substrate-induced conformational changes in glycosyltransferases

Substrate-induced conformationalchanges in glycosyltransferasesPradman K. Qasba1, Boopathy Ramakrishnan1,2 and Elizabeth Boeggeman1,2

1Structural Glycobiology Section, Laboratory of Experimental and Computational Biology, CCR, NCI-Frederick, MD 21702, USA2Basic Research Program, SAIC-Frederick, Laboratory of Experimental and Computational Biology, CCR, NCI-Frederick,

MD 21702, USA

Oligosaccharide chains of glycoproteins, glycolipids and

glycosaminoglycans are synthesized by glycosyltrans-

ferases by the transfer of specific glycosyl moieties from

activated sugar-nucleotide donors to specific acceptors.

Structural studies on several of these enzymes have

shown that one or two flexible loops at the substrate-

binding site of the enzymes undergo a marked confor-

mational change from an open to a closed conformation

on binding the donor substrate. This conformational

change, in which the loop acts as a lid covering the

bound donor substrate, creates an acceptor-binding

site. After the glycosyl unit is transferred from the

donor to the acceptor, the saccharide product is ejected

and the loop reverts to its native conformation, thereby

releasing the remaining nucleotide moiety. The speci-

ficity of the sugar donor is determined by a few residues

in the sugar-nucleotide-binding pocket of the enzyme

that are conserved among the family members from

different species.

Glycosyltransferases, a superfamily of enzymes, areinvolved in synthesizing the carbohydrate moieties ofglycoproteins, glycolipids and glycosaminoglycans. Thesecarbohydrate components have various specific roles incell growth and cell–cell interactions [1], cell adhesionincluding fertilization [2,3], modulation of growth factorreceptors [4], immune defense [5,6], inflammation [7], andboth viral and parasitic infections [8]. Profound changesoccur in oligosaccharide structures during cellulardevelopment, differentiation and tumorigenesis [9–11],and in many disease states [12,13].

Specific glycosyltransferases synthesize oligosaccharidesby the sequential transfer of the monosaccharide moietyof an activated sugar donor to an acceptor molecule(Figure 1). Many of these enzymes require a metal ioncofactor, generally a Mn2C ion, for activity [14]. Most ofthese enzymes in the eukaryotic cell are anchored in theGolgi compartment as type II membrane proteins. Theyhave a short N-terminal cytoplasmic domain, a mem-brane-spanning region, and a stem and a C-terminalcatalytic domain that face the Golgi lumen [15].

In glycosyltransferase catalysis, the monosaccharideunits glucose (Glc), galactose (Gal), N-acetylglucosamine(GlcNAc), N-acetylgalactosamine (GalNAc), glucuronic

Corresponding author: Qasba, P.K. ([email protected]).Available online 7 December 2004

www.sciencedirect.com 0968-0004/$ - see front matter Q 2004 Elsevier Ltd. All rights reserved

acid (GlcUA), galacturonic acid (GalUA) and xylose areactivated as uridine diphosphate (UDP)-a-D derivatives;arabinose is activated as a UDP-b-L derivative; mannose(Man) and fucose are activated as GDP-a-D and GDP-b-Lderivatives, respectively; and sialic acid (NeuAc) isactivated as a CMP derivative of b-D-NeuAc. Members ofthe glycosyltransferase superfamily, which are oftennamed after the sugar moiety that they transfer, aredivided into subfamilies on the basis of linkage that isgenerated between the donor and acceptor. Transfer ofthe sugar residue occurs with either the retention(by retaining glycosyltransferases) or the inversion(by inverting glycosyltransferases) of the configurationat the anomeric C1 atom (Figure 1).

Since the cloning of the first glycosyltransferase,b1,4-galactosyltransferase (Gal-T) [16,17], several mem-bers of this superfamily and their subfamilies have beencloned [18–22]. In the Gal-T family, for example, sub-families of inverting Gal-T, including b1–4-Gal-T (b4Gal-T)and b1–3-Gal-T (b3Gal-T), and retaining Gal-T, such asa1–3-Gal-T (a3-Gal-T) and a1–4-Gal-T (a4Gal-T), havebeen identified [23,24].All of these enzymesuseUDP-a-D-Galas the donor but generate b1–4, b1–3, a1–3 anda1–4 linkages, respectively (Figure 1). Cloning hasshown sequence homology among the members of eachsubfamily, although no sequence similarity is apparentbetween the subfamilies. Each subfamily member isexpressed in a tissue-specific manner. New glycosyltrans-ferases continue to be identified that have slightly differingsubstrate specificities from those of the known enzymes andthat can be used to synthesize an increasing variety ofoligosaccharides.Alackof,oralterationin,theactivityofsomeof these enzymes has been associated with disease [25,26].

