catalytic residue that is responsible for
nucleophilic attack on the substrate. A nucleophilic water molecule
completes the pathway by generating reaction products.
-glucanase H(A16-M) (
)(Keitel et al., 1993) suggests that
-glucan
hydrolysis takes place in a deep channel spanning one side of the
molecular surface and that residues Glu
,
Asp
, and Glu
(that correspond to
Glu
, Asp
, and Glu
in Bacillus macerans wild-type enzyme) are oriented toward the
active site cleft. Substitution by site-directed mutagenesis of
Glu
in B. macerans and of the corresponding
Glu
in Bacillus licheniformis
-glucanases
abolishes enzyme activity (Olsen, 1990; Planas et al., 1992).
Epoxybutyl-
-D-cellobioside (G4G-O-C
) has been
identified as the most effective inhibitor of Bacillus
-glucanase (Høj et al., 1992). The structure
analysis of this inhibitor bound to H(A16-M) revealed that the epoxide
is covalently attached to the side chain of Glu
(Keitel et al., 1993). Therefore it was suggested that Glu
acts by forming a covalent glycosyl enzyme intermediate or by
stabilizing the intermediate state through electrostatic interaction
with a transiently formed oxocarbonium ion.
-glucanase. In order to clarify the role of residues which
might be involved in the hydrolytic cleavage of
-glucan, we have
constructed different mutants of the B. macerans
-glucanase gene. Following expression in Escherichia
coli, mutant proteins substituted in putative catalytic residues
were characterized with regard to their enzymatic properties. The
results are discussed in relation to the crystal structure of the
enzyme which was determined at 2.3-Å resolution. In addition, the
observed differences in thermostability between B. macerans
-glucanase and H(A16-M) are considered in relation to the
crystal structures.
Crystallization, Diffraction Data Collection, and
Structure Analysis
The B. macerans
-glucanase was
concentrated to 6 mg/ml and stored in a 10 mM sodium acetate
buffer, pH 4.3, with 5 mM CaCl
. The precipitant
solution additionally contained 30%, w/v, ammonium sulfate and 20
mM MgCl
. Crystals were grown by mixing equal
volumes of protein and precipitant solution in a hanging-drop vapor
diffusion setup at room temperature. They were enlarged by macroseeding
to approximately 0.3 0.3
0.1 mm
within 2 or
more weeks. Two diffraction data sets with a resolution to 2.3 Å
were collected on a MAR-Research imaging plate detector mounted on an
Enraf-Nonius FR571 rotating anode x-ray generator. The space group was
identified by the autoindexing routine XDS (Kabsch, 1993) as C2 with
cell constants a = 203.68 Å, b =
42.41 Å, c = 60.70 Å, and
=
101.27°, suggesting a V
value (Matthews, 1968)
of 2.7 Å
/Da with two molecules in the asymmetric
unit. The data were processed with MOSFLM as part of the CCP4 program
suite (Collaborative Computational Project, Number 4, 1994).
-glucanase H(A16-M) (Keitel et al., 1993) as a
search model. Two peaks occurred in the rotation and Patterson
correlation functions that were used to orient the molecules. After
calculation of separate translation functions and combined rigid body
refinement a R-value of 35.4% for x-ray diffraction data
between 16 and 3 Å indicated that the molecules were located
correctly. The model was further refined with the simulated annealing
routine of X-PLOR (Brünger et al., 1990)
making use of non-crystallographic symmetry restraints. Positional and
temperature factor refinement was carried out with X-PLOR and for the
final steps of refinement with the program TNT (Tronrud et
al., 1987). Atomic coordinates and structure amplitudes have been
deposited in the Protein Data Bank, Brookhaven National Laboratory,
Upton, NY (entry code not yet assigned).Strains and Vectors
E. coli DH5
,
vector plasmid pTZ19R, and expression plasmid pUC13-M harboring the B. macerans
-glucanase gene have been described (Olsen et al., 1991). Expression plasmid pTZ19MAC is identical to
pUC13-M except for the vector sequences. Cells were grown in LB medium
supplemented with 100 µg/ml ampicillin when necessary.Mutagenesis
Site-directed mutagenesis was
performed by the polymerase chain reaction as described by Kadowaki et al. (1989). The mutated sequences were obtained by
mutagenic primer-directed fragment amplification. Afterwards, an
amplified sequence was introduced by replacing a cassette within the B. macerans gene. Plasmids pUC13-M and pTZ19-H(A16-M) were
used as template DNA for mutagenesis. In order to simplify
site-directed mutagenesis, an additional EcoRI site was
created at residue 108. The sequence of the primer
P1-EcoRI-Dir also covers the unique EcoRV restriction
site at residues 105-106: 5`-gat atc gaa ttc tta gga aaa gac aca
acg. The amplified DNA was cloned as EcoRV/HindIII
fragment into the B. macerans gene cut at the same restriction
sites. Primers DIR and dIII-LS specifying the 5` and 3` ends have been
described (Politz et al., 1993). Plasmids containing the
mutated sequences were checked by DNA sequencing.Protein Expression and Purification of Wild-type and
Mutant Enzymes
Proteins were expressed from E. coli cells harboring plasmids encoding the wild-type and mutant enzymes
essentially as described previously (Politz et al., 1993).
