Fold-recognition and comparative modeling of human β3GalT I, II, IV, V and VI and β3GalNAcT I: Prediction of residues conferring acceptor substrate specificity

Journal of Molecular Graphics and Modelling

Volumn 26, Issue 1, 2007, Pages 255-268

  Patel, Ronak Y ^a   Balaji, Petety V ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

3 Galactosyltransferase; Glycosyltransferase; GT A fold; Homology modeling; Specificity determining positions; Spore coat polysaccharide biosynthesis protein SpsA

Indexed keywords

RESIDUES CONFERRING ACCEPTOR; SUBSTRATE SPECIFICITY; TRANSMEMBRANE PROTEINS;

DATA ACQUISITION; MAPPING; MATHEMATICAL MODELS; MUTAGENESIS;

PROTEINS;

ALPHA 1,3 GALACTOSYLTRANSFERASE; BETA 1,3 GALACTOSYLTRANSFERASE; BETA3 GALACTOSYLTRANSFERASE; GALACTOSE; GLYCOSPHINGOLIPID; MEMBRANE PROTEIN; N ACETYLGALACTOSAMINE; N ACETYLGLUCOSAMINE; PROTEOGLYCAN; UNCLASSIFIED DRUG; URIDINE DIPHOSPHATE GALACTOSE;

ARTICLE; BINDING SITE; ENZYME SPECIFICITY; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN STRUCTURE; SITE DIRECTED MUTAGENESIS;

AMINO ACID SEQUENCE; ANIMALS; CARBOHYDRATE SEQUENCE; CATALYTIC DOMAIN; COMPUTER SIMULATION; GALACTOSYLTRANSFERASES; HUMANS; MICE; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; N-ACETYLGALACTOSAMINYLTRANSFERASES; OLIGOSACCHARIDES; PROTEIN CONFORMATION; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; SEQUENCE HOMOLOGY, AMINO ACID; SOFTWARE; SUBSTRATE SPECIFICITY;

EID: 34250832746     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmgm.2006.12.003     Document Type: Article

References (72)