The reaction catalyzed by these enzymes follows akinetic mechanism in which the metal ion and sugar-nucleotide bind to the enzyme first, followed by theacceptor (Figure 2) [27–29]. After the glycosyl moiety ofthe sugar-nucleotide donor is transferred to the acceptorwith the inversion or retention of the C1 configuration(Figure 1), the saccharide product is ejected. The releaseof the nucleotide and the metal ion follows, which returnsthe enzyme to its original state for a new round ofcatalysis.

X-ray crystal structures of the catalytic domain of manyglycosyltransferases, either free or bound to substrates,have been determined recently (Figure 3a,b). These

Review TRENDS in Biochemical Sciences Vol.30 No.1 January 2005

. doi:10.1016/j.tibs.2004.11.005

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Figure 1. The catalytic reaction of the Gal-T family. Enzymes of this family transfer galactose from the same activated sugar donor, UDP-a-D-galactose, to different acceptors,

generating a disaccharide unit with a specific glycosidic linkage between galactose and one of the hydroxyl groups of the acceptor. The configuration at the anomeric C1

carbon of the transferred galactose is either inverted (b) by an ‘inverting’ Gal-T enzyme or retained (a) by a ‘retaining’ Gal-T enzyme.


studies provide a structural basis for the ordered bindingof the donor and acceptor and for the proposed catalyticmechanism of these enzymes [30–34]. In this review, wediscuss the common features that emerge from thesestructural studies of sugar-nucleotide-dependent glycosyl-transferases, focusing on binding of the metal ion, therequired conformational change in a flexible loop afterbinding of the sugar-nucleotide donor, and the reorganiz-ation of the acceptor-binding site. We also describe themechanisms involved in inversion or retention of theconfiguration at the anomeric C1 atom of the transferredsugar.

Structural features of glycosyltransferases

Overall fold

Despite their significant sequence diversity, glycosyltrans-ferases show great structural similarity (Figure 3a,b) [35].

E

(m) (N-S) (A)

E–m (E–m–N–S) (E*–m–N–S)

(Em

[E inopenconf. (I)]

[E* inclosedconf.(II)]

Figure 2. Catalyticmechanismof glycosyltransferases. The catalytic reaction follows a seq

to the enzyme (E) first, followed by the sugar-nucleotide donor (N-S). Once the metal i

covers the sugar-nucleotide donor and creates a binding site for an acceptor (A). After ca

the acceptor, the product (S-A) is ejected. Release of the product is followed by a reversa

(m-N) is ejected. The enzyme can then enter a new cycle of catalysis.

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They are all globular proteins with two types of fold,termed GT-A and GT-B, which each have an N-terminaland a C-terminal domain [36].

The enzymes of the GT-A fold have two dissimilardomains. The N-terminal domain, which recognizes thesugar-nucleotide donor, comprises several b-strands thatare each flanked by a-helices as in a Rossmann-like fold,whereas the C-terminal domain, which contains theacceptor-binding site, consists largely of mixed b-sheets.By contrast, enzymes with the GT-B fold contain twosimilar Rossmann-like folds, with the N-terminal domainproviding the acceptor-binding site and the C-terminaldomain providing the donor-binding site. In both types ofenzyme, the two domains are connected by a linker regionand the active site is located between the two domains. Ametal-binding site is also located in the cleft in enzymes ofboth the GT-B and GT-A fold.

Ti BS

E

S-A m-N

*––N–S–A)

(E*–m–N–S–A)*

(E*–m–N)

uential orderedmechanism, in which ametal ion (m), if required for catalysis, binds

on and sugar-nucleotide have bound, a conformational change in the enzyme (E*)

talysis, in which the sugar moiety (S) of the sugar-nucleotide donor is transferred to

l of the enzyme conformation (E* to E), during which the metal-nucleotide complex


Retaining

Kre2p/Mnt1p

BGT

Inverting

MurG

GtfB

SpsA

CstII

LgtC

Blood group A/B-T

EXTL2

Retaining

α3GT

GnT I

GlcAT-P

Inverting

β4Gal-T1

Mammalian GT Microbial and bacteriophage GT

GlcAT-I

(a) (b)

Figure 3. Ribbon diagram of the overall structures of glycosyltransferases (GTs). Structures were drawn with MOLSCRIPT [70]. The flexible loop regions are shown either in

blue (where these regions of the structures have been traced) or in yellow (where they have not been traced and were generated by the program LOOK, V3.5, Molecular

Application Group). The bound substrates are shown in ball-and-stick notation. Metal ions are shown as gray spheres. In the BGT structure, bound DNA is shown as a red

ribbon. (a) Mammalian inverting and retaining glycosyltransferases. Shown are the inverting enzymes b4Gal-T1 (b-1,4-galactosyltransferase-1; Protein Data Bank accession

code 1O0R), which is responsible for the galactosylation of glycoproteins and glycolipids; GnT I (b-1,2-N-acetylglucosaminyltransferase; 1FOA), which is involved in

the biosynthetic pathway of N-linked oligosaccharides from the oligomannose core structure; and GlcAT-I (b-1,3-glucuronyltransferase I; 1FGG) and GlcAT-P