Whole cell extracts were prepared by ultrasonication and
diaultrafiltrated against 50 mM sodium acetate, pH 5.0, 10
mM CaCl
. The sample was applied to a column
containing CM-Sepharose CL-6B (Pharmacia) and eluted with a linear
gradient of 0-400 mM sodium chloride. Fractions
containing
-glucanase were collected and further purified by gel
chromatography using Sephacryl S-200 (Pharmacia). The proteins obtained
were separated by SDS-polyacrylamide gel electrophoresis and blotted
onto nitrocellulose filters. These were incubated with serum containing
antibodies raised against B. macerans
-glucanase.
Proteins reacting with the antibodies were detected using the Western
blot AP System (Promega).Characterization of
CD spectra of
wild-type and mutant
-Glucanases
-glucanases were recorded on a
J720-spectrophotometer (Jasco, Tokyo, Japan) between 180-260 and
250-340 nm. Enzyme was dissolved in 2 mM cacodylate, pH
6.0, 1 mM CaCl
at a final concentration of 0.5
mg/ml.
-Glucanase activity of purified wild-type and mutant
proteins was assayed by the release of reducing sugars from lichenan
(Olsen et al., 1991). Other biochemical analyses and
isoelectric focussing were performed as described (Politz et
al., 1993).
Crystal Structure of the
Endo-1,3-1,4-
Structure
refinement against all structure amplitudes > 2
-glucanase of B. macerans
between 8.0
and 2.3 Å converged at a R-value of 16.3%. One
Ca
ion per enzyme molecule and a total of 175 water
molecules were located. The diffraction data and refinement results are
summarized in Table 1and Table 2. In both independent
molecules in the asymmetric unit, residues 96-99 show temperature
factors up to 90 Å
and are poorly defined by electron
density. 87 and 85%, respectively, of the residues are in the most
favorable regions of the Ramachandran diagram as defined by Laskowski et al. (1993).
and 0.41 Å for equivalent backbone atoms.
Considering the mean error in the atomic coordinates of 0.25 Å as
given by a Luzzati(1952) analysis there are thus no significant
conformational differences between the molecules. They show a
considerable difference of about 10 Å
, however, in
the average thermal parameter indicating a higher flexibility of
molecule 1 in the crystal lattice. This may be related to the higher
number of intermolecular hydrogen bonds formed by molecule 2 in the
crystal (Table 3). In this evaluation, an upper limit of 3.5
Å is used for the donor-acceptor distance. It can be seen that
molecule 1 has seven hydrogen bonds compared with eleven of molecule 2
and, more important, molecule 1 is in contact with only three other
molecules in the lattice, whereas molecule 2 is in contact with six.
The conformational differences between the independent molecules are
most pronounced in the loop regions 51-55 and 94-102. These
residues are without contacts to symmetry-related molecules in the
crystal, but they are poorly defined by the diffraction data and have
large temperature factors. They seem to be flexible parts in the
molecular architecture with little structural influence.
-glucanase is an all-
protein with a sandwich-like jellyroll
architecture. The two sheets stacking atop of each other consist of
seven antiparallel strands each that are bent and thus create a channel
on one side of the protein where the substrate is bound and hydrolyzed.
