Fold-recognition and comparative modeling of human α2,3- sialyltransferases reveal their sequence and structural similarities to CstII from Campylobacter jejuni

BMC Structural Biology

Volumn 6, Issue , 2006, Pages

  Sujatha, M S ^a   Balaji, Petety V ^a  

^a INDIAN INSTITUTE OF TECHNOLOGY BOMBAY   (India)

Author keywords

[No Author keywords available]

Indexed keywords

ALPHA2,3 SIALYLTRANSFERASE DERIVATIVE ENZYME; BACTERIAL ENZYME; CST2 ENZYME; CYTIDINE PHOSPHATE N ACETYLNEURAMINIC ACID; GT29 SIALYLTRANSFERASE ENZYME; GT42 SIALYLTRANSFERASE ENZYME; SIALIC ACID; SIALYLTRANSFERASE; ST3GAL SIALYLTRANSFERASE 1 ENZYME; ST3GAL SIALYLTRANSFERASE 2 ENZYME; ST3GAL SIALYLTRANSFERASE 3 ENZYME; ST3GAL SIALYLTRANSFERASE 4 ENZYME; ST3GAL SIALYLTRANSFERASE 5 ENZYME; ST3GAL SIALYLTRANSFERASE 6 ENZYME; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CAMPYLOBACTER JEJUNI; CONTROLLED STUDY; ENZYME ACTIVE SITE; ENZYME ACTIVITY; ENZYME LOCALIZATION; ENZYME STRUCTURE; ENZYME SUBSTRATE COMPLEX; MEDICAL LITERATURE; MUTAGENESIS; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN FOLDING; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STEREOCHEMISTRY;

CAMPYLOBACTER JEJUNI; DATABASES, PROTEIN; HUMANS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN FOLDING; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, PROTEIN; SEQUENCE HOMOLOGY, AMINO ACID; SIALYLTRANSFERASES;

CAMPYLOBACTER JEJUNI; EUKARYOTA;

EID: 33745984208     PISSN: 14726807     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-6-9     Document Type: Article

References (71)