(b-1,3-glucuronyltransferase P; 1V84), which are involved in synthesis of the common carbohydrate linker regions of glycosaminoglycans and the HNK-1 carbohydrate

epitope, respectively. Also shown are the retaining enzymes EXTL2 (a-1–4-N-acetylhexosaminyl-transferase; 1ON8), which is involved in the synthesis of heparin and

heparan sulfate; a3GT (a-1–3-galactosyltransferase; 1GX4), which synthesizes the a-Gal epitope in many mammals, but not in humans, apes or Old World monkeys; and

the blood group B (a-1–3-galactosyltransferase B; 1R80) and A (a-1–3-galactosaminyltransferase A; 1R81) transferases which are involved in the synthesis of AB blood group

antigens. (b) Microbial and bacteriophage inverting and retaining glycosyltransferases. Shown are the inverting enzymes MurG (b-1–4-N-acetylglucosaminyltransferase)

from Escherichia coli (1NLM), which is involved in bacterial peptidoglycan biosynthesis; SpsA (b-1-X-nucleotidyltransferase) from Bacillus subtilis (1QGS), which is

implicated in spore coat formation; GtfB (b-1-X-glucosyltransferase; 1IIR), which is involved in synthesis of the aglycon portion of vancomycin family of antibiotics; CstII

(a-2–3-sialyltransferase; 1RO7) from the human mucosal pathogen Campylobacter jejuni; and BGT (T4 bacteriophage b1-glucosyltransferase; 1IXY), which transfers glucose

to the 5-hydroxymethylcytosine residues in T4 phage DNA. Also shown are the retaining enzymes LgtC (a-1–4-galactosyltransferase) fromNeisseria meningitidis (1G9R) and

Kre2p or Mnt1p (a-1–2-mannosyltransferase; 1S4P) from Saccharomyces cerevisiae.

Review TRENDS in Biochemical Sciences Vol.30 No.1 January 2005 55

The crystal structure of the bacteriophage T4 b-gluco-syltransferase (BGT), which transfers glucose fromUDP-Glc to 5-hydroxylmethylcytosine bases of phage T4DNA, was the first structure of a sugar-nucleotide-dependent glycosyltransferase to be determined [37],and was shown to have a fold similar to that of glycogenphosphorylase [30,37].

Motifs and metal ion coordination in GT-A type enzymes

A three-residue motif, Asp-X-Asp (DXD) or Glu-X-Asp(EXD), or its equivalent (see below), generally participatesin metal ion binding in enzymes of the GT-A fold (Table 1),although sialyltransferases such as a-2–3-sialyltransferaseCstII [38], a GT-A enzyme, do not require a metal ion


cofactor and lack a DXD motif. Enzymes of the GT-B foldsuch as the microbial glycosyltransferases MurG [39] andGtfB [40], and BGT [37], do not have a DXD motif or itsequivalent (Table 1), even though some, BGT for example,require a metal ion for activity.

In glycosyltransferases that require Mn2C ion ascofactor, the metal ion is bound in an octahedralcoordination (Figure 4). It interacts with one or bothacidic residues of the DXD or EXDmotif (Table 1) and withtwo oxygen atoms from the a-phosphate and b-phosphateof UDP. To satisfy the octahedral geometry, the threeremaining metal ion links are made either to watermolecules or to water in combination with other residuesof the protein. In several glycosyltransferases (Table 1 and


Table 1. Metal-binding motif and the flexible region in the glycosyltransferase structures

Glycosyltransferasea Protein fold Metal-binding

motif

Interactions of the acidic residues of

the motif

Residues of the

flexible region

Refs

First Second

Mammalian inverting type

b4Gal-T1 A DXD Water–metal Metal 313–316, 345–365 [42–44]

GnT I A EXD Water–metal Metal 318–330 [45]

GlcAT-I A DXD Water–metal Metal 140–152 [46–47]

GlcAT-P A DXD Water–metal Metal 150–162 [48]

Mammalian retaining type

EXTL2 A DXD Water–metal Metal 277–281 [50]

a3GT A DXD Metal Metal 358–368 [52–54]

Blood group A and B

transferases

A DXD Metal Metal 179–194 [51]

Microbial and bacteriophage inverting type

SpsA A DXD Metal Metal 134–136, 218–231 [49]

CstII (metal ion not

required)

A None – – 155–188 [38]

BGT B None – – – [37]

MurG B None – – – [39]

GtfB B None – – – [40]

Microbial retaining type

LgtC A None – – 75–80, 246–251 [56]

Kre2p/Mnt1p A EXD Metal – – [41]aEnzyme abbreviations: BGT, T4 bacteriophage b1-glucosyltransferase; blood group B and A transferases, CstII, a-2–3-sialyltransferase; a-1–3-galactosyltransferase B

and a-1–3-galactosaminyltransferase A, respectively; EXTL2, a-1–4-N-acetylhexosaminyl-transferase; b4Gal-T1, b-1,4-galactosyltransferase-1; GlcAT-I, b-1,3-glucuronyl-

transferase I; GlcAT-P, b-1,3-glucuronyltransferase; GnT I, b-1,2-N-acetylglucosaminyltransferase; a3GT, a-1–3-galactosyltransferase; GtfB, b-1-X-glucosyltransferase;

Kre2p or Mnt1p, a-1–2-mannosyltransferase; LgtC, a-1–4-galactosyltransferase; MurG, b-1–4-N-acetylglucosaminyltransferase; SpsA, b-1-X-nucleotidyltransferase.


