Sequence Fingerprints in the Evolution of the α-Amylase Family

Carbohydrate-Active Enzymes: Structure, Function and Applications

Volumn , Issue , 2008, Pages 45-63

  Janeček, Tefan ^a  

^a UNIVERSITY OF SS CYRIL AND METHODIUS   (Slovakia)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 77951738053     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1533/9781845695750.1.45     Document Type: Chapter

References (64)

1. Bahl H., Burchhardt G., Spreinat A., Haeckel K., Wienecke A., Schmidt B., Antranikian G. α-Amylase of Clostridium thermosulfurogenes EM1: nucleotide sequence of the gene, processing of the enzyme, and comparison of other α-amylases. Appl Environ Microbiol 1991, 57:1554-1559.
2. Coutinho P.M., Henrissat B. Carbohydrate-active enzymes: an integrated database approach. Recent Advances in Carbohydrate Bioengineering 1999, 3-12. The Royal Society of Chemistry, Cambridge. http://www.cazy.org/, H.J. Gilbert, G. Davies, B. Henrissat, B. Svensson (Eds.).
3. Da Lage J.L., Feller G., Janecek S. Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the α-amylase model. Cell Mol Life Sci 2004, 61:97-109.
4. Dijkstra B.W., Vujicic-Zagar A., Pijning T., Kralj S., Dijkhuizen L. Structural and functional characterization of a glucansucrase (δN-GTF180) from Lactobacillus reuteri 180, a GH family 70 enzyme 2007, Asco Arts & Sicence, Bratislava, Sep 23-27, 2007, 15. S. Janecek (Ed.).
5. Fort J., de la Ballina L.R., Burghardt H.E., Ferrer-Costa C., Turnay J., Ferrer-Orta C., Uson I., Zorzano A., Fernandez-Recio J., Orozco M., Lizarbe M.A., Fita I., Palacin M. The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. J Biol Chem 2007, 282:31444-31452.
6. Fraser C.M., Casjens S., Huang W.M., Sutton G.G., Clayton R., Lathigra R., White O., Ketchum K.A., Dodson R., Hickey E.K., Gwinn M., Dougherty B., Tomb J.F., Fleischmann R.D., Richardson D., Peterson J., Kerlavage A.R., Quackenbush J., Salzberg S., Hanson M., van Vugt R., Palmer N., Adams M.D., Gocayne J., Weidman J., Utterback T., Watthey L., McDonald L., Artiach P., Bowman C., Garland S., Fuji C., Cotton M.D., Horst K., Roberts K., Hatch B., Smith H.O., Venter J.C. Genomic sequence of a Lyme disease spirochaete Borrelia burgdorferi. Nature 1997, 390:580-586.
7. Friedberg F. On the primary structure of amylases. FEBS Lett 1983, 152:139-140.
8. Godany A., Vidova B., Janecek S. The unique glycoside hydrolase family 77 amylomaltase from Borrelia burgdorferi with only catalytic triad conserved. FEMS Microbiol Lett 2008, 284:84-91.
9. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 1991, 280:309-316.
10. Hutcheon G.W., Vasisht N., Bolhuis A. Characterisation of a highly stable α-amylase from the halophilic archaeon Haloarcula hispanica. Extremophiles 2005, 9:487-495.
11. Itkor P., Tsukagoshi N., Udaka S. Nucleotide sequence of the raw-starchdigesting amylase gene from Bacillus sp. B1018 and its strong homology to the cyclodextrin glucanotransferase genes. Biochem Biophys Res Commun 1990, 166:630-636.
12. 8-barrel domains. Biochem J 1992, 288:1069-1070.
13. Janecek S. Sequence similarities and evolutionary relationships of microbial, plant and animal α-amylases. Eur J Biochem 1994, 224:519-524.
14. Janecek S. Parallel β/α-barrels of α-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of β-amylase: evolutionary distance is a reflection of unrelated sequences. FEBS Lett 1994, 353:119-123.
15. 8-barrel glycosyl hydrolases suggested by the similarity of their fifth conserved sequence region. FEBS Lett 1995, 377:6-8.
16. Janecek S. Structural features and evolutionary relationships in the α-amylase family,. Glycoenzymes 2000, 19-54. Japan Scientific Societies Press, Karger Publishers, Tokyo, Basel. M. Ohnishi, T. Hayashi, S. Ishijima, T. Kuriki (Eds.).
17. Janecek S. How many conserved sequence regions are there in the α-amylase family?. Biologia 2002, 57(Suppl 11):29-41.
18. Janecek S., Leveque E., Belarbi A., Haye B. Close evolutionary relatedness of α-amylases from Archaea and plants. J Mol Evol 1999, 48:421-426.
19. Janecek S., MacGregor E.A., Svensson B. Characteristic differences in the primary structure allow discrimination of cyclodextrin glucanotransferases from α-amylases. Biochem J 1995, 305:685-686.
