PDBsum entry 1ga8

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Transferase PDB id
Jmol PyMol
Protein chain
278 a.a. *
Waters ×191
* Residue conservation analysis
PDB id:
Name: Transferase
Title: Crystal structure of galacosyltransferase lgtc in complex with donor and acceptor sugar analogs.
Structure: Galactosyl transferase lgtc. Chain: a. Engineered: yes. Mutation: yes
Source: Neisseria meningitidis. Organism_taxid: 487. Gene: lgtc. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
2.00Å     R-factor:   0.189     R-free:   0.226
Authors: K.Persson,H.D.Ly,M.Diekelmann,W.W.Wakarchuk,S.G.Withers, N.C.J.Strynadka
Key ref:
K.Persson et al. (2001). Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs. Nat Struct Biol, 8, 166-175. PubMed id: 11175908 DOI: 10.1038/84168
29-Nov-00     Release date:   14-Feb-01    
Go to PROCHECK summary

Protein chain
Pfam   ArchSchema ?
Q93EK7  (Q93EK7_NEIME) -  LgtC
311 a.a.
278 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class: E.C.  - Lipopolysaccharide 3-alpha-galactosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: UDP-alpha-D-galactose + [lipopolysaccharide] = UDP + 3-alpha-D- galactosyl-[lipopolysaccharide]
+ [lipopolysaccharide]
Bound ligand (Het Group name = UPF)
matches with 69.44% similarity
+ 3-alpha-D- galactosyl-[lipopolysaccharide]
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biochemical function     transferase activity, transferring glycosyl groups     2 terms  


    Key reference    
DOI no: 10.1038/84168 Nat Struct Biol 8:166-175 (2001)
PubMed id: 11175908  
Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs.
K.Persson, H.D.Ly, M.Dieckelmann, W.W.Wakarchuk, S.G.Withers, N.C.Strynadka.
Many bacterial pathogens express lipooligosaccharides that mimic human cell surface glycoconjugates, enabling them to attach to host receptors and to evade the immune response. In Neisseria meningitidis, the galactosyltransferase LgtC catalyzes a key step in the biosynthesis of lipooligosaccharide structure by transferring alpha-d-galactose from UDP-galactose to a terminal lactose. The product retains the configuration of the donor sugar glycosidic bond; LgtC is thus a retaining glycosyltranferase. We report the 2 A crystal structures of the complex of LgtC with manganese and UDP 2-deoxy-2-fluoro-galactose (a donor sugar analog) in the presence and absence of the acceptor sugar analog 4'-deoxylactose. The structures, together with results from site-directed mutagenesis and kinetic analysis, give valuable insights into the unique catalytic mechanism and, as the first structure of a glycosyltransferase in complex with both the donor and acceptor sugars, provide a starting point for inhibitor design.
  Selected figure(s)  
Figure 1.
Figure 1. Glycosyl transfer reactions. a, The LgtC catalyzed transfer of galactose from UDP-Gal to the LPS core oligosaccharide of Neisseria. b, Proposed catalytic mechanism of inverting -galactosyltransferases. c, Proposed catalytic mechanism of retaining -galactosyltransferases.
Figure 4.
Figure 4. The active site. a, The donor sugar UDP-Gal and the acceptor sugar lactose are shown, in stereo, as ball-and-stick models (with red and green sticks, respectively) in a refined 2F[o] - F[c] map contoured at 1.2 . Amino acids interacting with the substrates are labeled. The loops that fold over the active site (residues 75 -80 and 246 -251) are colored green. b, Molecular surface representation of the active site. UDP-Gal and 4'-deoxylactose are shown in ball-and-stick form. UDP-Gal is almost completely buried in the enzyme while 4'-deoxylactose is bound in an open pocket that is more accessible to solvent. c, Stereo view of the hydrogen bonding network of Gln 189 and the distance and angle to the anomeric carbon C1'. Distances are in .
  The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Biol (2001, 8, 166-175) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21267505 K.Descroix, and G.K.Wagner (2011).
