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377±386, 2003
DOI: 10.1093/glycob/cwg042
Introduction
Carbohydrates in the form of glycoproteins and glycolipids
play crucial roles in various signaling and molecular recog-
nition processes, affect the stability and structure of pro-
teins, and are epitopes recognized by the immune system
(Varki, 1993). A core a-galactosyl(1-3)galactose moiety is
the common structure of several oligosaccharide antigens
present on mammalian cell surfaces. These antigens have
been well characterized because of their importance for
Glycobiology vol. 13 no. 5 # Oxford University Press 2003; all rights reserved. 377
H. Heissigerova et al.
Table I. Specificity and reaction products of the glycosyltransferases related to blood group A and B synthases
a
The monosaccharides that carry the acceptor hydroxyl are indicated in boldface type.
(Keusch et al., 2000), and the histo-blood group A and B in substrate binding. First evidenced in inverting glycosyl-
glycosyltransferases (GTA and GTB) (Yamamoto et al., transferases for b2-GlcNAc transferase (U È nligil et al., 2000)
1990). and then b4-Gal transferase (Ramakrishnan and Qasba,
Enzymes belonging to this a3-Gal(NAc)T family share 2001), this conformational change has also been demon-
common features. They all use a UDP-nucleotide sugar as strated to occur in retaining glycosyltransferases (Boix et al.,
Loop regions display more variability, but their sizes are phosphate atoms through Lys359 (LBR-H) and Arg365
comparable, thus facilitating the modeling study. (LBR-I), both positions absolutely conserved among the
Because all glycosyltransferases belong to the SpsA fold enzymes studied here.
superfamily, the enzymes modeled here adopt a globular The Gal/GalNAc moiety interacts with different regions:
shape. Figure 2A displays the overall structure of the GTA LBR-B, -C, -E, and -F. Details of the hydrogen bonds
model. One face is responsible for binding the nucleotide- involving the sugar moiety have been listed in Table II.
sugar and the acceptor. Because the crystal structure of Depending on the model, five to seven hydrogen bonds
a3GalT complexed with UDP was taken as the reference are established between the sugar moiety and the proteins
molecule (Boix et al., 2001), all models are in their locked (see Figure 4 for GTA/GalNAc). Four of them are con-
Form II conformation, with the nucleotide-sugar almost served in the whole family: the first aspartate amino acid of
completely buried under the C-terminal region. The accep- the DXD motif (LBR-C) receives a hydrogen bond from O-
tor binding site appears as a deep crevice adjacent to the 3 hydroxyl group. An acidic amino acid from region LBR-F
nucleotide-binding site. These two binding sites are made (Asp316 in a3GalT) receives hydrogen bonds from both
up with residues belonging to nine peptide regions, identi- O-4 and O-6, this latest hydroxyl receiving a hydrogen
fied as ligand binding regions (LBRs) and labeled from A bond from the conserved Ser amino acid of LBR-B. The
to I in Figures 1 and 2. Because there is no significant Gal/GalNAc specificity is ensured by LBR-E, which con-
differences in loop size, the overall structure of the four tains the 277 FYYX(GA)(GA)282 motif. From our modeling,
proteins modeled here does not present large variation, it appears that the possibility to accept an N-acetyl group in
and only one has been displayed. the binding site is controlled by a pair of amino acids
facing each other (His280 and Ala282 in a3GalT). The
The nucleotide-sugar binding site: predicted interactions steric hindrance created by Met266/Ala268 in GTB and
between enzymes and UDP-Gal/GalNAc by His280/Ala282 in a3GalT (His253 in iGb3-S) is clearly
The UDP-sugar binding domain is located between the displayed in Figure 3A. The enzymes that can use GalNAc
central b-sheet (b2±b5) and two long a-helices (a3 and a4) have a glycine at one of these two positions (Leu266/Gly268
and is capped by the C-terminal region. Figure 3A gives in GTA and Gly261/Ala263 in Forss-S), therefore allowing
insights into the binding site pockets of four models. The for an opening of this subsite. These particular two residues
model for binding UDP-Gal by iGb3-S is very similar to the correspond to two of the four amino acids differentiating the
prediction for a3GalT and is not displayed. The Mn2 human blood group A and B glycosyltransferases.
binding site is made up by the 225 DVD227 (numbering rela-
tive to a3GalT), the very conserved LBR-C region. The The acceptor binding site: interactions between
uridine moiety is bound through the conserved enzyme and oligosaccharide acceptor
134
FA(IV)(GK)(KR)Y139 motif in LBR-A, whereas the Acceptors of various size (disaccharides and trisaccharides)
ribose ring interacts with amino acids of LBR-A, -B, and have been docked into protein models. The molecules that
-C. The C-terminal region makes direct contacts with the have been used in the modeling studies are those listed in
379
H. Heissigerova et al.
Table I, although the noncarbohydrate part (ceramide) have been color coded in Figure 3B where the proteins are
has not been taken into account in the modeling. When represented by their accessible surfaces. Minor contacts are
compared to the donor nucleotide sugar, it can be stated also established with residues of LBR-E (Tyr278 in a3GT).