A disulfide bond is formed between Cys
and
Cys
. Loops between the
-strands are mostly stabilized
by
-turns. In addition, the analysis of the secondary structure
and hydrogen bonding with the program DSSP (Kabsch and Sander, 1983)
reveals one turn with
-helical geometry (Fig. 1). On the
convex side of the molecule, remote from the active site, a calcium ion
is bound which has been suggested to play a role in stabilizing the
protein structure (Borriss et al., 1989; Keitel et
al., 1994; Welfle et al., 1994). In
pentahedral-bipyramidal geometry it is coordinated to the carbonyl
oxygen atoms of Pro
, Gly
, and Asp
and the O
1 atom of the latter as well as to three water
molecules. In the related
-glucanase H(A16-M), this binding site
is occupied either by an octahedrally coordinated calcium or a
trigonal-bipyramidally coordinated sodium ion (Keitel et al.,
1994).
-glucanase with
-strands drawn as arrows. The
calcium ion is drawn as a black ball, the S-S bridge between
residues 30 and 59 in ball-and-stick mode, and the
-helical turn between residues 188 and 191 as ribbon.
Some residue numbers are indicated to facilitate following the
polypeptide chain. This figure as well as Fig. 2Fig. 3Fig. 4were prepared with MOLSCRIPT
(Kraulis, 1991).
-glucanase. The side chains of the
hydrophilic amino acids Asn, Asp, Glu, Arg, Lys, and His in the channel
are shown in the top drawing. At the bottom the side chains of
the hydrophobic amino acids Phe, Tyr, Trp, Leu, Ala, Val, and Met are
shown.
-terminal region
of B. macerans
-glucanase and H(A16-M). Residues
15-212 of the former and 17-214 of the latter protein which
have identical sequence were matched in a least squares fit to
superimpose the NH
-terminal peptide portions. Residue
labels refer to the B. macerans protein (thick
lines). Hydrogen bonds are shown as dashed
lines.
-glucanase. On the left, the cellobiose part of an
inhibitor bound covalently to H(A16-M) (Keitel et al., 1993)
has been fitted into the active site channel by least squares
superposition of the two proteins. In the blow-up on the right, looking through the channel the side chains of those
amino acids that are involved in catalysis are drawn in ball-and-stick representation with hydrogen bonds indicated as dashed lines.
Comparison with H(A16-M) and Origin of Different
Thermostability
The hybrid H(A16-M) differs from the wild-type B. macerans
-glucanase only by the 16
NH
-terminal amino acids that are derived from the Bacillus amyloliquefaciens protein. As expected, the
three-dimensional structures of the proteins are very similar (see Table 2). This holds true although three protein molecules in
three different crystal environments are compared. It confirms the
remarkable conformational rigidity of the bacterial
-glucanases
observed earlier (Hahn et al., 1994). On the other hand,
differences in thermostability have been described for various hybrid
and parental
-glucanases (Politz et al., 1993). For
example, the temperature required to reduce the enzymatic activity to
50% within 10 min is 72.4 °C for the wild-type B. macerans
-glucanase studied here, but 75.0 °C for H(A16-M). Is it
possible to explain this small difference in stability from the crystal
structures?
-terminal region (Fig. 3). In both proteins the termini are close together in
space. The NH
-terminal
-strand of the wild-type enzyme
reaches from Ser
to Glu
, in H(A16-M) it is
shorter by 2 residues reaching from Phe
to Glu
.
In the B. macerans
-glucanase five main chain hydrogen
bonds are formed between residues 2, 4, and 6 of the
NH
-terminal strand and residues 211, 209, and 207 of the
COOH-terminal strand, respectively. Furthermore, the
NH
-terminal loop is stabilized internally by hydrogen bonds
from Asn
to Thr
and Trp
.
Conversely, in H(A16-M) only four main chain hydrogen bonds are found
between the NH
- and COOH-terminal strands and an additional
one between the NH
terminus and the loop from residue 67 to
residue 72, one of the four loops that connect the two seven-stranded
sheets. Thus, just by counting hydrogen bonds the small differences in
thermal stability cannot be explained. The size of a ``loop''
closed by a hydrogen bond may also play a role as well as subtle
differences in cation binding.Active Site Structure
The geometry of the active
site of B. macerans
-glucanase is shown in Fig. 4.
