Structural model for family 32 of glycosyl-hydrolase enzymes

Proteins: Structure, Function and Genetics

Volumn 33, Issue 3, 1998, Pages 383-395

  Pons, Tirso ^a   Olmea, Osvaldo ^b   Chinea, Glay ^a   Beldarraín, Alejandro ^a   Márquez, Gabriel ^a   Acosta, Niuris ^a   Rodríguez, Luis ^a   Valencia, Alfonso ^b  

^a CENTER FOR GENETIC ENGINEERING AND BIOTECHNOLOGY   (Cuba)

^b CENTRO NACIONAL DE BIOTECNOLOGÍA   (Spain)

Author keywords

Correlated mutations; Glycosidases; Phylogenic relationships; Protein structure prediction; Sequence space; Threading

Indexed keywords

BETA FRUCTOFURANOSIDASE; GLYCOSIDASE; INULINASE; LEVANASE; LEVANSUCRASE; SUCRASE;

AMINO ACID COMPOSITION; ARTICLE; BETA CHAIN; CATALYSIS; CIRCULAR DICHROISM; DIFFERENTIAL SCANNING CALORIMETRY; ENZYME ACTIVE SITE; ENZYME MECHANISM; ENZYME STRUCTURE; MOLECULAR MODEL; MUTATION; PHYLOGENY; PREDICTION; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BETA-FRUCTOFURANOSIDASE; CIRCULAR DICHROISM; GLYCOSIDE HYDROLASES; HEXOSYLTRANSFERASES; MOLECULAR SEQUENCE DATA; MUTATION; PHYLOGENY; PROTEIN CONFORMATION; SACCHAROMYCES CEREVISIAE;

EID: 0032533763     PISSN: 08873585     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1097-0134(19981115)33:3<383::AID-PROT7>3.0.CO;2-R     Document Type: Article

References (45)

