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Plant Physiol, February 2001, Vol. 125, pp. 527-531
SCIENTIFIC CORRESPONDENCE
Three-Dimensional Structures of UDP-Sugar Glycosyltransferases
Illuminate the Biosynthesis of Plant
Polysaccharides1
Simon J.
Charnock,
Bernard
Henrissat, and
Gideon J.
Davies*
Department of Chemistry, Structural Biology Laboratory, University
of York, Heslington, York YO10 5DD, United Kingdom (S.J.C., G.J.D.);
and Architecture et Fonction des Macromolécules Biologiques,
Unité Mixte de Recherche 6098, Centre National de la
Recherche Scientifique, Universités d'Aix-Marseille I and
II, 31 Chemin Joseph Aiguier, 13402 Marseille cedex 20, France
(B.H.)
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INTRODUCTION |
Cell-free preparations of the
bacterium Acetobacter xylinum were first reported to
synthesize cellulose from UDP-Glc over 40 years ago (Glaser, 1958 ).
Despite the elucidation of the primary sequence of the cellulose
synthase from this organism in 1990 (Wong et al., 1990), a consistent
mechanism to account for the biosynthesis of this and related
polysaccharides has remained elusive. Opposing views of the number of
catalytic centers and the molecular directionality of the synthesis
have been presented (for review, see Delmer, 1999). A
comprehensive classification of glycosyltransferases harnessed to
the recent structural determinations of UDP-sugar dependent
 -glycosyltransferases, including a cellulose synthase homolog,
permits a preliminary illumination of this controversial area. The
number of glycosyl transfer centers in the catalytic domain of
cellulose synthase remains controversial: a two-center model has been
proposed (Saxena et al., 1995), but we find it hard to reconcile with
the wealth of experimental data on the three-dimensional structure of glycosyltransferases.
The sequence family classification system, originally
developed for the glycoside hydrolases, has recently been extended to include the activated-sugar dependent glycosyltransferases (Campbell et
al., 1997). Forty-eight families are known at the present date and
may be found in a continuously updated database at
http://afmb.cnrs-mrs.fr/~pedro/CAZY/db. html (for review, see
Henrissat and Davies, 2000). Activated-sugar dependent transferases
account for the vast majority of glycosyl transfer on earth. The
activating group may be a phosphate, a lipid phosphate, or a
nucleotide, and the reaction mechanism proceeds with either retention
or inversion of the anomeric configuration of the donor sugar.
One of the features of the sequence-family classification is that
the reaction mechanism is conserved within each family. Cellulose
synthase, in family "GT-2," is an "inverting"
glycosyltransferase, i.e. it uses  -linked UDP-sugars to generate a
-linked product. Inverting transferases are assumed to use a single
displacement mechanism with nucleophilic attack by the acceptor species
at the C-1 (anomeric) carbon of the donor sugar. Such a mechanism is
generally believed to demand a base to activate the sugar acceptor for
nucleophilic attack by deprotonation because sugar hydroxyls are in
themselves quite poor nucleophiles. For most enzymes the reaction also
involves an additional carboxylate or carboxylates to coordinate a
divalent metal ion on the phosphate group(s) of the nucleotide (Fig.
1).
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Figure 1.
The putative mechanism for an inverting
nucleotide-sugar glycosyltransferase. Such a mechanism most
likely requires at least two catalytic carboxylates, one to function as
a base to activate the acceptor species and at least one more to
coordinate a divalent metal ion associated with the UDP-sugar. In many
enzymes the metal-ion coordination involves two carboxylates in what is
misleadingly (because it is often seen as DDx, xDD, DDD) termed the
"D(x) D" motif.
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THE THREE-DIMENSIONAL STRUCTURE OF A GLYCOSYLTRANSFERASE
FROM FAMILY GT-2 |
In the last few months, six different glycosyltransferases
structures from different sequence families have been published or presented (for review, see Ünligil and Rini, 2000). This
recent burst of structural activity began with the resolution of the three-dimensional structure of SpsA, a glycosyltransferase implicated in the sporulation response of Bacillus subtilis (Charnock
and Davies, 1999). This structure is particularly relevant to those studying the biosynthesis of plant polysaccharides, such as cellulose, because it is found in glycosyltransferase family GT-2, which includes
cellulose synthase and over 40 other open reading frames (ORFs)
in Arabidopsis alone (Henrissat et al., 2001).