For a better orientation, the cellobiose moiety of an inhibitor bound
covalently in the crystal of H(A16-M) (Keitel et al., 1993)
has been fitted into the active site channel by least squares
superposition of the protein atoms. Near the presumed catalytic site,
the side chains of Trp
, Glu
,
Asp
, and Glu
point toward the channel,
whereas those of Asp
, Ile
, and Ile
point into the hydrophobic interior of the enzyme. Trp
plays an important role in enzyme activity (see below), although
it is located in a flexible surface loop. The remaining catalytic site
residues are on one contiguous stretch of
-strand.
1 of Glu
and N
1 of
Trp
and between O
2 of Glu
and O
1
of Asp
. In the absence of bound substrate a proton has to
be bound between the side chains of Glu
and Asp
to allow the formation of this hydrogen bond which is conceivable
at the pH of crystallization of 4.3. However, the conformation and
hydrogen bonding pattern of these amino acids is identical in the
wild-type enzyme and in hybrid H(A16-M), even though the latter was
crystallized from a neutral buffer. Therefore, the active site geometry
shown here appears to be representative for the entire family of
bacterial
-glucanases. In a similar way as Glu
, the
side chain of Glu
is involved in stabilizing hydrogen
bonding via its carboxyl oxygen to N
2 of Gln
which
in turn hydrogen bonds to Trp
N
1 via its O
1
atom.Construction of Mutant Proteins
Single
substitutions of Trp
, Glu
,
Asp
, and Glu
were achieved by cassette
mutagenesis of the gene taking advantage of either a unique EcoRV restriction site in the vicinity of the site of the
mutational event or an artificial EcoRI restriction site
introduced at the codon of residue 108. In order to obtain
substitutions in Trp
, Glu
, and Asp
mutation primers containing degenerated oligonucleotides in the
desired mutation site and a silent mutation creating an additional EcoRI restriction were used as reverse primers (Fig. 5). DNA fragments encoding the NH
-terminal
part with the mutated sequence in the active site region of the
-glucanase were amplified, cut by BstEII and EcoRI, and ligated back into the
-glucanase gene sequence
with the appropriate deletion. The expected substitutions were screened
by DNA sequencing. Mutants W101F, W101Y, E103D, E103Q, E103K, D105N,
and D105K were isolated. Mutations within Glu
were
generated by using primer Mac-E107-Dir as direct primer for
amplification of a DNA fragment encoding the COOH-terminal part of the B. macerans
-glucanase. DNA sequencing revealed mutations
E107H, E107D, and E107Q. All mutant genes obtained in this way were
cloned into pTZ19R vector plasmid and transformed into E. coli DH5
cells.
-glucanase. A silent mutation was introduced
at residue 108 by site-directed mutagenesis to yield an EcoRI
restriction site. The four degenerated oligonucleotides shown were used
as primers to introduce changes in Trp
,
Glu
, Asp
, and Glu
. Altered
nucleotides are underlined and indicated by bold
letters. MAC-W101-Rev: W = 50% T, 50% A; MAC-E103-Rev: W
= 75% T, 25% A; MAC-D105-Rev: W = 75% A, 25% T;
MAC-E107-Dir: W = 75% A, 25% T and S = 75% G, 25%
C.
Characterization of Mutant Proteins
Analysis of
mutant and wild-type
-glucanases using polyclonal antibodies
raised against B. macerans
-glucanase revealed that E. coli cells expressed approximately the same amount of
precipitating material (Fig. 6). The mutant proteins were
purified from E. coli and their enzymatic properties were
compared. To ensure that the protein structures are not affected by
site-directed mutagenesis, CD spectra of the wild-type and mutated
variants were obtained. These revealed only subtle differences in
secondary structure (Fig. 7). Temperature optima of the enzyme
reactions catalyzed by the wild-type and the active mutant proteins
were found to be essentially similar except for mutant E105H in which
the optimum is slightly decreased.
-glucanases expressed in E.
coli. Extracts of DH5
cells harboring recombinant and vector
plasmid pTZ19R grown in LB medium were prepared and loaded onto
SDS-PAGE (15% acrylamide). Detection of
-glucanases was with
polyclonal antibodies raised against purified B. macerans
-glucanase.