Figure 3a,b), only the first [41] or the second [42–50] acidicresidue of the motif coordinates directly with the metalion. In some enzymes, the first acidic residue of the motifeither interacts directly with the sugar donor or the ribosemoiety or interacts via the water molecules coordinated tothe Mn2C ion. In blood group A and B and a3GTtransferases (Table 1 and Figure 3a), by contrast, bothaspartic acid residues of the DXDmotif directly coordinatethe metal ion [51–54].

Open and closed conformations of the flexible loop

The crystal structures of several glycosyltransferases ofeither the GT-A or GT-B fold show that at least oneflexible loop region has a crucial role in the catalyticmechanism of the enzyme (Figure 3a,b). Although theexact location of this loop differs among the transferases,it is invariably located in the vicinity of the sugar-nucleotide-binding site. Owing to the flexibility of thisregion, the loop structure cannot be traced in the apoform of the enzyme, which lacks bound substrate. In thesugar-nucleotide-bound structures, the loop either is ina closed conformation covering the bound donor sub-strate or is found disordered in the vicinity of the sugar-nucleotide-binding site.

Only in b4Gal-T1 have most of the residues in twoflexible loop regions – a short loop (residues 313–316) anda long loop (residues 345–365) – been traced in both theabsence and the presence of substrate (Figure 4) [42,55].In the apo structure, the active-site residues in the loopsare located away from the catalytic site (open confor-mation; Figure 4). In the a-1–4-Gal-T LgtC (Table 1), thetwo loops from opposite sides fold over the bound substrateUDP-2FGal [56]. By contrast, in the inverting glycosyl-transferases GnT I [45] and a-2–3-sialyltransferase CstII(Table 1) [38], the loops can be traced only in the complexwith bound donor substrate.


In each enzyme structure, the loop acts as a lid coveringthe bound sugar-nucleotide. In the inverting b-1,3-glucur-onyltransferases GlcAT-I [46] and GlcAT-P [48], themicrobial inverting glycosyltransferase SpsA [49], andthe retaining glycosyltransferases EXTL2 [50] and bloodgroup transferases A and B [51], the loops cannot be tracedeven in the donor-bound structures, although in eachstructure the loop lies near the sugar-nucleotide-bindingsite (Table 1 and Figure 3a,b). In another retainingglycosyltransferase, a3GT, the C-terminal 11-residueflexible loop changes its conformation when the sugar-nucleotide donor is bound [53].

Metal ion and sugar-nucleotide binding creates the

catalytic site

Metal ion binding

The active site of the enzyme is created by an orderedbinding of metal ion and sugar-nucleotide, followed by aconformational change that creates the acceptor-bindingsite (Figures 2,4,5). In b4Gal-T1, the metal ion binds to theapo form of the enzyme when both of the flexible loops arein an open conformation and located away from thecatalytic site (Figures 4,5) [34,42,57,58]. The metal ioninteracts with two residues, Met344 and Asp254 of theD252XD254 motif, and with four water molecules to form anoctahedral coordination [34,58]. The flexibility of theresidues close to the N terminus of the hinge region ofthe long loop in the open conformation is dampened bymetal ion binding [34,58]. In GnT I, the metal ion alsobinds near the N terminus of the flexible loop [45].

Sugar-nucleotide binding induces the change in the

flexible loop

UDP-Gal, in an unusual folded conformation, binds to themetal-bound form of b4Gal-T1 while the loop is still in theopen conformation (Figures 4–6) [44]. Two oxygen atoms,


Figure 4. Open and substrate-bound closed conformations of b4Gal-T. In the apo

form of the enzyme, the flexible loop (residues 345–365) in b4Gal-T is in an open

conformation (yellow). In the complex with UDP-a-D-Gal (UDP-Gal) and Mn2C, the

loop is in a closed conformation (green) and covers the sugar-nucleotide. TheMn2C

ion binds at the N-terminal region of the flexible loop through the repositioning and

coordination of His347 in the loop. Two other residues, Met344 and Asp254 of the

D252XD254 motif, coordinate the Mn2C ion. Two oxygen atoms, one from each

phosphate of UDP, coordinate and tether the Mn2C ion. By interacting with one

water molecule, Mn2C satisfies its octahedral coordination. The bound UDP-Gal

substrate adopts a conformation in which the phosphates (yellow) are perpen-

dicular to the plane of galactose. Trp314, which lies in a short flexible loop (residues

313–316) in the closed conformation, faces the binding pocket and holds the

UDP-Gal substrate in position by forming a hydrogen bond between its N3 atom

and the b-phosphate oxygen of UDP. Trp314 also makes hydrophobic interactions

with the hydrophobic face of the donor galactose and also with the acceptor

GlcNAc. The change in the flexible loop from an open to closed conformation

generates an a-helix from the random coil structure at the C terminus (residues

359–365) and the binding site for the acceptor chitobiose (GlcNAcb1-4GlcNAc). The

residues Arg359, Phe360 and Ile363 form a hydrophobic pocket that interacts with

the N-acetyl group of GlcNAc at the nonreducing end of the acceptor chitobiose.