20. Janecek S., Svensson B., Henrissat B. Domain evolution in the α-amylase family. J Mol Evol 1997, 45:322-331.
21. Janecek S., Svensson B., MacGregor E.A. A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31. FEES Lett 2007, 581:1261-1268.
22. 8-barrel domain and evolutionary relationship to other amylolytic enzymes. J Protein Chem 1993, 12:791-805.
23. Jespersen H.M., MacGregor E.A., Sierks M.R., Svensson B. Comparison of the domain-level organization of starch hydrolases and related enzymes. Biochem J 1991, 280:51-55.
24. Jones R.A., Jermiin L.S., Easteal S., Patel B.K., Beacham I.R. Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium. J Appl Microbiol 1999, 86:93-107.
25. Kadziola A., Sogaard M., Svensson B., Haser R. Molecular structure of a barley α-amylase-inhibitor complex: implications for starch binding and catalysis. J Mol Biol 1998, 278:205-217.
26. Kaper T., Talik B., Ettema T.J., Bos H., van der Maarel M.J., Dijkhuizen L. Amylomaltase of Pyrobaculum aerophilum IM2 produces thermoreversible starch gels. Appl Environ Microbiol 2005, 71:5098-5106.
27. Knegtel R.M., Wind R.D., Rozeboom H.J., Kalk K.H., Buitelaar R.M., Dijkhuizen L., Dijkstra B.W. Crystal structure at 2.3 ↗ resolution and revised nucleotide sequence of the thermostable cylodextrin glycosyltransferase from Themoanaerobacterium thermosulfurigenes EM1. J Mol Biol 1996, 256:611-622.
28. Kobayashi T., Kanai H., Aono R., Horikoshi K., Kudo T. Cloning, expression, and nucleotide sequence of the α-amylase gene from the haloalkaliphilic archaeon Natronococcus sp. strain Ah-36. J Bacteriol 1994, 176:5131-5134.
29. Kobayashi T., Kanai H., Hayashi T., Akiba T., Akaboshi R., Horikoshi K. Haloalkaliphilic maltotriose-forming α-amylase from the archaebacterium Natronococcus sp. strain Ah-36. J Bacteriol 1992, 174:3439-3444.
30. Kuriki T., Imanaka T. Nucleotide sequence of the neopullulanase gene from. Bacillus stearothermophilus', J Gen Microbiol 1989, 135:1521-1528.
31. Kuriki T., Imanaka T. The concept of the α-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng 1999, 87:5565-5575.
32. Kuriki T., Takata H., Yanase M., Ohdan K., Fujii K., Terada Y., Takaha T., Hondoh H., Matsuura Y., Imanaka T. The concept of the α-amylase family: a rational tool for interconverting glucanohydrolases/glucanotransferases, and their specificities. J Appl Glycosci 2006, 53:155-161.
33. Lee H.S., Kim M.S., Cho H.S., Kim J.I., Kim T.J., Choi J.H., Park C., Lee H.S., Oh B.H., Park K.H. Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other. J Biol Chem 2002, 277:21891-21897.
34. Leveque E., Haye B., Belarbi A. Cloning and expression of an α-amylase encoding gene from the hyperthermophilic archaebacterium Thermococcus hydrothermalis and biochemical characterisation of the recombinant enzyme. FEMS Microbiol Lett 2000, 186:67-71.
35. Linden A., Mayans O., Meyer-Klaucke W., Antranikian G., Wilmanns M. Differential regulation of a hyperthermophilic α-amylase with a novel (Ca,Zn) twometal center by zinc. J Biol Chem 2003, 278:9875-9884.
36. MacGregor E.A. α-Amylase structure and activity. J Protein Chem 1988, 7:399-415.
37. MacGregor E.A., Janecek S., Svensson B. Relationship of sequence and structure to specificity in the α-amylase family of enzymes. Biochim Biophys Acta 2001, 1546:1-20.
38. MacGregor E.A., Jespersen H.M., Svensson B. A circularly permuted α-amylase-type α/β-barrel structure in glucan-synthesizing glucosyltransferases. FEBS Lett 1996, 378:263-266.
39. MacGregor E.A., Svensson B. A supersecondary structure predicted to be common to several α-1,4-D-glucan-cleaving enzymes. Biochem J 1989, 259:145-152.
40. Machovic M., Janecek S. The invariant residues in the α-amylase family: just the catalytic triad. Biologia 2003, 58:1127-1132.
41. Matsuura Y., Kusunoki M., Harada W., Kakudo M. Structure and possible catalytic residues of Taka-amylase A. J Biochem 1984, 95:697-702.
42. Nakajima R., Imanaka T., Aiba S. Comparison of amino acid sequences of eleven different α-amylases. Appl Microbiol Biotechnol 1986, 23:355-360.