-glucanases. The
samples were buffered in 2 mM cacodylate, pH 6.0, 1 mM CaCl
, at a protein concentration of 0.5 mg/ml. The
measurements were performed with a J720 spectrometer
(Jasco).
and not K
. Replacement of
Trp
with another aromatic residue results in a
-glucanase variant with reduced, but clearly measurable, activity.
For glutamic acids 103 and 107 the isosteric replacement with a
glutamine side chain abolishes activity. Significantly reduced turnover
is observed when they are exchanged for aspartates preserving the
carboxylate function or, in the case of mutant E107H, with histidine.
The presence of ionizable groups at positions 103 and 107 thus appears
to be crucially important for catalysis. In contrast, the isosteric
replacement of the Asp
carboxylate with an amide function
in variant D105N leaves residual activity whereas
-glucan
hydrolysis by mutant D105K is no longer measurable. Hybrid H(A16-M)
-glucanase is identical with the B. macerans enzyme
except for 16 amino-terminal residues derived from B.
amyloliquefaciens
-glucanase (Olsen et al., 1991).
This polypeptide segment does not influence the enzymatic properties as
shown by introducing identical changes into the active site residues of
the hybrid H(A16-M) enzyme. The properties were found to be identical
with those of the B. macerans mutants. (
)
-glucanase
has been determined, and a number of key residues have been exchanged
in order to gain a basic understanding of the enzymatic function. The
three-dimensional structure of a Bacillus
-glucanase has
been described previously for the hybrid H(A16-M) (Keitel et
al., 1993), and site-directed mutagenesis experiments have been
reported for the B. licheniformis enzyme (Planas et
al., 1992; Juncosa et al., 1994). In the present study
x-ray crystallography and site-directed mutagenesis have been applied
to the same enzyme for the first time to define a framework for the
discussion of Bacillus
-glucanase function.
, Glu
, Asp
, and
Glu
show small or nonmeasurable residual activity. The
differential effects of the mutations can be discussed in the light of
the crystal structure. As indicated by the crystal structure of a
covalent H(A16-M)-inhibitor complex, the
-glucan substrate binds
to a pronounced channel on the molecular surface where the 4 residues
analyzed here form the catalytic site. For the wild-type B.
macerans enzyme studied here this view is supported by the
observation that those mutations in these residues which display
measurable residual activity tend to differ in k
much more than in K
. The such defined
catalytic site is quite unusual in that all four residues are on one
contiguous stretch of
-strand with connecting loop
(Trp
) where Glu
is tied in place by
hydrogen bonds to both Trp
and Asp
.
can no
longer be formed, and consequently the enzyme activity is reduced.
However, a conservation of function at this sequence position is not
mandatory for enzymatic activity. A similar reduction to less than 1%
of wild-type activity is brought about by the isosteric replacement of
Asp
by Asn, whereas the mutant D105K is inactive. This
seems to indicate that a conservation of shape is required at position
105, but not necessarily of function. We note that a hydrogen bond to
Glu
may very well be formed by the Asn
amide group. At positions 103 and 107 mutations tend to cause
more drastic reductions in catalytic efficiency suggesting a direct
role of these residues in catalysis. Isosteric exchanges of the two
glutamic acid residues with glutamine as in mutants E103Q and E107Q
lead to enzymatically inactive protein variants whereas the
isofunctional replacements with aspartic acid as in mutants E103D and
E107D yield low, but measurable, activities. This reduction in
enzymatic activity may arise from the shortening of the side chains by
one methylene group and connected rearrangements in the active site.
Interestingly, mutant E107H shows slightly higher activity than E107D
and a shift in pH optimum. Residue His
is closer in shape
to glutamic acid and can also take up and release a proton. In summary,
the enzymatic activity of
-glucanase appears to require ionizable
groups at positions 103 and 107 as well as conservation of shape and/or
hydrophobicity for sequence positions 101 and 105.
-glucanase action must take into account two general
considerations (Sinnot, 1990; Svensson and Søgaard, 1993).