that the acceptor oligosaccharides are more exposed to the Details of hydrogen bonds and hydrophobic contacts are
solvent and establish a limited number of contacts with the listed in Tables III and IV.
protein surface. Nevertheless, four regions seem to play an In all enzymes of this family, the primary acceptor is a
important role in binding the acceptor and defining the Gal or GalNAc residue. This can be correlated to a con-
specificity, namely, LBR-D, -F, -G, and -H. These regions served structural feature: LBR-F is almost invariant and
380
Molecular modeling of a3Gal(NAc)transferases
G268
A268 position.
L266 M266
For two of the enzymes, a3GalT and iGb3-S, a terminal
GTA GTB
galactose is required for acceptor, and no substitution is
tolerated at the C-2 position of this residue. Examination of
E297
S180 D316
S199 the models indicated that region LBR-H, and parti-
E298
E317 cularly the presence of an additional bulky Trp (Trp356
G261
in a3GalT), is responsible for the fine specificity. The
A263 H280 A282 Trp356 in a3GalT makes a barrier for any substitution on
Forss-S α3GalT
the Gal ring, whereas in the other enzymes the smaller Ala
or Thr residue together with basic residues 323 RK (Forss-S)
or 328 QL (GTA and GTB) form a pocket accommodating
either Fuc or NHAc group on C2 of the Gal ring. The size
B of the first amino acid of region LBR-H (Trp356 in
a3GalT) seems to distinguish whether the first monosac-
I316
GTA iGb3-S
W295 W314
H228 Q247
Y231
K340 K359
W250
W356
T337
G230
K324
R323 W249
H342
I343
Forss-S α3GalT
Table II. Analysis of the models: hydrogen bonds between the Gal or GalNAc of the nucleotide sugars and the amino acids of the different
glycosyltransferases
381
H. Heissigerova et al.
which uses lactose or N-acetyllactosamine as acceptor, LBR-E, which contains a variable sequence responsible
displays a Trp residue stacking with the Glc (or GlcNAc) for the specificity toward Gal and GalNAc.
ring at the reducing end, thus limiting the possibilities of The well-conserved region LBR-F mostly ensures specifi-
substitution or branching for this residue. This selection of city for galacto configuration of the acceptor terminal
the flat, ribbonlike conformationÐwhich can be adopted
residue.
by equatorial±equatorial linked carbohydrate (such as cel-
lulose and chitin, but also lactose and N-acetlyllactosamine) The variable LBR-H region defines the substitution that
by pavement of Trp residuesÐhas previously been observed can be accepted on this terminal sugar of the acceptor.
in polysaccharide-binding protein module. Blood group A This loop, together with the C-terminal peptide LBR-I,
and B transferases, which use either aFuc1-2bGal1- undergoes the conformational change that locks the
3GlcNAc (type 1) or aFuc1-2bGal1-4GlcNAc (type 2) nucleotide sugar in the binding site. Those two regions
acceptors, present a PG/S motif in the LBR-D region also make contacts with the pyrophosphate group.
instead of the AW motif characteristic of a3GalT. The variable LBR-D region plays a role in the specificity
for the reducing part of the acceptor.
Role of the nine ligand binding regions Finally, LBR-G only interacts with Fuc or NHAc
The present dissection of the acceptor binding site moiety of the acceptor in GTA, GTB, and Forss-S.
allows researchers to clarify the role of each binding
regions in cation, donor, and acceptor binding. The amino
acids that are predicted to directly interact with the substrate Discussion
Table III. Analysis of the models: hydrogen bonds between the acceptor sugar and the amino acids of the different glycosyltransferases
Table IV. Analysis of the models: amino acids of the different glycosyltransferases that are involved in van der Waals interaction with the acceptor sugar
382
Molecular modeling of a3Gal(NAc)transferases
Fig. 5. Alignments of the nine sequence motifs that are predicted to form the binding site. Residues labeling are as follows: plus sign, interacting with Mn2 ;
open squares, with uridine and ribose; filled diamonds, with pyrophosphate; open circles, with Gal or GalNAc of donor; and filled squares, with
oligosaccharidic acceptor. The amino acids that play a crucial role in specificity have been boxed.
rotation and translation movements of small amplitude C-terminal region interacts with the His78±Ile79 cluster.