43. Nitschke L., Heeger K., Bender H., Schulz G.E. Molecular cloning, nucleotide sequence and expression in Escherichia coli of the β-cyclodextrin glycosyltransferase gene from Bacillus circulans strain no. 8. Appl Microbiol Biotechnol 1990, 33:542-546.
44. Oh B.H. The same group of enzymes with different names: cyclomaltodextrinases, neopullulanases, and maltogenic amylases. Biologia 2003, 58:299-305.
45. Oslancova A., Janecek S. Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the α-amylase family defined by the fifth conserved sequence region. Cell Mol Life Sci 2002, 59:1945-1959.
46. Page R.D. TreeView: an application to display phylogenetic trees on personal computers. Comput Applic Biosci 1996, 12:357-358.
47. Park J.H., Kim H.J., Kim Y.H., Cha H., Kim Y.W., Kim T.J., Kim Y.R., Park K.H. The action mode of Thermus aquaticus YT-1 4α-glucanotransferase and its chimeric enzymes introduced with starch-binding domain on amylose and amylopectin. Carbohydr Polym 2007, 67:164-173.
48. Park K.H., Kim T.J., Cheong T.K., Kim J.W., Oh B.H., Svensson B. Structure, specificity and function of cyclomaltodextrinase, a multispecific enzyme of the α-amylase family. Biochim Biophys Acta 2000, 1478:165-185.
49. Przylas I., Tomoo K., Terada Y., Takaha T., Fujii K., Saenger W., Straeter N. Crystal structure of amylomaltase from Thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. J Mol Biol 2000, 296:873-886.
50. Raha M., Kawagishi I., Mueller V., Kihara M., Macnab R.M. Escherichia coli produces a cytoplasmic α-amylase AmyA. J Bacteriol 1992, 174:6644-6652.
51. Rogers J.C. Conserved amino acid sequence domains in α-amylases from plants, mammals, and bacteria. Biochem Biophys Res Commun 1985, 128:470-476.
52. Roujeinikova A., Raasch C., Burke J., Baker P.J., Liebl W., Rice D.W. The crystal structure of Thermotoga maritima maltosyltransferase and its implications for the molecular basis of the novel transfer specificity. J Mol Biol 2001, 312:119-131.
53. Stam M.R., Danchin E.G., Rancurel C., Coutinho P.M., Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng Des Sel 2006, 19:555-562.
54. Svensson B. Regional distant sequence homology between amylases, α-glucosidases and transglucanosylases. FEBS Lett 1988, 230:72-76.
55. Svensson B. Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol Biol 1994, 25:141-157.
56. Takata H., Kuriki T., Okada S., Takesada Y., Iizuka M., Minamiura N., Imanaka T. Action of neopullulanase. Neopullulanase catalyzes both hydrolysis and transglycosylation at α(14)- and alph-(16)-glucosidic linkages. J Biol Chem 1992, 267:18447-18452.
57. Terada Y., Fujii K., Takaha T., Okada S. Thermus aquaticus ATCC 33923 amylomaltase gene cloning and expression and enzyme characterization: production of cycloamylose. Appl Environ Microbiol 1999, 65:910-915.
58. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 1994, 22:4673-4680.
59. Toda H., Kondo K., Narita K. The complete amino acid sequence of Taka-amylase A. Proc Japan Acad 1982, B58:208-212.
60. Uitdehaag J.C., Mosi R., Kalk K.H., van der Veen B.A., Dijkhuizen L., Withers S.G., Dijkstra B.W. X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family. Nature Struct Biol 1999, 6:432-436.
61. van der Kaaij R.M., Janecek S., van der Maarel M.J., Dijkhuizen L. Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes. Microbiology 2007, 153:4003-4015.
62. Watanabe K., Kitamura K., Iha H., Suzuki Y. Primary structure of the oligo-1,6-glucosidase of Bacillus cereus ATCC7064 deduced from the nucleotide sequence of the cloned gene. Eur J Biochem 1990, 192:609-620.
63. Wind R.D., Liebl W., Buitelaar R.M., Penninga D., Spreinat A., Dijkhuizen L., Bahl H. Cyclodextrin formation by the thermostable α-amylase of Thermoanaerobacterium thermosulfurigenes EM1 and reclassification of the enzyme as a cyclodextrin glycosyltransferase. Appl Environ Microbiol 1995, 61:1257-1265.
64. Yuuki T., Nomura T., Tezuka H., Tsuboi A., Yamagata H., Tsukagoshi N., Udaka S. Complete nucleotide sequence of a gene coding for heat- and pH-stable α-amylase of Bacillus licheniformis: comparison of the amino acid sequences of three bacterial liquefying α-amylases deduced from the DNA sequences. J Biochem 1985, 98:1147-1156.