Relationships between SLH motifs from different glycoside hydrolase families

Biologia - Section Cellular and Molecular Biology

Volumn 60, Issue SUPPL. 16, 2005, Pages 115-121

  Zona, Richard ^a   Janeček, Štefan ^a  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

Author keywords

Alpha amylase family; Glycoside hydrolase; SLH motif

Indexed keywords

EID: 33751339757     PISSN: 13356399     EISSN: None     Source Type: Journal    
DOI: None     Document Type: Conference Paper

References (38)

1. APWEILER, R., BAIROCH, A., 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. & YEH, L.S. 2004. UniProt: the Universal Protein knowledgebase. Nucleic Acids Res. 32: D115-D119.
2. BATEMAN, A., BIRNEY, E., CERRUTI, L., DURBIN, R., ETWILLER, L., EDDY, S.R., GRIFFITHS-JONES, S., HOWE, K.L., MARSHALL, M. & SONNHAMMER, E.L. 2002. The Pfam protein families database. Nucleic Acids Res. 30: 276-280.
3. BENSON, D.A., KARSCH-MIZRACHI, I., LIPMAN, D.J., OSTELL, J. & WHEELER, D.L. 2004. GenBank: update. Nucleic Acids Res. 32: D23-D26.
4. BEVERIDGE, T.J., POUWELS, P.H., SARA, M., KOTIRANTA, A., LOUNATMAA, K., KARI, K., KEROSUO, E., HAAPASALO, M., EGELSEER, E.M., SCHOCHER, I., SLEYTR, U.B., MORELLI, L., CALLEGARI, M.L., NOMELLINI, J.F., BINGLE, W.H., SMIT, J., LEIBOVITZ, E., LEMAIRE, M., MIRAS, I., SALAMITOU, S., BEGUIN, P., OHAYON, H., GOUNON, P., MATUSCHEK, M. & KOVAL, S.F. 1997. Functions of S-layers. FEMS Microbiol. Rev. 20: 99-149.
5. BORASTON, A.B., BOLAM, D.N., GILBERT, H.J. & DAVIES, G.J. 2004. Carbohydrate-binding modules: fine-tuning polysaccharide recognition. Biochem. J. 382: 769-781.
6. BRECHTEL, E. & BAHL, H. 1999. In Thermoanaerobacterium thermosulfurigenes EM1 S-layer homology domains do not attach to peptidoglycan. J. Bacteriol. 181: 5017-5023.
7. BRECHTEL, E., MATUSCHEK, M., HELLBERG, A., EGELSEER, E.M., SCHMID, R. & BAHL, H. 1999. Cell wall of Thermoanaerobacterium thermosulfurigenes EM1: isolation of its components and attachment of the xylanase XynA. Arch. Microbiol. 171: 159-165.
8. CHANG-PI-HIN, F., ERRA-PUJADA, M., DAUCHEZ, M., DEBEIRE, P., DUCHIRON, F. &. O'DONOHUE, M.J. 2002. Expression and characterization of the catalytic domain of an archaeal family 57 pullulanase type II. Biologia, Bratislava 57 (Suppl. 11): 155-162.
9. CHEN, J.T., CHEN, M.C., CHEN, L.L. & CHU, W.S. 2001. Structure and expression of an amylopullulanase gene from Bacillus stearothermophilus TS-23. Biotechnol. Appl. Biochem. 33: 189-199.
10. COHEN, G.N., BARBE, V., FLAMENT, D., GALPERIN, M., HEILIG, R., LECOMPTE, O., POCH, O., PRIEUR, D., QUERELLOU, J., RIPP, R., THIERRY, J.C., VAN DER OOST, J., WEISSENBACH, J., ZIVANOVIC, Y. & FORTERRE, P. 2003. An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi. Mol. Microbiol. 47: 1495-1512.
11. COUTINHO, P. M. & HENRISSAT, B. 1999. Carbohydrate-Active Enzymes server; http://afmb.cnrs-mrs.fr/CAZY/.
12. ENGELHARDT, H. & PETERS, J. 1998. Structural research on surface layers: a focus on stability, surface layer homology domains, and surface layer-cell wall interactions. J. Struct. Biol. 124: 276-302.
13. ERRA-PUJADA, M., DEBEIRE, P., DUCHIRON, F. & O'DONOHUE, M.J. 1999. The type II pullulanase of Thermococcus hydrothermalis: molecular characterization of the gene and expression of the catalytic domain. J. Bacteriol. 181: 3284-3287.
14. ERRA-PUJADA, M., CHANG-PI-HIN, F., DEBEIRE, P., DUCHIRON, F. & O'DONOHUE, M. J. 2001. Purification and properties of the catalytic domain of the thermostable pullulanase type II from Thermococcus hydrothermalis. Biotechnol. Lett. 23: 1273-1277.
15. FELSENSTEIN, J. 1985. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783-791.
16. JANECEK, S. 2002. How many conserved sequence regions are there in the α-amylase family? Biologia, Bratislava 57 (Suppl. 11): 29-41.
17. JANECEK, S. & SEVCIK, J. 1999. The evolution of starch-binding domain. FEBS Lett. 456: 119-125.
18. JANECEK, Š., SVENSSON, B. & MACGREGOR, E.A. 2003. Relation between domain evolution, specificity, and taxonomy of the α-amylase family members containing a C-terminal starch-binding domain. Eur. J. Biochem. 270: 635-645.