The first C-glycosidic analogue of a novel galactosyltransferase inhibitor.
  Org Biomol Chem, 9, 1855-1863.  
21098513 N.Soya, Y.Fang, M.M.Palcic, and J.S.Klassen (2011).
Trapping and characterization of covalent intermediates of mutant retaining glycosyltransferases.
  Glycobiology, 21, 547-552.  
20655926 B.Schuman, M.Persson, R.C.Landry, R.Polakowski, J.T.Weadge, N.O.Seto, S.N.Borisova, M.M.Palcic, and S.V.Evans (2010).
Cysteine-to-serine mutants dramatically reorder the active site of human ABO(H) blood group B glycosyltransferase without affecting activity: structural insights into cooperative substrate binding.
  J Mol Biol, 402, 399-411.
PDB codes: 3i0c 3i0d 3i0e 3i0f 3i0g 3i0h 3i0i 3i0j 3i0k 3i0l
20672277 G.K.Wagner, and T.Pesnot (2010).
Glycosyltransferases and their assays.
  Chembiochem, 11, 1939-1949.  
20030628 R.Hurtado-Guerrero, T.Zusman, S.Pathak, A.F.Ibrahim, S.Shepherd, A.Prescott, G.Segal, and D.M.van Aalten (2010).
Molecular mechanism of elongation factor 1A inhibition by a Legionella pneumophila glycosyltransferase.
  Biochem J, 426, 281-292.
PDB codes: 2wzf 2wzg
20533489 T.Pesnot, M.M.Palcic, and G.K.Wagner (2010).
A novel fluorescent probe for retaining galactosyltransferases.
  Chembiochem, 11, 1392-1398.  
19691080 C.Goedl, and B.Nidetzky (2009).
Sucrose phosphorylase harbouring a redesigned, glycosyltransferase-like active site exhibits retaining glucosyl transfer in the absence of a covalent intermediate.
  Chembiochem, 10, 2333-2337.  
19750531 S.A.Allman, H.H.Jensen, B.Vijayakrishnan, J.A.Garnett, E.Leon, Y.Liu, D.C.Anthony, N.R.Sibson, T.Feizi, S.Matthews, and B.G.Davis (2009).
Potent fluoro-oligosaccharide probes of adhesion in Toxoplasmosis.
  Chembiochem, 10, 2522-2529.  
  18205830 C.Goedl, and B.Nidetzky (2008).
The phosphate site of trehalose phosphorylase from Schizophyllum commune probed by site-directed mutagenesis and chemical rescue studies.
  FEBS J, 275, 903-913.  
  19058170 C.J.Thibodeaux, C.E.Melançon, and H.W.Liu (2008).
Natural-product sugar biosynthesis and enzymatic glycodiversification.
  Angew Chem Int Ed Engl, 47, 9814-9859.  
18627619 C.J.Zea, G.Camci-Unal, and N.L.Pohl (2008).
Thermodynamics of binding of divalent magnesium and manganese to uridine phosphates: implications for diabetes-related hypomagnesaemia and carbohydrate biocatalysis.
  Chem Cent J, 2, 15.  
18192272 J.A.Alfaro, R.B.Zheng, M.Persson, J.A.Letts, R.Polakowski, Y.Bai, S.N.Borisova, N.O.Seto, T.L.Lowary, M.M.Palcic, and S.V.Evans (2008).
ABO(H) blood group A and B glycosyltransferases recognize substrate via specific conformational changes.
  J Biol Chem, 283, 10097-10108.
PDB codes: 2rit 2rix 2riy 2riz 2rj0 2rj1 2rj4 2rj5 2rj6 2rj7 2rj8 2rj9
18518825 L.L.Lairson, B.Henrissat, G.J.Davies, and S.G.Withers (2008).
Glycosyltransferases: structures, functions, and mechanisms.
  Annu Rev Biochem, 77, 521-555.  
18390549 M.W.Vetting, P.A.Frantom, and J.S.Blanchard (2008).
Structural and enzymatic analysis of MshA from Corynebacterium glutamicum: substrate-assisted catalysis.