First, the hydrolysis of the glycosyl bond can proceed either under
overall retention or inversion of the configuration at the anomeric
carbon C1. Since NMR analysis of the products of
-glucan cleavage
by the homologous B. licheniformis
-glucanase has proven
retention of configuration (Malet et al., 1993), we may safely
assume the same stereochemical course for the B. macerans enzyme. Overall retention of configuration requires two functional
groups of the enzyme present in an appropriate spatial setting and
acting as nucleophile (or by providing electrostatic assistance) and as
general acid, respectively, in a double displacement reaction. Second,
the reaction may proceed via an oxocarbonium ion or a covalently
enzyme-bound intermediate. This ambiguity cannot be resolved based on
the available data, although the covalent binding of epoxyalkyl
cellobioside inhibitors to Bacillus
-glucanases
(Høj et al., 1989, 1992; Keitel et al., 1993)
lends some support to the latter possibility.
-glucanase are consistent with a model that assigns a role as
general acid to Glu
and a role as catalytic nucleophile
or in electrostatic stabilization of an oxocarbonium ion to
Glu
. The crucial importance of the latter residue is also
evident from chemical modification studies of Bacillus
-glucanases which show it to be the site of inhibitor
attachment (Høj et al., 1992; Keitel et al.,
1993) and from further mutagenesis studies (Juncosa et al.,
1994). In this view, the general acid Glu
would activate
a water molecule for binding to the anomeric carbon. In the
three-dimensional structure, the networks of hydrogen bonds apparently
serving to position both the Glu
and Glu
carboxylate groups underline their functional importance.
-glucanases appear to have some resemblance (Borriss et
al., 1990; Planas et al., 1992).
, Asp
, Glu
, and
Gly
are conserved throughout the compared sequences (Fig. 8, numbering according to B. macerans protein).
In the case of Gly
no function in catalysis is assumed,
but glycine tends to be conserved when space is scarce. Other amino
acids like isoleucines 102 and 104 are also highly invariant. The
changes from Ile to Val observed in the F. succinogenes and B. circulans enzymes maintain the apolar character of the side
chain. Starting with Glu
and ending with Phe
there is a strict alternation of polar (acidic) and nonpolar side
chains in the catalytic sites of the
endo-1,3-1,4-
-glucanases which reflects the regular way in
which side chains subtend from a
-strand toward the hydrophobic
interior or the surface of the protein. This pattern is disturbed in
the endo-1,3-
-glucanases by insertion of a methionine residue
between Ile
and Glu
of B. macerans
-glucanase. Assuming generally similar active site geometry
and catalytic mechanism this residue must be accommodated by formation
of a
-bulge (Richardson et al., 1978) which would allow
the Met side chain to point toward the hydrophobic core and the Glu to
subtend into the channel and to participate in catalysis. The
concomitant structural rearrangements of the active site are proposed
to cause the changed substrate specificity toward
-1,3 linkages of
the laminarinases. However, B. macerans
-glucanase
variants carrying an inserted methionine in the active site region were
found to be enzymatically inactive, suggesting that further
modifications are necessary to extend the substrate specificity of Bacillus
-glucanases.
-glucanase and endo-1,3-
-glucanase
sequences. The numbering is according to the B. macerans enzyme. Lichenases (Lic) are from B. macerans (Borriss et al., 1990), B. amyloliquefaciens (Hofemeister et al., 1986), B. licheniformis (Lloberas et al., 1991), Bacillus subtilis (Murphy et al., 1984), Bacillus polymyxa (Gosalbes et al., 1991), B. brevis (Louw and
Reid, 1993), C. thermocellum (Schimming et al.,
1992), R. flavefaciens (Flint et al., 1993) and F. succinogenes (Teather and Erfle, 1990).
``Laminarinases'' (Lam) are from Rhodothermus marinus (Spilliaert et al., 1994), C. thermocellum (W.
Schwarz, personal communication) and B. circulans (Yahata et al., 1990).
)
-glucanase with residues 1-16 derived from the B.
amyloliquefaciens enzyme and residues 17-214 from the B.
macerans enzyme; W101F . . . etc. (see ``Construction of
Mutant Proteins'' under ``Results''), mutant B.
macerans
-glucanase with a single site substitution of
Trp
with Phe . . . etc.; r.m.s., root mean square.