The O4 atom of GlcNAc is positioned close to the C1 atom of the galactose for

nucleophilic attack. The closed conformation was generated from the structures of

the b4Gal-T–UDP-Gal–Mn2C complex (1O0R) and the b4Gal-T–UDP-hexanolamine–

Mn2C–chitobiose complex (1TW5); the open conformation was generated from the

structure of b4Gal-T (1FGX). The molecular surface of the protein is colored on the

basis of charge, where red indicates negative and blue indicates positive charge.

This figure was generated using GRASP [71].


one from the a-phosphate and one from the b-phosphate ofUPD, replace two of the four water molecules that arecoordinated to the metal ion [34,58]. This replacementinduces changes in the conformation of the flexible loops,which restructure the binding site. His347 at the hingeregion of the flexible loop repositions itself (Figure 4) andreplaces the third bound water molecule to coordinatewith the Mn2C ion [34,58], which thereby retains itsoctahedral coordination. The conformation of the smallflexible loop also changes such that the side chain ofTrp314 is oriented towards, and makes interactions with,the sugar-nucleotide. The residues from the long loopregion interact with uridine, the diphosphate and thesugar moiety of the sugar-nucleotide, covering them andreducing the accessibility of the site to the solvent. At thesame time, the acceptor-binding site becomes moreaccessible to solvent. Thus, an ordered binding of thedonor and acceptor substrates is ensured.

The distorted conformation of the bound sugar donorUDP-Gal in b4Gal-T1 is also observed in the sugar-nucleotide complexes of GlcAT-I (Figure 6) [47], GlcAT-P[48], EXTL2 [50], blood group A and B transferases [51],


a3GT [54], LgtC [56] and CstII [38]. In this conformation,the diphosphate of UDP is perpendicular to the planeof the sugar donor. The two oxygen atoms from the a- andb-phosphates remain tethered to the metal ion. In GnT I,by contrast, UDP-GlcNAc binds in an extended confor-mation [45]. The hydroxyl side chain of Thr315 and thecarbonyl of Gly317 – amino acids that are located atthe N-terminal hinge region of the 13-residue flexible loop– reorient to form hydrogen bonds with the watermolecules coordinating the metal ion.

Regardless of whether its conformation is folded orextended, the sugar donor moiety is buried deep in thecatalytic pocket of the respective enzymes with itsanomeric C1 atom available for nucleophilic attack(Figures 4 and 6). The hydroxyl groups of the sugardonor form hydrogen bonds with protein residues and thehydrophobic face of the sugar moiety stacks againstaromatic residues, namely, phenylalanine, tryptophanand tyrosine. Thus, the donor sugar and the uridine ringare held in position by several hydrogen bonds and bystacking interactions with specific protein residues, someof which belong to the flexible loop (Figure 4) [43–45,53].

The nature of the interactions of the sugar moiety ofthe donor also determines the conformational change inthe flexible loop. In b4Gal-T1, for example, less-preferredsugar-nucleotide substrates such as UDP-Glc and UDP-GalNAc, which do not make the same interactions asUDP-Gal, dissociate from the sugar-nucleotide enzymecomplex. It seems that the flexible loops do not efficientlychange to the closed conformation needed for efficientcatalysis [59,60].

Additional roles of the metal ion

In addition to its role in inducing the conformationalchange in the flexible loop, the metal ion participates information and stabilization of the transition state complexduring catalysis in b4Gal-T1 [57]. The metal ion interactsnot only with the aspartic acid residues of the DXD motif,but also with other residues of the protein, namelyMet344, that have a vital role in catalysis.

When Met344 is replaced with histidine, for example,the mutant still binds a Mn2C ion and causes theUDP-Gal-induced conformational change in the flexibleloop. No catalysis occurs, however, because the enzymeforms an abortive complex in which the flexible loop failsto return to the open conformation [57]. Notably, thismutant can bind an Mg2C ion and undergo the confor-mational change, and catalysis does occur because the loopreverts to the open conformation [57]. At position 344in b4Gal-T1, therefore, either a methionine residue incombination with a Mn2C ion or a histidine residue incombination with a Mg2C ion performs two functions: itinduces a conformational change in the flexible loop and itaids in formation and stabilization of the transition statecomplex, thereby resulting in efficient catalysis.