1. Henrissat, B. A classification of glycosyl-hydrolases based on amino acid sequence similarities. Biochem. J. 280:309-316, 1991.
2. Henrissat, B., Bairoch, A. New families in the classification of glycosyl-hydrolases based on amino acid sequence similarities. Biochem. J. 293:781-788, 1993.
3. nd edit. 1960.
4. Reddy, V.A., Maley, F. Studies on identifying the catalytic role of Glu-204 in the active site of yeast invertase. J. Biol. Chem. 271:13953-13958, 1996.
5. Reddy, V.A., Maley, F. Identification of an active-site residue in yeast invertase by affinity labeling and site-directed mutagenesis. J. Biol. Chem. 265:10817-10820, 1990.
6. Rost, B. PHD:predicting one-dimensional protein structure by profile based neuronal networks. Methods Enzymol. 266:525-539, 1996.
7. Casari, G., Sander, C., Valencia, A. A method to predict functional residues in proteins. Nat. Struct. Biol. 2:171-178, 1995.
8. Göbel, U., Sander, C., Schneider, R., Valencia, A. Correlated mutations and residue contacts in proteins. Proteins 18:309-317, 1994.
9. Davies, G., Henrissat, B. Structures and mechanisms of glycosyl-hydrolases. Structure 3:853-859, 1995.
10. Scharf, M., Schneider, R., Casari, G. et al. GeneQuiz: A workbench for sequence analysis. In: Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology." Altman, R., Brutlog, D., Karp, P., Lathrop, R., Searls, D. (eds.). Menlo Park, California: AAAI Press, 1994:348-353.
11. Casari, G., Ouzounis, C., Valencia, A., Sander, C. GeneQuiz II: Automatic function assignment for genome sequence analysis. In; "Proceedings of the First Annual Pacific Symposium on Biocomputing." Hawaii: USA-World Scientific, 1996:707-709.
12. Henikoff, J.G., Henikoff, S. Blocks database and its applications. Methods Enzymol. 266:88-105, 1996.
13. Pearson, W.R. Effective protein sequence comparison. Methods Enzymol. 266:227-258, 1996.
14. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTALW: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, positions-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680, 1994.
15. Sander, C., Schneider, R. Database of homology-derived protein structures and the structural meaning of sequence alignment. Proteins 9:56-68, 1991.
16. Gribskov, M., McLachlan, A.D., Eisenberg, D. Profile analysis: Detection of distantly related proteins. Proc. Natl. Acad. Sci. USA 84:4355-4358, 1987.
17. Maciukenas, M. Treetool version 1.0. A phylogenetic data visualizer editor and tree formatter. Ribosomal Database Project University of Illinois. Copyright © 1992.
18. Rost, B., Sander, C. Combining evolutionary information and neural networks to predict protein secondary structure. Proteins 19:55-77, 1994.
19. Rost, B. TOPITS: Threading one-dimensional predictions into three-dimensional structures. In: "The Third International Conference on Intelligent Systems for Molecular Biology (ISMB)." Rawlings C., Clark D., Altman R., Hunter L., Lengauer T., Wodak S. (eds.). Menlo Park, California: AAAI Press, 1995:314-321.
20. Jones, D.T., Taylor, W.R., Thornton, J.M. Anew approach to protein fold recognition. Nature 358:86-89, 1992.
21. Olmea, O., Valencia, A. Improving contact prediction by the combination of correlated mutations and other sources of information. Folding & Design 2:S25-S32, 1997.
22. Vriend, G. WHATIF, a molecular modelling and drug design program. J. Mol. Graph. 8:52-56, 1990.
23. Montesino, R., Cremata, J., Rodríguez, L., Delgado, J. Low level of glycosylation of invertase secreted by methylotrophic yeast Hansenula polymorpha. Biotecnologia Aplicada 9:22-30, 1992.
24. Perczel, A., Park, K., Fasman, G.D. Analysis of the circular dichroism spectrum of proteins using the convex constraint algorithm: A practical guide. Anal. Biochem. 203:32-44, 1992.
25. Sreerama, N., Woody, R.W. A self-consistent method for the analysis of protein secondary structure from circular dichroism. Anal. Biochem. 209:32-44, 1993.
26. Cortijo, M., Beldarraín, A., Molina, A., Lapy-Lacomba, J. Digital control of a differential scanning microcalorimeter. Meas. Sci. Technol. 6:1086-1092, 1995.
27. Gunasekaran, P., Karunakaran, B., Cami, B., Mukundan, A.G., Preziosi, L., Baratti J. Cloning and sequencing of the saca gene: characterization of a sucrase from Zymomonas mobilis. J. Bacteriol. 172:6727-6735, 1990.
28. Chávez, F.P., Pons, T., Delgado, J.M., Rodríguez, L. Cloning and sequence analysis of the gene encoding invertase (INV1) from the yeast Candida utilis. Yeast, (in press).
29. Chothia, C., Lesk, A.M. The relation between the divergence of sequence and structure in proteins. EMBO J. 5:823-826, 1986.
30. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B. et al. The protein data bank: A computer-based archival file for macromolecular structures. J. Mol. Biol. 112:535-542, 1977.
31. Rost, B., Schneider, R., Sander, C. Protein fold recognition by prediction-based threading. J. Mol. Biol. 267:471-480, 1997.
32. Holm, L., Sander, C. The FSSP database of structurally aligned protein fold families. Nucleic Acids Res. 22:3600-3609, 1994.
33. Crennell, S.J., Garman, E.F., Laver, G.L., Virm, E.R., Taylor, G.L. Crystal structure of a bacterial sialidase (from Salmonella typhimurium LT2) shows the same fold as an influenza virus neuraminidase. Proc. Natl. Acad. Sci. USA, 90:9852-9856, 1993.
34. Bryant, S.H., Altschul, S.F. Statistics of sequence-structure threading. Curr. Opin. Struct. Biol 5:236-244, 1995.
35. Hobohm, U., Houthaeve, T., Sander, C. Amino acid analysis and protein database compositional search as a rapid and inexpensive method to identify proteins. Anal. Biochem. 222:202-209, 1994.
36. Ortiz, A.R., Kolinski, A., Skolnick, J. Native like topology assembly of small proteins using predicted restraints in Monte Carlo folding simulations. Proc. Natl. Acad. Sci. USA 95:1020-1025, 1998.
37. Ortiz, A.R., Kolinski, A., Skolnick, J. Fold assembly of small proteins using Monte Carlo simulations driven by restraints derived from multiple sequence alignments. J. Mol. Biol. 277:419-448, 1998.
38. Kabsch, W., Sander, C. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 22:2577-2637, 1983.
39. Sánchez-Ruíz, J.M. Theoretical analysis of Lumry-Eyring models in differential scanning calorimetry. Biophys. J. 61:921-935, 1992.
40. Sprenger, N., Bortlik, K., Brandt, A., Boller, T., Wiemkem, A. Purification, cloning, and functional expression of sucrose: fructan 6-fructosyltransferase, a key enzyme of fructan synthesis in barley. Proc. Natl. Acad. Sci. USA 92:11652-11656, 1995.
41. Bryant, S.H. Evaluation of threading specificity and accuracy. Proteins 26:172-185, 1996.
42. Rothe, B., Roggentin, P., Schauer, R. The sialidase gene from Clostridium septicum: Cloning, sequencing, expression in Escherichia coli and identification of conserved sequences in sialidases and other proteins. Mol. Gen. Genet. 226:190-197, 1991.
43. Sippl, M.J., Flöckner, H. Threading thrills and threats. Structure 4:15-19, 1996.
44. Batista, F.R., Hernández, L., Fernández, J.R., Arrieta, J., Menéndez, C., Pons, T. Site-directed mutagenesis of Asp309 in the RDP motif of the Acetobacter diazotrophicus levansucrase dramatically decreases the enzyme activity. 1998 (submitted).
45. Insight II. San Diego, California: Biosym Technologies, Inc.