1. Amado M., Almeida R., Schwientek T., and Clausen H. Identification and characterization of large galactosyltransferase gene families: galactosyltransferases for all functions. Biochim. Biophys. Acta 1473 (1999) 35-53
2. Hennet T. The galactosyltransferase family. Cell. Mol. Life Sci. 59 (2002) 1081-1095
3. Bai X., Zhou D., Brown J.R., Crawford B.E., Hennet T., and Esko J.D. Biosynthesis of the linkage region of glycosaminoglycans: cloning and activity of galactosyltransferase II, the sixth member of the β1,3-galactosyltransferase family (β3GalT6). J. Biol. Chem. 276 (2001) 48189-48195
4. Isshiki S., Togayachi A., Kudo T., Nishihara S., Watanabe M., Kubota T., Kitajima M., Shiraishi N., Sasaki K., Andoh T., and Narimatsu H. Cloning, expression, and characterization of a novel UDP-galactose:β-N-acetylglucosamine β1,3-galactosyltransferase (β3Gal-T5) responsible for synthesis of type 1 chain in colorectal and pancreatic epithelia and tumor cells derived there from. J. Biol. Chem. 274 (1999) 12499-12507
5. Ju T., Brewer K., D'Souza A., Cummings R.D., and Canfield W.M. Cloning and expression of human core 1 β1,3-galactosyltransferase. J. Biol. Chem. 277 (2002) 178-186
6. Amado M., Almeida R., Carneiro F., Levery S.B., Holmes E.H., Nomoto M., Hollingsworth M.A., Hassan H., Schwientek T., Nielsen P.A., Bennett E.P., and Clausen H. A family of human β3-galactosyltransferases. Characterization of four members of a UDP-galactose:β-N-acetyl-glucosamine/β-N-acetylgalactosamine β-1,3-galactosyltransferase family. J. Biol. Chem. 273 (1998) 12770-12778
7. Malissard M., Dinter A., Berger E.G., and Hennet T. Functional assignment of motifs conserved in β1,3-glycosyltransferases. Eur. J. Biochem. 269 (2002) 233-239
8. Kurowski M.A., and Bujnicki J.M. GeneSilico protein structure prediction meta-server. Nucleic Acids Res. 31 (2003) 3305-3307
9. Cuff J.A., and Barton G.J. Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 40 (1999) 502-511
10. J. Meiler, M. Mueller, A. Zeidler, F. Schmaeschke, JUFO: Secondary Structure Prediction for Proteins, 2002, www.jens-meiler.de.
11. Ouali M., and King R.D. Cascaded multiple classifiers for secondary structure prediction. Protein Sci. 9 (2000) 1162-1176
12. B. Rost, PROF: predicting one-dimensional protein structure by profile based neural networks, 2000, unpublished.
13. Jones D.T. Protein secondary structure prediction based on position-specific scoring matrices. J. Mol. Biol. 292 (1999) 195-202
14. Krogh A., Larsson B., von Heijne G., and Sonnhammer E.L.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305 (2001) 567-580
15. Rice P., Longden I., and Bleasby A. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16 (2000) 276-277
16. Alexandrov N.N., Nussinov R., and Zimmer R.M. Fast protein fold recognition via sequence to structure alignment and contact capacity potentials. In: Hunter L., and Klein T.E. (Eds). Pacific Symposium on Biocomputing'96 (1995), World Scientific Publishing Co., Singapore 53-72
17. Kelley L.A., MacCallum R.M., and Sternberg M.J.E. Enhanced genome annotation using structural profiles in the program 3D-PSSM. J. Mol. Biol. 299 (2000) 499-520
18. Jaroszewski L., Rychlewski L., Li Z., Li W., and Godzik A. FFAS03: a server for profile-profile sequence alignments. Nucleic Acids Res. 33 (2005) W284-W288
19. Fischer D. 3D-SHOTGUN: a novel, cooperative, fold-recognition meta-predictor. Proteins 51 (2003) 434-441
20. Fischer D., and Eisenberg D. Protein fold recognition using sequence-derived predictions. Protein Sci. 5 (1996) 947-955
21. Zhou H., and Zhou Y. Fold recognition by combining sequence profiles derived from evolution and from depth-dependent structural alignment of fragments. Proteins 58 (2005) 321-328
22. Kalinina O.V., Novichkov P.S., Mironov A.A., Gelfand M.S., and Rakhmaninova A.B. SDPpred: a tool for prediction of amino acid residues that determine differences in functional specificity of homologous proteins. Nucleic Acids Res. 32 (2004) W424-W428
23. Crooks G.E., Hon G., Chandonia J.M., and Brenner S.E. WebLogo: a sequence logo generator. Genome Res. 14 (2004) 1188-1190
24. Hall T.A. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp. Ser. 41 (1999) 95-98
25. Sayle R.A., and Milner-White E.J. RASMOL: biomolecular graphics for all. Trends Biochem. Sci. 20 (1995) 374