)
We are grateful to W. Schwarz for communicating the
sequence of the laminarinase (licA) prior to publication. W. Saenger,
O. Simon, and H. Welfle are thanked for providing laboratory facilities
and for support in purification and CD analysis of wild-type and mutant
-glucanases. Cloning of active site mutants into hybrid H(A16-M)
glucanase by K. Piotukh and helpful comments on the manuscript by D.
von Wettstein, J. J. Müller, and Ch.
Förster are gratefully acknowledged.
-glucanases. Ph.D. thesis, Aarhus University, Aarhus, Denmark
©1995 by The American Society for Biochemistry and Molecular Biology, Inc.
![]()
CiteULike
Complore
Connotea
Del.icio.us
Digg
Reddit
Technorati What's this?
This article has been cited by other articles:
![]() |
C. Deutsch and B. Krishnamoorthy Four-Body Scoring Function for Mutagenesis Bioinformatics, November 15, 2007; 23(22): 3009 - 3015. [Abstract] [Full Text] [PDF] |
||||
![]() |
V. S. T. Van Sandt, Y. Guisez, J.-P. Verbelen, and K. Vissenberg Analysis of a xyloglucan endotransglycosylase/hydrolase (XTH) from the lycopodiophyte Selaginella kraussiana suggests that XTH sequence characteristics and function are highly conserved during the evolution of vascular plants J. Exp. Bot., September 1, 2006; 57(12): 2909 - 2922. [Abstract] [Full Text] [PDF] |
||||
![]() |
P. Johansson, H. Brumer III, M. J. Baumann, A. M. Kallas, H. Henriksson, S. E. Denman, T. T. Teeri, and T. A. Jones Crystal Structures of a Poplar Xyloglucan Endotransglycosylase Reveal Details of Transglycosylation Acceptor Binding PLANT CELL, April 1, 2004; 16(4): 874 - 886. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Allouch, M. Jam, W. Helbert, T. Barbeyron, B. Kloareg, B. Henrissat, and M. Czjzek The Three-dimensional Structures of Two {beta}-Agarases J. Biol. Chem., November 21, 2003; 278(47): 47171 - 47180. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. D. Palumbo, R. F. Sullivan, and D. Y. Kobayashi Molecular Characterization and Expression in Escherichia coli of Three {beta}-1,3-Glucanase Genes from Lysobacter enzymogenes Strain N4-7 J. Bacteriol., August 1, 2003; 185(15): 4362 - 4370. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Walter, N. C. K. Heng, W. P. Hammes, D. M. Loach, G. W. Tannock, and C. Hertel Identification of Lactobacillus reuteri Genes Specifically Induced in the Mouse Gastrointestinal Tract Appl. Envir. Microbiol., April 1, 2003; 69(4): 2044 - 2051. [Abstract] [Full Text] [PDF] |
||||
![]() |
K.-P. Fuchs, V. V. Zverlov, G. A. Velikodvorskaya, F. Lottspeich, and W. H. Schwarz Lic16A of Clostridium thermocellum, a non-cellulosomal, highly complex endo-{beta}-1,3-glucanase bound to the outer cell surface Microbiology, April 1, 2003; 149(4): 1021 - 1031. [Abstract] [Full Text] [PDF] |
||||
![]() |
C. Ma and M. R. Kanost A beta 1,3-Glucan Recognition Protein from an Insect, Manduca sexta, Agglutinates Microorganisms and Activates the Phenoloxidase Cascade J. Biol. Chem., March 10, 2000; 275(11): 7505 - 7514. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. Aÿ, F. Gotz, R. Borriss, and U. Heinemann Structure and function of the Bacillus hybrid enzyme GluXyn-1: Native-like jellyroll fold preserved after insertion of autonomous globular domain PNAS, June 9, 1998; 95(12): 6613 - 6618. [Abstract] [Full Text] [PDF] |
||||
![]() |
J. J. Muller, K. K. Thomsen, and U. Heinemann Crystal Structure of Barley 1,3-1,4-beta -Glucanase at 2.0-A Resolution and Comparison with Bacillus 1,3-1,4-beta -Glucanase J. Biol. Chem., February 6, 1998; 273(6): 3438 - 3446. [Abstract] [Full Text] [PDF] |
||||
![]() < |