  J Biol Chem, 283, 15834-15844.
PDB codes: 3c48 3c4q 3c4v
19015727 P.J.Pereira, N.Empadinhas, L.Albuquerque, B.Sá-Moura, M.S.da Costa, and S.Macedo-Ribeiro (2008).
Mycobacterium tuberculosis glucosyl-3-phosphoglycerate synthase: structure of a key enzyme in methylglucose lipopolysaccharide biosynthesis.
  PLoS ONE, 3, e3748.
PDB codes: 3e25 3e26
18394902 T.Jank, and K.Aktories (2008).
Structure and mode of action of clostridial glucosylating toxins: the ABCD model.
  Trends Microbiol, 16, 222-229.  
18667419 Z.Fulton, A.McAlister, M.C.Wilce, R.Brammananth, L.Zaker-Tabrizi, M.A.Perugini, S.P.Bottomley, R.L.Coppel, P.K.Crellin, J.Rossjohn, and T.Beddoe (2008).
Crystal Structure of a UDP-glucose-specific Glycosyltransferase from a Mycobacterium Species.
  J Biol Chem, 283, 27881-27890.
PDB codes: 3ckj 3ckn 3cko 3ckq 3ckv
17850816 A.L.Milac, N.V.Buchete, T.A.Fritz, G.Hummer, and L.A.Tabak (2007).
Substrate-induced conformational changes and dynamics of UDP-N-acetylgalactosamine:polypeptide N-acetylgalactosaminyltransferase-2.
  J Mol Biol, 373, 439-451.  
17465952 B.Hosseini-Maaf, J.A.Letts, M.Persson, E.Smart, P.Y.LePennec, H.Hustinx, Z.Zhao, M.M.Palcic, S.V.Evans, M.A.Chester, and M.L.Olsson (2007).
Structural basis for red cell phenotypic changes in newly identified, naturally occurring subgroup mutants of the human blood group B glycosyltransferase.
  Transfusion, 47, 864-875.
PDB code: 2i7b
17603109 G.Devasahayam, D.J.Burke, and T.W.Sturgill (2007).
Golgi manganese transport is required for rapamycin signaling in Saccharomyces cerevisiae.
  Genetics, 177, 231-238.  
17220972 L.L.Lairson, W.W.Wakarchuk, and S.G.Withers (2007).
Alternative donor substrates for inverting and retaining glycosyltransferases.
  Chem Commun (Camb), (), 365-367.  
17631498 M.D.Leipold, E.Vinogradov, and C.Whitfield (2007).
Glycosyltransferases involved in biosynthesis of the outer core region of Escherichia coli lipopolysaccharides exhibit broader substrate specificities than is predicted from lipopolysaccharide structures.
  J Biol Chem, 282, 26786-26792.  
17090541 M.D.Leipold, N.A.Kaniuk, and C.Whitfield (2007).
The C-terminal Domain of the Escherichia coli WaaJ glycosyltransferase is important for catalytic activity and membrane association.
  J Biol Chem, 282, 1257-1264.  
17574762 P.Molina, R.M.Knegtel, and B.A.Macher (2007).
Site-directed mutagenesis of glutamate 317 of bovine alpha-1,3Galactosyltransferase and its effect on enzyme activity: implications for reaction mechanism.
  Biochim Biophys Acta, 1770, 1266-1273.  
17901056 T.Jank, T.Giesemann, and K.Aktories (2007).
Clostridium difficile glucosyltransferase toxin B-essential amino acids for substrate binding.
  J Biol Chem, 282, 35222-35231.  
17850743 Y.Zhang, Y.Xiang, J.L.Van Etten, and M.G.Rossmann (2007).
Structure and function of a chlorella virus-encoded glycosyltransferase.
  Structure, 15, 1031-1039.