Creation of the oligosaccharide acceptor-binding site

Inmany enzymes, the conformational change in the flexibleloop generates a helical structure in the C-terminal region(Figure 4) [43–45,53]. In b4Gal-T1, the C terminus of theflexible loop (residues 359–365) generates an a-helix from


Ti BS

M

A

MN

S–NS–A

(ii)

(iii)(iv)

(i)

(v)

Figure 5. The catalytic cycle of metal-ion-dependent glycosyltransferases. (i) The

enzyme is shown as a two-domain protein in an open conformationwith the flexible

loop (light blue ribbon) as a random coil. (ii) The metal ion (M) binds to the enzyme

in the open conformation. (iii) The sugar-nucleotide (S-N) binds to the metal–

enzyme complex and the loop changes its conformation (dark blue ribbon), creating

a lid-like structure that covers the buried sugar-nucleotide. A helical structure is

formed at the C-terminal region of the loop that becomes part of the acceptor-

binding site. (iv) The acceptor is held in the acceptor-binding site with its

nonreducing end close to the sugar moiety of the donor, while rest of the molecule

is exposed to the solvent. (v) After catalysis, during which the sugar from the sugar-

nucleotide is transferred to the acceptor, the product (S-A) is ejected from the

binding site, while the UDP–metal complex remains buried under the loop. (i) The

loop reverts to the open conformation, facilitating release of the UDP–metal

complex and enabling the free enzyme to start a new catalytic cycle.

Figure 6. A single amino acid determines sugar donor specificity. (a) Tyr289 in bovine b4G

UDP-Gal sugar donor. UDP-GalNAc is a poor substrate for b4Gal-T. The hydroxyl of Tyr28

a molecular brake, restricting its transfer to the acceptor GlcNAc. Mutation of Tyr289 t

Tyr289Leu can transfer GalNAc from UDP-GalNAc as efficiently as the wild-type enzyme

b4Gal-T in complex with UDP-GalNAc–Mn2C (1OQM) was made possible by co-crystal

superposition of the GlcNAcmoiety from the b4Gal-T–GlcNAc–LA complex (1NQI). (b) In

bonds with the 2-hydroxyl of GlcUA of the donor sugar-nucleotide UDP-GlcUA and deter

at the nonreducing end of the acceptor Galb1-3Gal (from the PDB file 1FGG) is positione

mutated to arginine, the mutant GlcAT-I enzyme, in contrast to the wild-type enzyme, ca

high efficiency. TheMn2C ion in (a), although it has octahedral geometry, is shown coordi

molecular surfaces of the proteins are colored on the basis of charge, where red indic

GRASP [71].



the random coil structure that becomes part of theextended oligosaccharide acceptor-binding site of theenzyme [43,44]. Residues Arg359, Phe360 and Ile363 inthe helical region of the C terminus form a hydrophobicpocket, which facilitates binding of the N-acetyl group ofGlcNAc [34,43]. This extended binding site is also part of abinding site for a-lactalbumin (a-LA), a lactating mam-mary-gland-specific protein that alters the acceptorspecificity of the enzyme from GlcNAc to glucose, therebyenabling the synthesis of milk lactose [61]. a-LA interactswith the extended sugar-binding site and brings glucoseinto the monosaccharide-binding pocket. The side chainsof residues 359–365 in the helical region adjust to makemaximum contacts with glucose [43,62], thus makingglucose the preferred acceptor by decreasing its Michaelisconstant (Km) by a thousand-fold.

In GnT I, another inverting mammalian enzyme, theloop (residues 318–330) forms a flap that partially coversthe UDP-GlcNAc substrate [45]. As in b4Gal-T1, theC-terminal region (residues 324–330) makes one completeturn of an a-helix, whereas residues 320–323 form a typeIV b-turn. Central to this loop structuring is the side chainof Val321 at the tip of the loop, which interacts with anapolar pocket. Phe327, which is located in the loop helix,lies buried against Arg318 of the loop and the non-loopresidues Thr315, Leu331 and Lys332. The two loopresidues Ser322 and Phe326 are also present in thedeep acceptor pocket [45]. In the inverting enzymea-2–3-sialyltransferase CstII, the lid-like structure isformed by residues 175–187, which fold over the activesite and cover the intact CMP-NeuAc substrate [38],whereas in the inverting microbial glycosyltransferase

al-T (or Tyr286 in human b4Gal-T) determines the specificity of the enzyme towards

9 interacts with theN-acetyl group of the GalNAcmoiety of UDP-GalNAc and acts as

o leucine, isoleucine or asparagines relieves this steric hindrance, and the mutant

can transfer galactose from UDP-Gal to GlcNAc. Determination of the structure of

lizing the complex with a-LA. The GlcNAc residue in the picture was generated by

the crystal structure of GlcAT-I–UDP-GlcUA–Mn2C (1KWS), N32 of His308 hydrogen

mines the specificity of GlcAT-1 towards the sugar donor. The O3 atom of galactose

d close to the C1 atom of the GlcUA moiety for nucleophilic attack. When His308 is

n transfer mannose, glucose and GlcNAc from their respective UDP derivatives with

nating to only two oxygen atoms of UDP, one each from the a- and b-phosphate. The

ates negative and blue indicates positive charge. This figure was generated using



SpsA the nucleotide in the UDP–Mn2C complex seems tobe buried under the loop [49].