1. Angata K, Fukuda M: Polysialyltransferases: major players in polysialic acid synthesis on the neural cell adhesion molecule. Biochimie 2003, 85:195-206.
2. Dall'Olio F, Chiricolo M: Sialyltransferases in cancer. Glycoconj J 2001, 18:841-850.
3. Harduin-Lepers A, Vallejo-Ruiz V, Krzewinski-Recchi MA, Samyn-Petit B, Julien S, Delannoy P: The human sialyltransferase family. Biochimie 2001, 83:727-737.
4. Tsuji S: Molecular cloning and functional analysis of sialyltransferases. J Biochem 1996, 120:1-13.
5. Harduin-Lepers A, Mollicone R, Delannoy P, Oriol R: The animal sialyltransferases and sialyltransferase-related genes: a phylogenetic approach. Glycobiology 2005, 15:805-817.
6. Datta AK, Paulson JC: Sialylmotifs of sialyltransferases. Indian J Biochem Biophys 1997, 34(1-2):157-165.
7. Jeanneau C, Chazalet V, Auge C, Soumpasis DM, Harduin-Lepers A, Delannoy P, Imberty A, Breton C: Structure-function analysis of the human sialyltransferase ST3Gal I: role of N-glycosylation and novel conserved sialylmotif. J Biol Chem 2004, 279:13461-13468.
8. Datta AK, Paulson JC: The sialyltransferase "sialylmotif" participates in binding the donor substrate CMP-NeuAc. J Biol Chem 1995, 270:1497-1500.
9. Datta AK, Sinha A, Paulson JC: Mutation of the sialyltransferase S-sialylmotif alters the kinetics of the donor and acceptor substrates. J Biol Chem 1998, 273:9608-9614.
10. Kitazume-Kawaguchi S, Kabata S, Arita M: Differential biosynthesis of polysialic or disialic acid structure by ST8Sia II and ST8Sia IV. J Biol Chem 2001, 276:15696-15703.
11. Patel RY, Balaji PV: Identification of linkage-specific sequence motifs in sialyltransferases. Glycobiology 2006. DOI 101093/glycob/cwj046.
12. Murzin AG, Brenner SE, Hubbard T, Chothia C: SCOP: a structural classification of proteins database for the investigation of sequences and structures. J Mol Biol 1995, 247:536-540.
13. Chiu CPC, Watts AG, Lairson LL, Gilbert M, Lim D, Wakarchuk WW, Withers SG, Strynadka NCJ: Structural analysis of the sialyltransferase CstII from Campylobacter jejuni in complex with substrate analog. Nat Struct Mol Biol 2004, 11:163-170.
14. Venclovas C, Thelen MP: Structure-based predictions of Rad1, Rad9, Hus1 and Rad17 participation in sliding clamp and clamp-loading complexes. Nucleic Acids Res 2000, 28:2481-2493.
15. Fukuda M, Marth JD: ST3Gal-I. In Handbook of glycosyltransferases and related genes Edited by: Taniguchi N, Honke K, Fukuda M. Springer-Verlag, Tokyo; 2002:267-273.
16. Hamamoto T, Tsuji S: ST3Gal-II (SAT-IV). In Handbook of glycosyltransferases and related genes Edited by: Taniguchi N, Honke K, Fukuda M. Springer-Verlag, Tokyo; 2002:274-278.
17. Kitazume-Kawaguchi S, Tsuji S: ST3Gal-III. In Handbook of glycosyltransferases and related genes Edited by: Taniguchi N, Honke K, Fukuda M. Springer-Verlag, Tokyo; 2002:279-283.
18. Kitazume-Kawaguchi S, Tsuji S: ST3Gal-IV. In Handbook of glycosyltransferases and related genes Edited by: Taniguchi N, Honke K, Fukuda M. Springer-Verlag, Tokyo; 2002:284-288.
19. Saito S, Ishii A: ST3Gal-V (GM3 synthase, SAT-I). In Handbook of glycosyltransferases and related genes Edited by: Taniguchi N, Honke K, Fukuda M. Springer-Verlag, Tokyo; 2002:289-294.
20. Okajima T, Fukumoto S, Miyazaki H, Ishida H, Kiso M, Furukawa K, Urano T, Furukawa K: Molecular cloning of a novel α2,3-sialyltransferase (ST3Gal VI) that sialylates type II lactosamine structures on glycoproteins and glycolipids. J Biol Chem 1999, 274:11479-11486.
21. Datta AK, Chammas R, Paulson JC: Conserved cysteines in the sialyltransferase sialylmotifs form an essential disulphide bond. J Biol Chem 2001, 276:15200-15207.
22. Gilbert M, Watson DC, Cunningham AM, Jennings MP, Young NM, Wakarchuk WW: Cloning of the lipooligosaccharide α2,3-sialyltransferase from the bacterial pathogens Neisseria meningitidis and Neisseria gonorrhoeae. J Biol Chem 1996, 271:28271-28276.
