An evolving hierarchical family classification for glycosyltransferases

Journal of Molecular Biology

Volumn 328, Issue 2, 2003, Pages 307-317

  Coutinho, Pedro M ^a   Deleury, Emeline ^a   Davies, Gideon J ^b   Henrissat, Bernard ^a  

^a AIX MARSEILLE UNIVERSITY   (France)

^b UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Classification; Genomic annotations; Glycosyltransferases; Modular structure; Protein families

Indexed keywords

CARBOHYDRATE DERIVATIVE; GLYCOCONJUGATE; GLYCOSIDASE; GLYCOSYLTRANSFERASE; OLIGOSACCHARIDE; OXOCARBENIUM; POLYSACCHARIDE; SUGAR; UNCLASSIFIED DRUG;

ARTICLE; CARBOHYDRATE ANALYSIS; CATALYSIS; CYTOLOGY; ENZYME ANALYSIS; ENZYME MECHANISM; MOLECULAR EVOLUTION; OPEN READING FRAME; PRIORITY JOURNAL; PROTEIN FAMILY;

EID: 0037466315     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0022-2836(03)00307-3     Document Type: Article

References (50)

1. Rudd P.M., Elliott T., Cresswell P., Wilson I.A., Dwek R.A. Glycosylation and the immune system. Science. 291:2001;2370-2376.
2. Wells L., Vosseller K., Hart G.W. Glycosylation of nucleocytoplasmic proteins: signal transduction and O-GlcNAc. Science. 291:2001;2376-2378.
3. Bertozzi C.R., Kiessling L.L. Chemical glycobiology. Science. 291:2001;2357-2364.
4. Kleene R., Berger E.G. The molecular and cell biology of glycosyltransferases. Biochim. Biophys. Acta. 1154:1993;283-325.
5. Sharon N. The conquest of the last frontier of molecular and cell biology. Biochimie. 83:2001;555.
6. Davies G.J., Henrissat B. Structural enzymology of carbohydrate-active enzymes: implications for the post-genomic era. Biochem. Soc. Trans. 30:2002;291-297.
7. Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes. 1992;Academic Press, London.
8. Campbell J.A., Davies G.J., Bulone V., Henrissat B. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem. J. 326:1997;929-939.
9. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 280:1991;309-316.
10. Henrissat B., Bairoch A. New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem. J. 293:1993;781-788.
11. Henrissat B., Bairoch A. Updating the sequence-based classification of glycosyl hydrolases. Biochem. J. 316:1996;695-696.
12. Campbell J.A., Davies G.J., Bulone V.V., Henrissat B. A classification of nucleotide-diphospho-sugar glycosyltransferases based on amino acid sequence similarities. Biochem. J. 329:1998;719.
13. Henrissat B., Coutinho P.M., Davies G.J. A census of carbohydrate-active enzymes in the genome of Arabidopsis thaliana. Plant Mol. Biol. 47:2001;55-72.
14. 12 structures for a reducing hexasaccharide: the isomer barrier to development of single-method saccharide sequencing or synthesis systems. Glycobiology. 4:1994;759-767.
15. Seto N.O., Compston C.A., Evans S.V., Bundle D.R., Narang S.A., Palcic M.M. Donor substrate specificity of recombinant human blood group A, B and hybrid A/B glycosyltransferases expressed in Escherichia coli. Eur. J. Biochem. 259:1999;770-775.
16. Wrabl J.O., Grishin N.V. Homology between O-linked GlcNAc transferases and proteins of the glycogen phosphorylase superfamily. J. Mol. Biol. 314:2001;365-374.
17. Gaboriaud C., Bissery V., Benchetrit T., Mornon J.-P. Hydrophobic cluster analysis: an efficient new way to compare and analyse amino acid sequences. FEBS Letters. 224:1987;149-155.
18. Altschul S.F., Madden T.L., Schaffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl. Acids Res. 25:1997;3389-3402.
19. Ünligil U., Zhou S., Yuwaraj S., Sarkar M., Schachter H., Rini J. X-ray crystal structure of rabbit N-acetylglucosaminyltransferase I: catalytic mechanism and a new protein superfamily. EMBO J. 19:2000;5269-5280.
20. Bourne Y., Henrissat B. Glycoside hydrolases and glycosyltransferases: families and functional modules. Curr. Opin. Struct. Biol. 11:2001;593-600.
21. Tarbouriech N., Charnock S.J., Davies G.J. Three-dimensional structures of the Mn and Mg dTDP complexes of the family GT-2 glycosyltransferase SpsA: a comparison with related NDP-sugar glycosyltransferases. J. Mol. Biol. 314:2001;655-661.
22. Hu Y., Walker S. Remarkable structural similarities between diverse glycosyltransferases. Chem. Biol. 9:2002;1287-1296.
23. Davies G., Henrissat B. Structures and mechanisms of glycosyl hydrolases. Structure. 3:1995;853-859.
24. Henrissat B., Davies G. Structural and sequence-based classification of glycoside hydrolases. Curr. Opin. Struct. Biol. 7:1997;637-644.
25. Gibson R.P., Turkenburg J.P., Charnock S.J., Lloyd R., Davies G.J. Insights into trehalose synthesis provided by the structure of the retaining glucosyltransferase OtsA. Chem. Biol. 9:2002;1337-1346.
26. Withers S.G., Wakarchuk W.W., Strynadka N.C. One step closer to a sweet conclusion. Chem. Biol. 9:2002;1270-1273.