In the retainingmammalianGal-T a3GT, theC-terminalloop residues (358–368) adopt a highly ordered structureon binding UDP-Gal, in which residues 361–364 form adefinite a-helical structure and residues 354–356 make ashort b-strand [53]. This change is associated with anincrease in therigidityofall of theresidues in this regionandthe formation of hydrogen bonds between the phosphates ofUDP and residues Lys359, Tyr361 and Arg365. The lastresidue interacts directlywith thehydroxyl groupofTyr139,which in turn interacts with the a-phosphate of UDP andmakes stacking interactions against the uracil ring. Mutat-ing either one of these residues disrupts the catalyticfunction of the enzyme [63,64].

Acceptor substrate binding

In disaccharide- or trisaccharide-bound complexes of theinverting glycosyltransferases b4Gal-T1, GlcAT-I andGlcAT-P and the retaining glycosyltransferases EXTL2and a3GT, the non-reducing end of the acceptor is burieddeep in the cleft, close to the donor sugar (Figure 6), and issurrounded mostly by aromatic residues, specificallytryptophan, of the protein. Because the acceptor-bindingsite is largely solvent accessible, the hydroxyl groups ofthe pyranose rings of each monosaccharide unit makehydrogen-bond interactions with water molecules andwith the side chains of polar residues such as asparticacid, glutamic acid, arginine and/or tyrosine. At the cata-lytic center, a tryptophan residue – Trp314 in b4Gal-T1[43,55], Trp284 in EXTL2 [50] or Trp314 in a3GT [63] –generally makes stacking interactions with the hydro-phobic face of both the acceptor and the donor sugars. Theaspartic or glutamic acid residues form hydrogen bondswith the attacking hydroxyl group of the monosaccharideunit at the nonreducing end, rendering it a nucleophile.

The second monosaccharide residue of the di- ortrisaccharide in the accepter-binding pocket makes non-bonded interactions with phenylalanine, tryptophan ortyrosine residues and bonded interactions with the polarresidues. The third monosaccharide unit of the trisacchar-ide in complexes of GlcAT-I and GlcAT-P are not visible inthe crystal structures, which suggests that the bindingsite cannot accommodate more than a disaccharide unit.In b4Gal-T1, however, the acceptor-binding site is pre-dicted to be longer [44] and has been recently shown toaccommodate trisaccharides that are part of N-glycanstructures [65].

A single amino acid change alters the donor specificity

Interactions between the sugar-nucleotide donor and afew protein residues seem to determine the specificity ofthe glycosyltransferases for their donor substrate. Forexample, a highly conserved tyrosine residue in b4Gal-Tsubfamily members (Tyr289 in bovine b4Gal-T), deter-mines enzyme specificity towards the galactose moiety ofthe sugar donor (Figure 6a) [60]. It restricts transfer of theGalNAc moiety from UDP-GalNAc by forming a hydrogenbond with its N-acetyl group. Mutation of Tyr289 toleucine, isoleucine or asparagine, however, makes the


enzyme equally efficient as a galactose or GalNActransferase [60].

In GlcAT-I, the N32 nitrogen of His308 (His311 inGlcAT-P) forms a hydrogen bond with the 2-hydroxyl ofGlcUA (Figure 6b) [47,48], which determines enzymespecificity towards UDP-GlcUA as the sugar donor.Substitution of His308 with arginine in GlcAT-I enablesthe enzyme to use efficiently UDP-Glc, UDP-Man orUDP-GlcNAc as the donor substrates [66]. Met266 andAla268 in the blood group B Gal-T, and Leu266 andGly268 in the blood group A GalNAc transferase deter-mine specificity towards their respective sugar donors,UDP-Gal and UDP-GalNAc [67].

In a3Gal-T, His280 interacts with the 2-hydroxyl of thegalactose moiety, setting its orientation suitable forcatalysis and thereby determining the donor specificity[63]. Mutation of His280 does not alter the specificity ofthe enzyme, however, although its activity is reduced [63].Spontaneous mutation of a residue that confers donorspecificity to a residue that broadens it, such as tyrosine toisoleucine in b4Gal-T1 or histidine to arginine in GlcAT-I,will result in cellular glycans with altered sugar residuesand could have significant effects on normal cellularprocesses.