23. Gilbert M, Brisson JR, Karwaski MF, Michniewicz J, Cunningham AM, Wu Y, Young NM, Wakarchuk WW: Biosynthesis of ganglioside mimics in Campylobacter jejuni OH4384. Identification of the glycosyltransferase genes, enzymatic synthesis of model compounds, and characterization of nanomole amounts by 600-mhz (1)h and (13)c NMR analysis. J Biol Chem 2000, 275:3896-3906.
24. Hood DW, Cox AD, Gilbert M, Makepeace K, Walsh S, Deadman ME, Cody A, Martin A, Mansson M, Schweda EK, Brisson JR, Richards JC, Moxon ER, Wakarchuk WW: Identification of a lipopolysaccharide alpha-2,3-sialyltransferase from Haemophilus influenzae. Mol Microbiol 2001, 39:341-350.
25. Jones PA, Samuels NM, Phillips NJ, Munson RS Jr, Bozue JA, Arseneau JA, Nichols WA, Zaleski A, Gibson BW, Apicella MA: Haemophilus influenzae type b strain A2 has multiple sialyltransferases involved in lipooligosaccharide sialylation. J Biol Chem 2002, 277:14598-14611.
26. Shen GJ, Datta AK, Izumi M, Koeller KM, Wong CH: Expression of alpha2,8/2,9-polysialyltransferase from Escherichia coli K92. Characterization of the enzyme and its reaction products. J Biol Chem 1999, 274:35139-35146.
27. Yamamoto T, Nakashizuka M, Terada I: Cloning and expression of a marine bacterial beta-galactoside alpha2,6-sialyltransferase gene from Photobacterium damsela JT0160. J Biochem 1998, 123:94-100.
28. Coutinho PM, Deleury E, Davies GJ, Henrissat B: An evolving hierarchical family classification of glycosyltransferases. J Mol Biol 2003, 328:307-317.
29. Qasba PK, Ramakrishnan B, Boeggeman E: Substrate-induced conformational changes in glycosyltransferases. Trends Biochem Sci 2005, 30:53-62.
30. Ramakrishnan B, Boeggeman E, Ramasamy V, Qasba PK: Structure and catalytic cycle of β1,4-galactosyltransferase. Curr Opin Struct Biol 2004, 14:593-600.
31. Zhang Y, Deshpande A, Xie Z, Natesh R, Acharya KR, Brew K: Roles of active site tryptophans in substrate binding and catalysis by α1,3-galactosyltransferase. Glycobiology 2004, 14:1295-1302.
32. Khidekel N, Arndt S, Lamarre-Vincent N, Lippert A, Poulin-Kerstien KG, Ramakrishnan B, Qasba PK, Hsieh-Wilson LC: A chemoenzymatic approach toward the rapid and sensitive detection of O-GlcNAc posttranslational modifications. J Am Chem Soc 2003, 125:16162-16163.
33. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE: The protein data bank. Nucl Acids Res 2000, 28:235-242.
34. Andreeva A, Howorth D, Brenner SE, Hubbard TJP, Chothia C, Murzin AG: SCOP database in 2004: refinements integrate structure and sequence family data. Nucl Acids Res 2004, 32:D226-D229.
35. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ: Basic local alignment search tool. J Mol Biol 1990, 215:403-410.
36. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucl Acids Res 1997, 25:3389-3402.
37. Jaroszewski L, Rychlewski L, Li Z, Li W, Godzik A: FFAS03: a server for profile-profile sequence alignments. Nucl Acids Res 2005, 33:W284-W288.
38. Shi J, Blundell TL, Mizuguchi K: FUGUE: sequence-structure homology recognition using environment-specific substitution tables and structure- dependent gap penalties. J Mol Biol 2001, 310:243-257.
39. Kelley LA, MacCallum RM, Sternberg MJE: Enhanced Genome Annotation using Structural Profiles in the Program 3D-PSSM. J Mol Biol 2000, 299:499-520.
40. Karplus K, Karchin R, Draper J, Casper J, Mandel-Gutfreund Y, Diekhans M, Hughey R: Combining local-structure, fold-recognition, and new-fold methods for protein structure prediction. Proteins 2003, 53:491-496.
41. Kurowski MA, Bujnicki JM: GeneSilico protein structure prediction meta-server. Nucleic Acids Res 2003, 31:3305-3307.
42. Notredame C, Higgins D, Heringa J: T-Coffee: a novel method for multiple sequence alignments. J Mol Biol 2000, 302:205-217.
43. Poirot O, Suhre K, Abergel C, O'Toole E, Notredame C: 3DCoffee: a web server for mixing sequences and structures into multiple sequence alignments. Nucl Acids Res 2004, 32:W37-40.