that allow it to maximize the number of hydrogen bonds When ordering these two regions in our model of GTA,
in the site. additional contacts are established between the protein and
Our docking of N-acetyllactosamine in the acceptor site the nucleotide-sugar: Lys346 (LBR-H) and Arg252 (LBR-I)
was also done from the a3GalT/UDP complex. Because the of the C-terminal domain make salt bridges to the phos-
crystal structure of the enzyme in complex with LacNAc has phate groups, whereas Val184 (LBR-B) interacts with the
been recently published (Boix et al., 2002), this gives a direct uracil ring. The GalNAc moiety of the nucleotide-sugar
comparison between the model and the crystal structure also presents additional contact with the protein. The orien-
The substitution Gly235Ser is located in the acceptor site crystal structures that have been determined recently, all
(region LBR-D) and may be involved in small differences in of the enzymes for which Mn2 is required for activity
acceptor recognition that have been defined by chemical share the same fold, despite a lack of sequence similarities.
mapping of the acceptors (see later discussion). Arg176Gly In such cases, fold recognition methods are a powerful tool
mutation does not affect the A-specificity but gives an 11- for identifying family of enzymes that can share the same
fold increase in kcat (Seto et al., 1997). This amino acid is fold (Breton et al., 2002). Combination of fold recognition
not involved in the substrate binding but is located at the study and molecular modeling may help in predicting the
surface of the enzyme. Analysis of the surface indicates that acceptor specificities of putative glycosyltransferase
it is located about 8 AÊ from LBR-A, which closes the site sequences from newly determined genomes. This approach
above the nucleotide sugar. Depending on the orientation may be helpful in the emerging area of glycogenomics.
of the Arg176 side chain, it can participate to a basic cluster
with K123 and K124 of LBR-A, two basic amino acids of A
and B transferases at the surface of the binding site. Mod- Materials and methods
ifying this basic cluster could affect the turnover of the
nucleotide-sugar and the catalysis products. Progress in Multiple alignment of amino acid sequences was performed
the understanding of the catalytic mechanism is needed to with the ClustalX program (Thompson et al., 1994) using
explain fully the role of these residues. the following sequences: bovine a3GalT (GenBank acces-
Chemical mapping studies with modified synthetic accep- sion number J04989), canine Forss-S (U66140), human
tors demonstrated a special role for O-4 of the galactose GTA (J05175) and GTB (AF134414), and rat iGb3-S
384
Molecular modeling of a3Gal(NAc)transferases
force field (Clark et al., 1989) in the Sybyl package with Imberty, A., Bettler, E., Karababa, M., Mazeau, K., Petrova, P., and
addition of energy parameters developed for carbohydrates Perez, S. (1999) Building sugars: The sweet part of structural biology.
In Vijayan, M., Yathindra, N., and Kolaskar, A.S. (eds.), Perspectives
(Imberty et al., 1999). in structural biology. Indian Academy of Sciences and Universities
Validation of the models was performed by superimposi- Press, Hyderabad, pp. 392±409.
tion with the crystal structure of GTA and GTB enzymes Keusch, J.J., Manzella, S.M., Nyame, K.A., Cummings, R.D., and
complexed with UDP and disaccharidic acceptor analog Baenziger, J.U. (2000) Expression cloning of a new member of the
(code 1LZI and 1LZJ; Patenaude et al., 2002). ABO blood group glycosyltransferases, iGb3 synthase, that directs
the synthesis of isoglobo-glycosphingolipids. J. Biol. Chem., 275,
25308±25314.
Laskowski, R.A., MacArthur, M.W., Moss, D.S., and Thornton, J.M.
Acknowledgments (1993) PROCHECK: a program to check the stereochemical quality of
protein structures. J. Appl. Crystallogr., 26, 283±291.
H.H. is supported by a grant from the French Ministere des Lowary, T.L. and Hindsgaul, O. (1993) Recognition of synthetic deoxy
Affaires Etrangeres. This research was partially supported and deoxyfluoro analogs of the acceptor alpha-L-Fuc p-(1 ! 2)-beta-
by the Assocation pour la Recherche contre le Cancer. D-Gal p-OR by the blood-group A and B gene-specified glycosyl-
transferases. Carbohydr. Res., 249, 163±195.
Lowary, T.L. and Hindsgaul, O. (1994) Recognition of synthetic
O-methyl, epimeric, and amino analogues of the acceptor alpha-L-
Abbreviations Fuc p-(1 ! 2)-beta-D-Gal p-OR by the blood-group A and B gene-
GT, glycosyltransferase; GTA, blood group A transferase; specified glycosyltransferases. Carbohydr. Res., 251, 33±67.
GTB, blood group B transferase; Forss-S, Forssman Ly, H.D., Lougheed, B., Wakarchuk, W.W., and Withers, S.G. (2002)
385
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