26. DeLano W.L. The PyMOL Molecular Graphics System (2002), DeLano Scientific, San Carlos, CA, USA
27. Bond C.S. TopDraw: a sketchpad for protein structure topology cartoons. Bioinformatics 19 (2003) 311-312
28. Marti-Renom M.A., Stuart A., Fiser A., Sanchez R., Melo F., and Sali A. Comparative protein structure modeling of genes and genomes. Annu. Rev. Biophys. Biomol. Struct. 29 (2000) 291-325
29. Sali A., and Blundell T.L. Comparative protein modeling by satisfaction of spatial restraints. J. Mol. Biol. 234 (1993) 779-815
30. Sippl M.J. Recognition of errors in three-dimensional structures of proteins. Proteins 17 (1993) 355-362
31. Canutescu A.A., Shelenkov A.A., and Dunbrack Jr. R.L. A graph theory algorithm for protein side-chain prediction. Protein Sci. 12 (2003) 2001-2014
32. Thompson J.D., Higgins D.G., and Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22 (1994) 4673-4680
33. Notredame C., Higgins D., and Heringa J. T-Coffee: a novel method for multiple sequence alignments. J. Mol. Biol. 302 (2000) 205-217
34. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32 (2004) 1792-1797
35. Okajima T., Nakamura Y., Uchikawa M., Haslam D.B., Numata S.I., Furukawa K., Urano T., and Furukawa K. Expression cloning of human globoside synthase cDNAs. Identification of β3Gal-T3 as UDP-N-acetylgalactosamine:globotriaosylceramide β1,3-N-acetylgalactosaminyltransferase. J. Biol. Chem. 275 (2000) 40498-40503
36. Bairoch A., Apweiler R., Wu C.H., Barker W.C., Boeckmann B., Ferro S., Gasteiger E., Huang H., Lopez R., Magrane M., Martin M.J., Natale D.A., O'Donovan C., Redaschi N., and Yeh L.S. The universal protein resource (UniProt). Nucleic Acids Res. 33 (2005) D154-D159
37. Altschul S.F., Madden T.L., Schaeffer A.A., Zhang J., Zhang Z., Miller W., and Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25 (1997) 3389-3402
38. Hubbard T., Andrews D., Caccamo M., Cameron G., Chen Y., Clamp M., Clarke L., Coates G., Cox T., Cunningham F., Curwen V., Cutts T., Down T., Durbin R., Fernandez-Suarez X.M., Gilbert J., Hammond M., Herrero J., Hotz H., Howe K., Iyer V., Jekosch K., Kahari A., Kasprzyk A., Keefe D., Keenan S., Kokocinsci F., London D., Longden I., McVicker G., Melsopp C., Meidl P., Potter S., Proctor G., Rae M., Rios D., Schuster M., Searle S., Severin J., Slater G., Smedley D., Smith J., Spooner W., Stabenau A., Stalker J., Storey R., Trevanion S., Ureta-Vidal A., Vogel J., White S., Woodwark C., and Birney E. Ensembl 2005. Nucleic Acids Res. 33 (2005) D447-D453
39. Burge C., and Karlin S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268 (1997) 78-94
40. Bowie J.U., Luthy R., and Eisenberg D. A method to identify protein sequences that fold into a known three-dimensional structure. Science 253 (1991) 164-170
41. Luthy R., Bowie J.U., and Eisenberg D. Assessment of protein models with three-dimensional profiles. Nature 356 (1992) 83-85
42. Melo F., and Feytmans E. Assessing protein structures with a non-local atomic interaction energy. J. Mol. Biol. 277 (1998) 1141-1152
43. Melo F., and Feytmans E. Novel knowledge-based mean force potential at atomic level. J. Mol. Biol. 267 (1997) 207-222
44. Wallner B., and Elofsson A. Identification of correct regions in protein models using structural, alignment, and consensus information. Protein Sci. 15 (2006) 900-913
45. Pontius J., Richelle J., and Wodak S.J. Deviations from standard atomic volumes as a quality measure for protein crystal structures. J. Mol. Biol. 264 (1996) 121-136
46. Sasin M., and Bujnicki JM. COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res. 32 (2004) W586-W589 Web Server issue
47. Gastinel L.N., Bignon C., Misra A.K., Hindsgaul O., Shaper J.H., and Joziasse D.H. Bovine α1,3-galactosyltransferase catalytic domain structure and its relationship with ABO histo-blood group and glycosphingolipids glycosyltransferases. EMBO J. 20 (2001) 638-649
48. Murzin A.G., Brenner S.E., Hubbard T., and Chothia C. SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol. 247 (1995) 536-540
49. Kikuchi N., Kwon Y.D., Gotoh M., and Narimatsu H. Comparison of glycosyltransferase families using the profile hidden Markov model. Biochem. Biophys. Res. Commun. 310 (2003) 574-579
50. Breton C., Snajdrova L., Jeanneau C., Koea J., and Imberty A. Structures and mechanisms of glycosyltransferases superfamily. Glycobiology 16 (2006) 29R-37R