The three-dimensional structure of both native and Mn-UDP
complexes of SpsA revealed a mixed / protein with two domains and
featuring a central -sheet core flanked by -helices, Figure 2a. The N-terminal region of SpsA
(residues 1-99) is a classical nucleotide-binding domain of four
parallel -strands flanked on either side by two -helices and is
the binding site for UDP. Many of the "signature motifs" of family
GT-2 are contained in this N-terminal UDP binding domain, which
equates to the "A-domain" described for cellulose synthase,
Figure 2b. The Rib and Mn phosphate are coordinated by Asp-98 and
Asp-99 which correspond to the "D(x) D" motif found in many
families of glycosyltransferase. The second, C-terminal, domain is the
site for binding of the acceptor species, and we predicted that
Asp-191, in this acceptor-binding region, would function as the
catalytic base in the inverting mechanism.
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Figure 2.
A, The three-dimensional structure of a
family GT-2 UDP-sugar-dependent glycosyltransferase, SpsA, from
Bacillus subtilis. The conserved N-terminal
nucleotide-binding domain is shown in green and the C-terminal acceptor
domain in red. Four aspartates, 39, 98, 99, and 191 discussed in the
text are shown in ball-and-stick representation as is the UDP molecule.
The Mn2+ ion is shown as a shaded sphere. Plant
sequences also contain insertions in the basic core structure. Within
the N-terminal UDP-binding domain there is a "P-CR" insertion of
approximately 115 residues in the Arabidopsis RSW1 and IRX3 cellulose
synthases and the length of this region varies from approximately 70 to
approximately 190 residues for other plant cellulose synthase homologs.
This insertion occurs between strand -3 and -4 in the
three-dimensional structure as indicated. Plant cellulose synthases
also have an insertion in the "B" domain termed an "HVR" domain
(not shown; Pear et al., 1996). There are no extensive insertions in
the bacterial cellulose synthases such as the Acetobacter
enzyme whose catalytic core domain is essentially the same size as SpsA
(Saxena et al., 1995). This figure was drawn with MOLSCRIPT/BOBSCRIPT
(Kraulis, 1991; Esnouf, 1997). B, Schematic representation of family
GT-2 and related glycosyltransferases (from families 7, 13, and 43 whose three-dimensional structures are known) indicating the position
of important catalytic and UDP-binding residues. "TM" indicates the
presence of extensive transmembrane segments. ORF MTH457 from
Methanobacterium thermoautotrophicum has been cited as an
enzyme containing just a "B" domain. Close examination of the
nucleotide sequence, however, shows that this is not the case. The
apparent lack of the "A" domain results purely from an incorrect
start codon in the genome-annotation, compounded by a frame-shift
error. Errors associated with this ORF are therefore shown for
reference.
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THREE-DIMENSIONAL STRUCTURES OF OTHER INVERTING
GLYCOSYLTRANSFERASES |
In addition to SpsA, three additional glycosyltransferase
structures of relevance to the synthesis of plant polysaccharides have
also recently been determined: the -galactosyl transferase from
family GT-7 (Gastinel et al., 1999), the rabbit GalNAc transferase from
family GT-13 (Ünligil et al., 2000), and the human
-1,3-glucuronyltransferase I from family GT-43 (Pedersen et al.,
2000). The striking feature of these four structures is their
structural and mechanistic similarity, despite insignificant sequence
identity (Ünligil and Rini, 2000). The N-terminal UDP-binding
domain is well-conserved and the critical amino acids "D... D(x)
D" that interact with UDP are invariant. Biochemical confirmation of
the roles of these residues also comes from site-directed mutagenesis
on another family GT-2 enzyme, ExoM from Sinorhizobium
mellioti (Garinot-Schneider et al., 2000). All four structures
present a C-terminal acceptor-binding domain and it is particularly
important that the residue predicted to be the catalytic base in SpsA
(Charnock and Davies, 1999), Asp-191, has correspondence in all
four enzyme families. In the structures from families 2, 7, and
13 this residue is an Asp, in family GT-43 it is a Glu. In the family
GT-43 human -1,3-glucuronyltransferase structure, the sugar
acceptor species is seen hydrogen bonding to the base in position for
nucleophilic attack on the UDP-sugar donor. Therefore, these
enzyme families use a minimum of four carboxylates to form a single
catalytic center: Three aspartates are involved in UDP coordination
whereas a fourth residue in the acceptor domain, Asp or Glu, acts as
the catalytic base.