PDB codes: 2p6w 2p72 2p73
16407247 B.Ma, G.F.Audette, S.Lin, M.M.Palcic, B.Hazes, and D.E.Taylor (2006).
Purification, kinetic characterization, and mapping of the minimal catalytic domain and the key polar groups of Helicobacter pylori alpha-(1,3/1,4)-fucosyltransferases.
  J Biol Chem, 281, 6385-6394.  
16385447 D.B.Sparrow, G.Chapman, M.A.Wouters, N.V.Whittock, S.Ellard, D.Fatkin, P.D.Turnpenny, K.Kusumi, D.Sillence, and S.L.Dunwoodie (2006).
Mutation of the LUNATIC FRINGE gene in humans causes spondylocostal dysostosis with a severe vertebral phenotype.
  Am J Hum Genet, 78, 28-37.  
16829524 J.E.Pak, P.Arnoux, S.Zhou, P.Sivarajah, M.Satkunarajah, X.Xing, and J.M.Rini (2006).
X-ray crystal structure of leukocyte type core 2 beta1,6-N-acetylglucosaminyltransferase. Evidence for a convergence of metal ion-independent glycosyltransferase mechanism.
  J Biol Chem, 281, 26693-26701.
PDB codes: 2gak 2gam
17057723 L.L.Lairson, A.G.Watts, W.W.Wakarchuk, and S.G.Withers (2006).
Using substrate engineering to harness enzymatic promiscuity and expand biological catalysis.
  Nat Chem Biol, 2, 724-728.  
16434399 T.A.Fritz, J.Raman, and L.A.Tabak (2006).
Dynamic association between the catalytic and lectin domains of human UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferase-2.
  J Biol Chem, 281, 8613-8619.
PDB codes: 2ffu 2ffv
16105839 B.D.Lazarus, M.D.Roos, and J.A.Hanover (2005).
Mutational analysis of the catalytic domain of O-linked N-acetylglucosaminyl transferase.
  J Biol Chem, 280, 35537-35544.  
15951819 J.Flint, E.Taylor, M.Yang, D.N.Bolam, L.E.Tailford, C.Martinez-Fleites, E.J.Dodson, B.G.Davis, H.J.Gilbert, and G.J.Davies (2005).
Structural dissection and high-throughput screening of mannosylglycerate synthase.
  Nat Struct Mol Biol, 12, 608-614.
PDB codes: 2bo4 2bo6 2bo7 2bo8
15980069 L.Cuthbertson, J.Powers, and C.Whitfield (2005).
The C-terminal domain of the nucleotide-binding domain protein Wzt determines substrate specificity in the ATP-binding cassette transporter for the lipopolysaccharide O-antigens in Escherichia coli serotypes O8 and O9a.
  J Biol Chem, 280, 30310-30319.  
15831490 M.Sobhany, J.Dong, and M.Negishi (2005).
Two-step mechanism that determines the donor binding specificity of human UDP-N-acetylhexosaminyltransferase.
  J Biol Chem, 280, 23441-23445.  
15653326 P.K.Qasba, B.Ramakrishnan, and E.Boeggeman (2005).
Substrate-induced conformational changes in glycosyltransferases.
  Trends Biochem Sci, 30, 53-62.  
15849187 T.D.Hurley, S.Stout, E.Miner, J.Zhou, and P.J.Roach (2005).
Requirements for catalysis in mammalian glycogenin.
  J Biol Chem, 280, 23892-23899.
PDB codes: 1zct 1zcu 1zcv 1zcy 1zdf 1zdg
14730352 C.P.Chiu, A.G.Watts, L.L.Lairson, M.Gilbert, D.Lim, W.W.Wakarchuk, S.G.Withers, and N.C.Strynadka (2004).
Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with a substrate analog.
  Nat Struct Mol Biol, 11, 163-170.
PDB codes: 1ro7 1ro8
15122633 J.C.Biffinger, H.W.Kim, and S.G.DiMagno (2004).
The polar hydrophobicity of fluorinated compounds.
  Chembiochem, 5, 622-627.  
  15215454 K.Ginalski, M.von Grotthuss, N.V.Grishin, and L.Rychlewski (2004).
Detecting distant homology with Meta-BASIC.