Catalytic mechanisms of inverting and retaining

glycosyltransferases

Although the catalytic mechanisms of both inverting andretaining glycosyltransferases have been proposed, onlythe mechanism of the inverting glycosyltransferases iswell characterized. Crystal structures of donor–acceptorcomplexes of the inverting glycosyltransferases b4Gal-T1,GnT I and GlcAT-I have provided evidence for theorientation of donor and acceptor in the catalytic pockets(Figure 6) [43–45,47]. In these enzymes, part of the donoris covered and protected from solvent by the flexible loop,while the nonreducing monosaccharide unit of theoligosaccharide acceptor is held in a position close to thesugar donor by interactions with protein residues, somebelonging to the flexible loop. The rest of the oligo-saccharide is exposed to solvent.

The acceptor hydroxyl group is positioned at a distanceof 3 A to the C1 atom of the sugar donor (Figure 6). Aglutamic or aspartic acid residue of the protein that iswithin the hydrogen-bonding distance deprotonates thehydroxyl group of the acceptor, which then acts as acatalytic base and makes a nucleophilic attack on the C1atom of the sugar donor. The Mn2C ion helps the UDPgroup to leave by neutralizing the negative charge thatdevelops on the b-phosphate. The C1 atom of the sugardonor forms an oxocarbenium-ion-like transition state,leading to the formation of a glycosidic bond between theacceptor and sugar donor with inversion of the configur-ation at C1, consistent with the SN2-type displacementreaction mechanism.

This transition state has been recently trapped inb4Gal-T1 during transfer of the GalNAc sugar fromUDP-GalNAc to glucose in the presence of a-LA [58]. Afterthe glycosidic bond is formed, the oligosaccharide productis ejected from the binding site (Figure 5) while theUDP–Mn2C complex still lies buried under a part of the



flexible loop. Owing to a lack of interactions with the sugarmoiety, the loop reverts to a completely open conformation,enabling the UDP–Mn2C nucleotide complex to diffuse outof the enzyme (Figure 5).

By contrast, the mechanism used by the retainingglycosyltransferases is not yet settled. A double displace-ment mechanism has been proposed [52] in which thedonor sugar is first transferred to a suitable group on theprotein with an inversion of the configuration at C1, and isthen transferred to the acceptor with the C1 atomreverting to its original configuration. In the retainingGal-T LgtC, intermediates of the donor sugar and proteinhave been identified that support a double displacementmechanism [56,68]. The crystal structures of EXTL2 [33,50]and a3GT [54] with bound sugar donors or UDP andacceptors, however, do not support a double displacementmechanism. On the basis of the structural evidence forthese enzymes, a substitution nucleophilic internal(SNi)-like mechanism has been proposed in which theacceptor attaches on the same side that the sugar groupleaves the donor.

Concluding remarks

The structures of nine inverting and five retainingglycosyltransferases show that these enzymes are mono-meric proteins that have either one of two types of fold.Glycosyltransferases of the GT-A fold have an N-terminalnucleotide-binding domain with a Rossmann-type fold anda DXD motif if they are metal ion dependent. By contrast,glycosyltransferases of the GT-B fold have two domainswith a Rossmann-type fold: the N-terminal domain is theacceptor-binding domain, whereas the C-terminal domainbinds the sugar-nucleotide donor.

Enzymes of both folds have a loop region that plays animportant part in the catalytic mechanism. On binding ofthe metal ion (in the enzymes that require it) and thesugar donor to the enzyme, the loop restructures andmoves effectively to act as a lid covering the buried sugardonor (Figures 4,5). Thus, this conformational changein loop structure depends on the ability of the sugardonor and the metal ion (in the metal-ion-dependentenzymes) to create, or to reorganize, a region in theenzyme for binding the acceptor. This offers a structuralbasis for the ordered binding of the donor and acceptor tothe enzyme [30,31,34,54]. Specificity towards the sugardonor is generally determined by a few crucial residues inthe binding pocket, because mutation of these residuesbroadens the donor specificity.

During catalysis by the inverting enzymes, the C1anomeric carbon atom of the sugar donor is attacked bythe deprotonated hydroxyl group of the acceptor, resultingin the formation of a glycosidic bond between the sugardonor and acceptor and inversion of the configuration atC1. During catalysis by the retaining glycosyltrans-ferases, the acceptor either attacks from the same sideas the donor [33] or follows a double displacementmechanism [56,68], resulting in the formation of aglycosidic bond between the sugar donor and acceptorwith retention of the configuration at C1.

The detailed structural information obtained so farhas already facilitated the design of new and novel


glycosyltransferases with broader or requisite donor andacceptor specificities [60,69]. In turn, this has facilitatedthe synthesis of specific complex carbohydrates in additionto aiding the design of specific inhibitors for theseenzymes.

AcknowledgementsWe thank Soma Kumar and Xinhua Ji of the Molecular CrystallographyLaboratory at the National Cancer Institute, and Velavan Ramasamy ofthe Structural Glycobiology Section for critically reading the manuscriptand helpful discussions. The content of this publication does notnecessarily reflect the view or policies of the Department of Healthand Human Services, nor does mention of trade names, commercialproducts or organizations imply endorsement by the US Government.This project has been funded in part by federal funds from the NationalCancer Institute, National Institutes of Health, under contract numberN01-C0–12400.

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