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THE BIOSYNTHESIS OF CELLULOSE: CONFLICTING
PROPOSALS? |
The mode of action of polymerizing family GT-2 enzymes such
as cellulose synthase has been plagued by contradicting speculations (for review, see Davies and Charnock, 1999). Are these polymers extended at their reducing or non-reducing ends, does the mechanism involve lipid pyrophosphate intermediates or direct transfer from the
nucleotide-sugar donor, and are there one or more catalytic centers per
peptide chain?
14C-pulse-chase experiments with
Acetobacter xylinum favored extension at the reducing end
(Han and Robyt, 1998). [14C]UDP work suggested
a similar mechanism for hyaluronan synthase, a related family GT-2
enzyme (for review, see DeAngelis, 2000). However, numerous experiments
have demonstrated recently that elongation by family 2 enzymes occurs
by polymerization at the non-reducing end of the growing
polysaccharide. Electron crystallography provided the first
experimental evidence for cellulose synthesis (Koyama et al.,
1997), and this has been followed by numerous reports unambiguously
demonstrating non-reducing end elongation by direct transfer from the
nucleotide-sugar (DeAngelis, 1999; Kamst et al., 1999; Cartee et
al., 2000).
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THE "TWO-CENTER" MODEL FOR CELLULOSE
SYNTHASE |
Cellulose is a -1,4-linked polymer of D-Glc, in
which adjacent monosaccharides are rotated through 180° with respect
to one another, and thus the "structural" repeating unit is
considered to be cellobiose. One can speculate that in the case of
cellulose, this alternating orientation of monomers provides a
"torsional" problem for catalysis. Likewise, for the synthesis of
hyaluronan two different sugars, with two different linkages, need to
be added sequentially. Attempts to relieve these perceived problems led
to the proposal of a dual active-center model for "processive" or
polymerising enzymes (Saxena et al., 1995).
Hydrophobic cluster analysis of family GT-2
-glycosyltransferases correctly identified that these
glycosyltransferases were two domain proteins. The A-domain contained
the conserved family GT-2 motifs "D... D(x) D," which were
common to both polymerizing and single-addition transferases. The
B-domain contained a fourth invariant Asp, which in the polymerizing
enzymes only, was followed by a characteristic QxxRW motif (Saxena et
al., 1995). The two-domain architecture, coupled to observation of four
conserved aspartates spread over these two domains, led to the
development of a two catalytic center model in which the A and B
domains were each proposed to function as glycosyl transfer centers.
The effective addition of a disaccharide occurred via the dual addition
of monosaccharides.
The double addition of monosaccharides provided an extremely
seductive solution to potential problems associated with the synthesis
of cellulose. Furthermore, it could also explain the synthesis of
hyaluronan (a polymer of alternating -1,4-linked N-acetylglucosamine and -1,3-linked GlcA) by class-I
hyaluronan synthases. The two-center model initially featured
reducing-end elongation with three UDP-sugar binding sites and two
glycosyl transfer centers (Saxena et al., 1995). It later evolved to
feature two centers for glycosyl transfer and two UDP-sugar binding
sites when direct addition to the non-reducing end became favored
(Koyama et al., 1997; Saxena and Brown, 1997; Carpita and Vergara,
1998).
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IS THE TWO CENTER MODEL CONSISTENT WITH RECENT
THREE- DIMENSIONAL STRUCTURES? |
The release of single, monosaccharide adducts by root
nodulation factor, NodC (another polymerising family GT-2 enzyme) is not consistent with the dual addition mechanism (Kamst et al., 1999).
Furthermore, on many systems mutations of the
conserved aspartates, in either domain, tends to abolish catalytic
activity completely, consistent with the notion that together these
residues form just a single transfer center (Yoshida et al., 2000).
What do the three-dimensional structures of glycosyltransferases tell us about this confusing area?