  Nucleic Acids Res, 32, W576-W581.  
15075344 L.L.Lairson, C.P.Chiu, H.D.Ly, S.He, W.W.Wakarchuk, N.C.Strynadka, and S.G.Withers (2004).
Intermediate trapping on a mutant retaining alpha-galactosyltransferase identifies an unexpected aspartate residue.
  J Biol Chem, 279, 28339-28344.
PDB code: 1ss9
15148316 M.L.Rosén, M.Edman, M.Sjöström, and A.Wieslander (2004).
Recognition of fold and sugar linkage for glycosyltransferases by multivariate sequence analysis.
  J Biol Chem, 279, 38683-38692.  
15155763 N.A.Kaniuk, E.Vinogradov, J.Li, M.A.Monteiro, and C.Whitfield (2004).
Chromosomal and plasmid-encoded enzymes are required for assembly of the R3-type core oligosaccharide in the lipopolysaccharide of Escherichia coli O157:H7.
  J Biol Chem, 279, 31237-31250.  
14570926 R.P.Gibson, C.A.Tarling, S.Roberts, S.G.Withers, and G.J.Davies (2004).
The donor subsite of trehalose-6-phosphate synthase: binary complexes with UDP-glucose and UDP-2-deoxy-2-fluoro-glucose at 2 A resolution.
  J Biol Chem, 279, 1950-1955.
PDB codes: 1uqt 1uqu
15486088 T.A.Fritz, J.H.Hurley, L.B.Trinh, J.Shiloach, and L.A.Tabak (2004).
The beginnings of mucin biosynthesis: the crystal structure of UDP-GalNAc:polypeptide alpha-N-acetylgalactosaminyltransferase-T1.
  Proc Natl Acad Sci U S A, 101, 15307-15312.
PDB code: 1xhb
14752117 Y.D.Lobsanov, P.A.Romero, B.Sleno, B.Yu, P.Yip, A.Herscovics, and P.L.Howell (2004).
Structure of Kre2p/Mnt1p: a yeast alpha1,2-mannosyltransferase involved in mannoprotein biosynthesis.
  J Biol Chem, 279, 17921-17931.
PDB codes: 1s4n 1s4o 1s4p
15094797 Y.Zheng, R.J.Roberts, and S.Kasif (2004).
Segmentally variable genes: a new perspective on adaptation.
  PLoS Biol, 2, E81.  
12676935 B.Ma, G.Wang, M.M.Palcic, B.Hazes, and D.E.Taylor (2003).
C-terminal amino acids of Helicobacter pylori alpha1,3/4 fucosyltransferases determine type I and type II transfer.
  J Biol Chem, 278, 21893-21900.  
12824488 J.Liu, and A.Mushegian (2003).
Three monophyletic superfamilies account for the majority of the known glycosyltransferases.
  Protein Sci, 12, 1418-1431.  
12562774 L.C.Pedersen, J.Dong, F.Taniguchi, H.Kitagawa, J.M.Krahn, L.G.Pedersen, K.Sugahara, and M.Negishi (2003).
Crystal structure of an alpha 1,4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis.
  J Biol Chem, 278, 14420-14428.
PDB codes: 1omx 1omz 1on6 1on8
12913004 S.M.Arnold, and R.J.Kaufman (2003).
The noncatalytic portion of human UDP-glucose: glycoprotein glucosyltransferase I confers UDP-glucose binding and transferase function to the catalytic domain.
  J Biol Chem, 278, 43320-43328.  
12538870 Y.Hu, L.Chen, S.Ha, B.Gross, B.Falcone, D.Walker, M.Mokhtarzadeh, and S.Walker (2003).
Crystal structure of the MurG:UDP-GlcNAc complex reveals common structural principles of a superfamily of glycosyltransferases.
  Proc Natl Acad Sci U S A, 100, 845-849.
PDB code: 1nlm
14500887 Z.Zhang, S.Kochhar, and M.Grigorov (2003).
Exploring the sequence-structure protein landscape in the glycosyltransferase family.