19. LEE, S.P., MORIKAWA, M., TAKAGI, M. & IMANAKA, T. 1994. Cloning of the aapT gene and characterization of its product, α-amylase-pullulanase (AapT), from thermophilic and alkaliphilic Bacillus sp. strain XAL601. Appl. Environ. Microbiol. 60: 3764-3773.
20. LEMAIRE, M., OHAYON, H., GOUNON, P., FUJINO, T. & BÉGUIN, P. 1995. OlpB, a new outer layer protein of Clostridium thermocellum, and binding of its S-layer-like domains to components of the cell envelope. J. Bacteriol. 177: 2451-2459.
21. LUPAS, A., ENGELHARDT, H., PETERS, J., SANTARIUS, U., VOLKER, S. & BAUMEISTER, W. 1994. Domain structure of the Acetogenium kivui surface layer revealed by electron crystallography and sequence analysis. J. Bacteriol. 176: 1224-1233.
22. MACGREGOR, E.A. 2005. An overview of clan GH-H and distantly-related families. Biologia, Bratislava 60 (Suppl. 16): 5-12.
23. MACGREGOR, E.A., JANECEK, S. & SVENSSON, B. 2001. Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim Biophys Acta 1546: 1-20.
24. MATUSCHEK, M., BURCHHARDT, G., SAHM, K. & BAHL, H. 1994. Pullulanase of Thermoanaerobacterium thermosulfurigenes EM1 (Clostridium thermosulfurogenes): molecular analysis of the gene, composite structure of the enzyme, and a common model for its attachment to the cell surface. J. Bacteriol. 176: 3295-3302.
25. MATUSCHEK, M., SAHM, K., ZIBAT, A. & BAHL, H. 1996. Characterization of genes from Thermoanaerobacterium thermosulfurigenes EM1 that encode two glycosyl hydrolases with conserved S-layer-like domains. Mol. Gen. Genet. 252: 493-496.
26. MESNAGE, S., TOSI-COUTURE, E. & FOUET, A. 1999. Production and cell surface anchoring of functional fusions between the SLH motifs of the Bacillus anthracis S-layer proteins and the Bacillus subtilis levansucrase. Mol. Microbiol. 31: 927-936.
27. MESNAGE, S., FONTAINE, T., MIGNOT, T., DELEPIERRE, M., MOCK, M. & FOUET, A. 2000. Bacterial SLH domain proteins are non-covalently anchored to the cell surface via a conserved mechanism involving wall polysaccharide pyruvylation. EMBO J. 19: 4473-4484.
28. MIZUNO, M., TONOZUKA, T., ICHIKAWA, K., KAMITORI, S., NISHIKAWA, A. & SAKANO, Y. 2005. Three-dimensional structure of glucodextranase, a glycoside hydrolase family 15 enzyme. Biologia, Bratislava 60 (Suppl. 16): 171-177.
29. MIZUNO, M., TONOZUKA, T., SUZUKI, S., UOTSU-TOMITA, R., KAMITORI, S., NISHIKAWA, A. & SAKANO, Y. 2004. Structural insight into substrate specificity and function of glucodextranase. J. Biol. Chem. 279: 10575-10583.
30. PAGE, R.D. 1996. TREEVIEW: an application to display phylogenetic trees on personal computers. Comput. Applic. Biosci. 12: 357-358.
31. PETERS, J., PETERS, M., LOTTSPEICH, F. & BAUMEISTER, W. 1989. S-layer protein gene of Acetogenium kivui: cloning and expression in Escherichia coli and determination of the nucleotide sequence. J. Bacteriol. 171: 6307-6315.
32. RODRIGUEZ-SANOJA, R., OVIEDO, N. & SANCHEZ, S. 2005. Microbial starch-binding domain. Curr. Opin. Microbiol. 8: 260-267.
33. SAITOU, N. & NEI, M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
34. SCHWARZ, W.H., ZVERLOV, V.V. & BAHL, H. 2004. Extracellular glycosyl hydrolases from clostridia. Adv. Appl. Microbiol. 56: 215-261.
35. STOLL, D., STALBRAND, H. & WARREN, R.A.J. 1999. Mannan-degrading enzymes from Cellulomonas fimi. Appl. Environ. Microbiol. 65: 2598-2605.
36. SVENSSON, B., JENSEN, M.T., MORI, H., BAK-JENSEN, K.S., BŘNSAGER, B., NIELSEN, P.K., KRAMHŘFT, B., PRTORIUS-IBBA, M., NŘHR, J., JUGE, N., GREFFE, L., WILLIAMSON, G. & DRIGUEZ, H. 2002. Fascinating facets of function and structure of amylolytic enzymes of glycoside hydrolase family 13. Biologia, Bratislava 57 (Suppl. 11): 5-19.
37. THOMPSON, J.D., HIGGINS, D.G. & GIBSON, T.J. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position specific gap penalties and weight matrix choice. Nucleic Acids Res. 22: 4673-4680.
38. ZONA, R., CHANG-PI-HIN, F., O'DONOHUE, M.J. & JANECEK, S. 2004. Bioinformatics of the glycoside hydrolase family 57 and identification of catalytic residues in amylopullulanase from Thermococcus hydrothermalis. Eur. J. Biochem. 271: 2863-2872.