51. Charnock S.J., and 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
52. Wiggins C.A., and 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. U.S.A. 95 (1998) 7945-7950
53. Gotting C., Muller S., Schottler M., Schon S., Prante C., Brinkmann T., Kuhn J., and Kleesiek K. Analysis of the DXD motifs in human xylosyltransferase I required for enzyme activity. J. Biol. Chem. 279 (2004) 42566-42573
54. Li J., Rancour D.M., Allende M.L., Worth C.A., Darling D.S., Gilbert J.B., Menon A.K., and Young Jr. W.W. The DXD motif is required for GM2 synthase activity but is not critical for nucleotide binding. Glycobiology 11 (2001) 217-229
55. Munro S., and Freeman M. The notch signalling regulator fringe acts in the Golgi apparatus and requires the glycosyltransferase signature motif DXD. Curr. Biol. 10 (2000) 813-820
56. Ramakrishnan B., and Qasba P.K. Structure-based design of beta 1,4-galactosyltransferase I (beta 4Gal-T1) with equally efficient N-acetylgalactosaminyltransferase activity: point mutation broadens beta 4Gal-T1 donor specificity. J. Biol. Chem. 277 (2002) 20833-20839
57. Marcus S.L., Polakowski R., Seto N.O., Leinala E., Borisova S., Blancher A., Roubinet F., Evans S.V., and Palcic M.M. A single point mutation reverses the donor specificity of human blood group B-synthesizing galactosyltransferase. J. Biol. Chem. 278 (2003) 12403-12405
58. Thoden J.B., Henderson J.M., Fridovich-Keil J.L., and Holden H.M. Structural analysis of the Y299C mutant of Escherichia coli UDP-galactose 4-epimerase. Teaching an old dog new tricks. J. Biol. Chem. 277 (2002) 27528-27534
59. Coutinho P.M., Deleury E., Davies G.J., and Henrissat B. An evolving hierarchical family classification for glycosyltransferases. J. Mol. Biol. 328 (2003) 307-317
60. Ramakrishnan B., Balaji P.V., and Qasba P.K. Crystal structure of beta1,4-galactosyltransferase complex with UDP-Gal reveals an oligosaccharide acceptor binding site. J. Mol. Biol. 318 (2002) 491-502
61. Almeida R., Levery S.B., Mandel U., Kresse H., Schwientek T., Bennett E.P., and Clausen H. Cloning and expression of a proteoglycan UDP-galactose: β-xylose β1,4-galactosyltransferase I. A seventh member of the human β4-galactosyltransferase gene family. J. Biol. Chem. 274 (1999) 26165-26171
62. Boix E., Swaminathan G.J., Zhang Y., Natesh R., Brew K., and Acharya K.R. Structure of UDP complex of UDP-galactose:β-galactoside-α-1,3-galactosyltransferase at 1. 53-A resolution reveals a conformational change in the catalytically important C terminus. J. Biol. Chem. 276 (2001) 48608-48614
63. Unligil U.M., and Rini J.M. Glycosyltransferase structure and mechanism. Curr. Opin. Struct. Biol. 10 (2000) 510-517
64. Schneider T.D., and Stephens R.M. Sequence logos: a new way to display consensus sequences. Nucleic Acids Res. 18 (1990) 6097-6100
65. Mount D.W. Bioinformatics. Sequence and Genome Analysis (2003), CBS Publishers and Distributors, New Delhi pp. 196-198
66. Lupyan D., Leo-Macias A., and Ortiz A.R. A new progressive-iterative algorithm for multiple structure alignment. Bioinformatics 21 (2005) 3255-3263
67. Hennet T., Dinter A., Kuhnert P., Mattu T.S., Rudd P.M., and Berger E.G. Genomic cloning and expression of three murine UDP-galactose: β-N-acetylglucosamine β1,3-galactosyltransferase genes. J. Biol. Chem. 273 (1998) 58-65
68. Kolbinger F., Streiff M.B., and Katopodis A.G. Cloning of a human UDP-galactose:2-acetamido-2-deoxy-d-glucose 3β-galactosyltransferase catalyzing the formation of type 1 chains. J. Biol. Chem. 273 (1998) 433-440
69. Miyazaki H., Fukumoto S., Okada M., Hasegawa T., and Furukawa K. Expression cloning of rat cDNA encoding UDP-galactose:GD2 β1,3-galactosyltransferase that determines the expression of GD1b/GM1/GA1. J. Biol. Chem. 272 (1997) 24794-24799
70. Zhou D., Henion T.R., Jungalwala F.B., Berger E.G., and Hennet T. The β1,3-galactosyltransferase β3GalT-V is a stage-specific embryonic antigen-3 (SSEA-3) synthase. J. Biol. Chem. 275 (2000) 22631-22634
71. Zhou D., Berger E.G., and Hennet T. Molecular cloning of a human UDP-galactose: GlcNAcβ1,3GalNAc β1,3galactosyltransferase gene encoding an O-linked core3-elongation enzyme. Eur. J. Biochem. 263 (1999) 571-576
72. Sanchez R., and Sali A. Large-scale protein structure modeling of the Saccharomyces cerevisiae genome. Proc. Natl. Acad. Sci. U.S.A. 95 (1998) 13597-13602