44. Krogh A, Larsson B, von Heijne G, Sonnhammer ELL: Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 2001, 305:567-580.
45. Raghava GPS: Protein secondary structure prediction using nearest neighbor and neural network approach. CASP4 2000:75-76.
46. Cuff JA, Barton GJ: Application of enhanced multiple sequence alignment profiles to improve protein secondary structure prediction. Proteins 2000, 40:502-511.
47. Kneller DG, Cohen FE, Langridge R: Improvements in protein secondary structure prediction by an enhanced neural network. J Mol Biol 1990, 214:171-182.
48. Ouali M, King RD: Cascaded multiple classifiers for secondary structure prediction. Protein Sci 2000, 9:1162-1176.
49. McGuffin LJ, Bryson K, Jones DT: The PSIPRED protein structure prediction server. Bioinformatics 2000, 16:404-445.
50. Karplus K, Hu B: Evaluation of protein multiple alignments by SAM-T99 using the BAliBASE multiple alignment test set. Bioinformatics 2001, 17:713-720.
51. Geourjon C, Deleage G: SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci 1995, 11:681-684.
52. Pollastri G, Przybylski D, Rost B, Baldi P: Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 2002, 47:228-235.
53. Bowie JU, Luthy R, Eisenberg D: A method to identify protein sequences that fold into a known three-dimensional structure. Science 1991, 253:164-170.
54. Luthy R, Bowie JU, Eisenberg D: Assessment of protein models with three-dimensional profiles. Nature 1992, 356:83-85.
55. Sasin JM, Bujnicki JM: COLORADO3D, a web server for the visual analysis of protein structures. Nucleic Acids Res 2004, 32(Web Server):W586-W589.
56. Holm L, Sander C: Mapping the protein universe. Science 1996, 273:595-602.
57. Krissinel E, Henrick K: Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions. Acta Crystallogr D Biol Crystallogr 2004, 60(Pt 12 Pt 1):2256-2268.
58. Crooks GE, Hon G, Chandonia JM, Brenner SE: WebLogo: a sequence logo generator. Genome Res 2004, 14:1188-1190.
59. Hall TA: BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Series 1999, 41:95-98.
60. Guex N, Peitsch MC: SWISS-MODEL and the Swiss-Pdb-Viewer: an environment for comparative protein modeling. Electrophoresis 1997, 18:2714-2723.
61. Sayle R: RASMOL molecular visualization program. Biomolecular Structure Group, Glaxo Research and Development, Greenford, Middlesex, UK; 1994.
62. DeLano WL: The PyMOL molecular graphics system DeLano Scientific, San Carlos, CA, USA; 2002.
63. Marti-Renom MA, Stuart A, Fiser A, Sanchez R, Melo F, Sali A: Comparative protein structure modeling of genes and genomes. Annu Rev Biophys Biomol Struct 2000, 29:291-325.
64. Sali A, Blundell TL: Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 1993, 234:779-815.
65. Laskowski RA, MacArthur MW, Moss DS, Thornton JM: PROCHECK: a program to check the stereochemical quality of protein structures. J Appl Cryst 1993, 26:283-291.
66. Morris AL, MacArthur MW, Hutchinson EG, Thornton JM: Stereochemical quality of protein structure coordinates. Proteins 1992, 12:345-364.
67. Kitagawa H, Paulson JC: Differential expression of five sialyltransferase genes in human tissues. J Biol Chem 1994, 269:17872-17878.
68. Kim YJ, Kim KS, Kim SH, Kim CH, Ko JH, Choe IS, Tsuji S, Lee YC: Molecular cloning and expression of human Galα1,3GalNAcα2,3- sialytransferase (hST3Gal II). Biochem Biophys Res Commun 1996, 228:324-327.
69. Kitagawa H, Paulson JC: Cloning and expression of human Galβ1,3(4)GlcNAcα2,3-sialyltransferase. Biochem Biophys Res Commun 1993, 194:375-382.
70. Kitagawa H, Paulson JC: Cloning of a novel α2,3-sialyltransferase that sialylates glycoprotein and glycolipid carbohydrate groups. J Biol Chem 1994, 269:1394-1401.
71. Ishii A, Ohta M, Watanabe Y, Matsuda K, Ishiyama K, Sakoe K, Nakamura M, Inokuchi J, Sanai Y, Saito M: Expression cloning and functional characterization of human cDNA for ganglioside GM3 synthase. J Biol Chem 1998, 273:31652-31655.