27. Campbell R.E., Mosimann S.C., Tanner M.E., Strynadka N.C. The structure of UDP-N-acetylglucosamine 2-epimerase reveals homology to phosphoglycosyl transferases. Biochemistry. 39:2000;14993-15001.
28. Brown K., Pompeo F., Dixon S., Mengin-Lecreulx D., Cambillau C., Bourne Y. Crystal structure of the bifunctional N-acetylglucosamine 1-phosphate uridyltransferase from Escherichia coli: a paradigm for the related pyrophosphorylase superfamily. EMBO J. 18:1999;4096-4107.
29. Henrissat B., Romeu A. Families, superfamilies and subfamilies of glycosyl hydrolases. Biochem. J. 311:1995;350-351.
30. Costa A.A., Gomez F.J., Pereira M., Felipe M.S., Jesuino R.S., Deepe G.S. Jr, de Almeida Soares C.M. Characterization of a gene which encodes a mannosyltransferase homolog of Paracoccidioides brasiliensis. Microb. Infect. 4:2002;1027-1034.
31. Stolz J., Munro S. The components of the Saccharomyces cerevisiae mannosyltransferase complex M-Pol I have distinct functions in mannan synthesis. J. Biol. Chem. 277:2002;44801-44808.
32. Wiggins C.A., Munro S. Activity of the yeast MNN1 α-1,3-mannosyltransferase requires a motif conserved in many other families of glycosyltransferases. Proc. Natl Acad. Sci. USA. 95:1998;7945-7950.
33. Breton C., Bettler E., Joziasse D.H., Geremia R.A., Imberty A. Sequence-function relationships of prokaryotic and eukaryotic galactosyltransferases. J. Biochem. (Tokyo). 123:1998;1000-1009.
34. Pedersen L.C., Tsuchida K., Kitagawa H., Sugahara K., Darden T.A., Negishi M. Heparan/chondroitin sulfate biosynthesis: structure and mechanism of human glucuronyltransferase I. J. Biol. Chem. 275:2000;34580-34585.
35. Henrissat B., Davies G.J. Glycoside hydrolases and glycosyltransferases: families, modules and implications for genomics. Plant Physiol. 124:2000;1515-1519.
36. Jing W., DeAngelis P.L. Dissection of the two transferase activities of the Pasteurella multocida hyaluronan synthase: two active sites exist in one polypeptide. Glycobiology. 10:2000;883-889.
37. DeAngelis P.L., White C.L. Identification and molecular cloning of a heparosan synthase from Pasteurella multocida type D. J. Biol. Chem. 277:2002;7209-7213.
38. DeAngelis P.L., Padgett-McCue A.J. Identification and molecular cloning of a chondroitin synthase from Pasteurella multocida type F. J. Biol. Chem. 275:2000;24124-24129.
39. Iwai H., Masaoka N., Ishii T., Satoh S. A pectin glucuronyltransferase gene is essential for intercellular attachment in the plant meristem. Proc. Natl Acad. Sci. USA. 99:2002;16319-16324.
40. Pedersen L.C., Dong J., Taniguchi F., Kitagawa H., Krahn J., Pedersen L.G., et al. Crystal structure of an α 1, 4-N-acetylhexosaminyltransferase (EXTL2), a member of the exostosin gene family involved in heparan sulfate biosynthesis. J. Biol. Chem. 2003;. In press.
41. Hochstenbach F., Klis F.M., van den Ende H., van Donselaar E., Peters P.J., Klausner R.D. Identification of a putative alpha-glucan synthase essential for cell wall construction and morphogenesis in fission yeast. Proc. Natl Acad. Sci. USA. 95:1998;9161-9166.
42. Charnock S.J., Davies G.J. Structure of the nucleotide-diphospho-sugar transferase, SpsA from Bacillus subtilis, in native and nucleotide-complexed forms. Biochemistry. 38:1999;6380-6385.
43. Gastinel L.N., Cambillau C., Bourne Y. Crystal structures of the bovine β 4-galactosyltransferase catalytic domain and its complex with uridine diphosphogalactose. EMBO J. 18:1999;3546-3557.
44. Gastinel L.N., Bignon C., Misra A.K., Hindsgaul O., Shaper J.H., Joziasse D.H. Bovine α 1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipid glycosyltransferases. EMBO J. 20:2001;638-649.
45. Persson K., Ly H.D., Dieckelmann M., Wakarchuk W.W., Withers S.G., Strynadka N.C. Crystal structure of the retaining galactosyltransferase LgtC from Neisseria meningitidis in complex with donor and acceptor sugar analogs. Nature Struct. Biol. 8:2001;166-175.
46. Gibbons B.J., Roach P.J., Hurley T.D. Crystal structure of the autocatalytic initiator of glycogen biosynthesis, glycogenin. J. Mol. Biol. 319:2002;463-477.
47. Mulichak A.M., Losey H.C., Walsh C.T., Garavito R.M. Structure of the UDP-glucosyltransferase GtfB that modifies the heptapeptide aglycone in the biosynthesis of vancomycin group antibiotics. Structure. 9:2001;547-557.
48. Ha S., Walker D., Shi Y., Walker S. The 1.9 Å crystal structure of Escherichia coli MurG, a membrane-associated glycosyltransferase involved in peptidoglycan biosynthesis. Protein Sci. 9:2000;1045-1052.
49. Vrielink A., Ruger W., Driessen H.P., Freemont P.S. Crystal structure of the DNA modifying enzyme β-glucosyltransferase in the presence and absence of the substrate uridine diphosphoglucose. EMBO J. 13:1994;3413-3422.
50. Goldsmith E.J., Sprang S.R., Hamlin R., Xuong N.H., Fletterick R.J. Domain separation in the activation of glycogen phosphorylase a. Science. 245:1989;528-532.