  Protein Sci, 12, 2291-2302.  
12426326 A.Piekarowicz, and D.C.Stein (2002).
Biochemical properties of Neisseria gonorrhoeae LgtE.
  J Bacteriol, 184, 6410-6416.  
12045108 C.R.Raetz, and C.Whitfield (2002).
Lipopolysaccharide endotoxins.
  Annu Rev Biochem, 71, 635-700.  
12011052 E.Boix, Y.Zhang, G.J.Swaminathan, K.Brew, and K.R.Acharya (2002).
Structural basis of ordered binding of donor and acceptor substrates to the retaining glycosyltransferase, alpha-1,3-galactosyltransferase.
  J Biol Chem, 277, 28310-28318.
PDB codes: 1gwv 1gww 1gx0 1gx4
11784313 H.Ihara, Y.Ikeda, S.Koyota, T.Endo, K.Honke, and N.Taniguchi (2002).
A catalytically inactive beta 1,4-N-acetylglucosaminyltransferase III (GnT-III) behaves as a dominant negative GnT-III inhibitor.
  Eur J Biochem, 269, 193-201.  
11950836 L.C.Pedersen, T.A.Darden, and M.Negishi (2002).
Crystal structure of beta 1,3-glucuronyltransferase I in complex with active donor substrate UDP-GlcUA.
  J Biol Chem, 277, 21869-21873.
PDB code: 1kws
12199709 M.Tenno, S.Toba, F.J.Kézdy, A.P.Elhammer, and A.Kurosaka (2002).
Identification of two cysteine residues involved in the binding of UDP-GalNAc to UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 1 (GalNAc-T1).
  Eur J Biochem, 269, 4308-4316.  
12453217 N.A.Kaniuk, M.A.Monteiro, C.T.Parker, and C.Whitfield (2002).
Molecular diversity of the genetic loci responsible for lipopolysaccharide core oligosaccharide assembly within the genus Salmonella.
  Mol Microbiol, 46, 1305-1318.  
11943783 P.E.Pummill, and P.L.DeAngelis (2002).
Evaluation of critical structural elements of UDP-sugar substrates and certain cysteine residues of a vertebrate hyaluronan synthase.
  J Biol Chem, 277, 21610-21616.  
12135481 S.Bhattacharyya, A.Kerzmann, and A.L.Feig (2002).
Fluorescent analogs of UDP-glucose and their use in characterizing substrate binding by toxin A from Clostridium difficile.
  Eur J Biochem, 269, 3425-3432.  
12198488 S.I.Patenaude, N.O.Seto, S.N.Borisova, A.Szpacenko, S.L.Marcus, M.M.Palcic, and S.V.Evans (2002).
The structural basis for specificity in human ABO(H) blood group biosynthesis.
  Nat Struct Biol, 9, 685-690.
PDB codes: 1lz0 1lz7 1lzi 1lzj
  11592969 E.Boix, G.J.Swaminathan, Y.Zhang, R.Natesh, K.Brew, and K.R.Acharya (2001).
Structure of UDP complex of UDP-galactose:beta-galactoside-alpha -1,3-galactosyltransferase at 1.53-A resolution reveals a conformational change in the catalytically important C terminus.
  J Biol Chem, 276, 48608-48614.
PDB code: 1k4v
11606199 P.Petrová, J.Koca, and A.Imberty (2001).
Molecular dynamics simulations of solvated UDP-glucose in interaction with Mg2+ cations.
  Eur J Biochem, 268, 5365-5374.  
11717264 V.Chazalet, K.Uehara, R.A.Geremia, and C.Breton (2001).
Identification of essential amino acids in the Azorhizobium caulinodans fucosyltransferase NodZ.
  J Bacteriol, 183, 7067-7075.  
11785761 Y.Bourne, and B.Henrissat (2001).
Glycoside hydrolases and glycosyltransferases: families and functional modules.
  Curr Opin Struct Biol, 11, 593-600.  
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.