The two catalytic-center model is based upon the assumption
that four aspartates, spread over two domains in a
230-amino-acid fragment, are sufficient to constitute two discrete
glycosyl transfer centers (Saxena et al., 1995). Yet, the family 2, 7, 13, and 43 glycosyltransferase structures reveal that four such
residues are required to form a single viable catalytic center. These
proteins all display two domains, one of which binds the UDP-sugar and the other the acceptor. The N-terminal UDP binding domain of these proteins (approximately 100 amino acids) contains the "D... D(x) D" motif. It is equivalent to the complete A-domain of cellulose synthase. It is extremely hard for these authors to reconcile demonstration that this domain is a UDP-binding domain and thus uses
the three aspartates merely to bind UDP with proposals that it may
function as a discrete catalytic entity, the A-domain, in a two
catalytic-center protein.
We therefore propose that the catalytic core domain of cellulose
synthase (and related polymerizing family GT-2 enzymes) is similar to
these four glycosyltransferases. They all consist of a two-domain
protein in which the N-terminal A-domain binds the UDP-sugar and the
C-terminal B-domain forms the acceptor binding region and completes the
single transfer center by provision of the catalytic base. A few
enzymes in family GT-2, such as the type-II hyaluronan synthases do
possess two repeats of both of the UDP and acceptor domains in a
genuine two-center enzyme whose two catalytic centers are consequently
spread over 6 to 700 amino acids (Jing and DeAngelis, 2000). In
contrast with the results on cellulose synthase or the type-I
hyaluronan synthase (Yoshida et al., 2000) mutation of the
aspartates in this genuine two-center type-II hyaluronan
synthase abolish just one transfer activity.
How a polypeptide with a single active-site could account for the
synthesis of an alternating polysaccharide such as hyaluronan is not
understood. A general feature of polymerizing glycosyltransferases is
that the reaction product of one addition becomes the acceptor for a
subsequent events. One can speculate that the last residue added on the
growing hyaluronan chain (either a GlcNAc or a GlcA), once in the
acceptor site, may tune the affinity of the donor site for the
complementary sugar-nucleotide. This may be controlled in part by the
negatively charged carboxylate of the GlcA moiety. Small changes in the
active center environment are known to change the specificity of
transferases. The specificity "switch" from blood group -Gal to
-GalNAc transferase demands just a single amino acid substitution
(Seto et al., 1999) and the Campylobacter jejuni enzyme,
Cst-II, changes its regioselectivity depending on the nature of the
acceptor species (Gilbert et al., 2000).
These recent results on the three-dimensional structures and
mechanisms of inverting glycosyltransferases begin to reveal the
intimate details of oligosaccharide biosynthesis. Although these
enzymes appear unrelated to plant biochemistry, they actually have
great relevance for plant polysaccharides. Many of the unresolved issues may now be placed on a stronger experimental foundation. In
particular, the roles of many of the conserved motifs in cellulose synthase and related enzymes may now been assigned. By far the vast
majority of data point to polymer elongation at the non-reducing end by
direct transfer from the nucleotide sugar donor. Furthermore, we
propose that most family GT-2 transferases, including cellulose synthase, use the A and B domains, and the four conserved aspartates to
form a single center for glycosyl transfer. The three-dimensional structure of the GT-2 enzyme SpsA does not rule out all possible two-center models such as dimerization or the recruitment of other domains for catalysis. If the majority of family 2 enzymes use a single
center, perceived problems with torsional stress and addition of
alternating sugars require new explanations. Only when the
three-dimensional structure of a polymerizing family GT-2
glycosyltransferase is reported will these issues be fully resolved.
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FOOTNOTES |
Received September 20, 2000; returned for revision October 10, 2000; accepted November 9, 2000.
1
This work was supported by the European
Commission, the Biotechnology and Biological Science Research Council,
the Wellcome Trust, the University of York, and the Centre National de
la Recherche Scientifique. G.J.D is a Royal Society University Research Fellow.
*
Corresponding author; e-mail davies{at}ysbl.york.ac.uk; fax
44-1904-410519.
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© 2001 American Society of Plant Physiologists
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TOP
INTRODUCTION
THE THREE-DIMENSIONAL STRUCTURE...