α-Amylase: An enzyme specificity found in various families of glycoside hydrolases

Cellular and Molecular Life Sciences

Volumn 71, Issue 7, 2014, Pages 1149-1170

  Janeček, Štefan ^a   Svensson, Birte ^b   MacGregor, E Ann ^c  

^a INSTITUTE OF CHEMISTRY   (Slovakia)

^b TECHNICAL UNIVERSITY OF DENMARK   (Denmark)

^c NONE   (United Kingdom)

Author keywords

Catalytic machinery; Conserved sequence regions; Evolutionary relationships; GH13, GH57, GH119, GH126; Glycoside hydrolase families; Amylase

Indexed keywords

AMYLASE; GLYCOSIDASE;

AMINO ACID SEQUENCE; CHEMISTRY; CLASSIFICATION; ENZYME ACTIVE SITE; ENZYME SPECIFICITY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; PHYSIOLOGY; PROTEIN TERTIARY STRUCTURE; REVIEW; SEQUENCE ALIGNMENT;

ALPHA-AMYLASES; AMINO ACID SEQUENCE; CATALYTIC DOMAIN; CONSERVED SEQUENCE; EVOLUTION, MOLECULAR; GLYCOSIDE HYDROLASES; MOLECULAR SEQUENCE DATA; PHYLOGENY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY;

EID: 84899863334     PISSN: 1420682X     EISSN: 14209071     Source Type: Journal    
DOI: 10.1007/s00018-013-1388-z     Document Type: Review

References (260)

1. Henrissat B (1991) A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 280:309-316
2. Henrissat B, Bairoch A (1993) New families in the classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J 293:781-788
3. Henrissat B, Bairoch A (1996) Updating the sequence-based classification of glycosyl hydrolases. Biochem J 316:695-696
4. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for glycogenomics. Nucleic Acids Res 37:D233-D238
5. Henrissat B, Davies GJ (1997) Structural and sequence-based classification of glycoside hydrolases. Curr Opin Struct Biol 7:637-644
6. Stam MR, Danchin EG, Rancurel C, Coutinho PM, Henrissat B (2006) Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of α-amylase-related proteins. Protein Eng Des Sel 19:555-562
7. Aspeborg H, Coutinho PM, Wang Y, Brumer H 3rd, Henrissat B (2012) Evolution, substrate specificity and subfamily classification of glycoside hydrolase family 5 (GH5). BMC Evol Biol 12:186
8. St John FJ, Gonzalez JM, Pozharski E (2010) Consolidation of glycosyl hydrolase family 30: a dual domain 4/7 hydrolase family consisting of two structurally distinct groups. FEBS Lett 584:4435-4441
9. MacGregor EA (1988) α-Amylase structure and activity. J Protein Chem 7:399-415
10. MacGregor EA, 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
11. Brzozowski AM, Davies GJ (1997) Structure of the Aspergillus oryzae α-amylase complexed with the inhibitor acarbose at 2.0 Å resolution. Biochemistry 36:10837-10845
12. Aghajari N, Roth M, Haser R (2002) Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic α-amylase. Biochemistry 41:4273-4280
13. Ramasubbu N, Ragunath C, Mishra PJ (2003) Probing the role of a mobile loop in substrate binding and enzyme activity of human salivary amylase. J Mol Biol 325:1061-1076
14. Li C, Begum A, Numao S, Park KH, Withers SG, Brayer GD (2005) Acarbose rearrangement mechanism implied by the kinetic and structural analysis of human pancreatic α-amylase in complex with analogues and their elongated counterparts. Biochemistry 44:3347-3357
15. Brzozowski AM, Lawson DM, Turkenburg JP, Bisgaard-Frantzen H, Svendsen A, Borchert TV, Dauter Z, Wilson KS, Davies GJ (2000) Structural analysis of a chimeric bacterial α-amylase. High-resolution analysis of native and ligand complexes. Biochemistry 39:9099-9107
16. Janecek S, Svensson B, MacGregor EA (1995) Characteristic differences in the primary structure allow discrimination of cyclodextrin glucanotransferases from α-amylases. Biochem J 305:685-686
17. Ficko-Blean E, Stuart CP, Boraston AB (2011) Structural analysis of CPF-2247, a novel α-amylase from Clostridium perfringens. Proteins 79:2771-2777
18. Svensson B (1988) Regional distant sequence homology between amylases, α-glucosidases and transglucanosylases. FEBS Lett 230:72-76
19. Kuriki T, Imanaka T (1989) Nucleotide sequence of the neopullulanase gene from Bacillus stearothermophilus. J Gen Microbiol 135:1521-1528
20. MacGregor EA, Svensson B (1989) A super-secondary structure predicted to be common to several α-1,4-d-glucan-cleaving enzymes. Biochem J 259:145-152
21. Jespersen HM, MacGregor EA, Sierks MR, Svensson B (1991) Comparison of the domain-level organization of starch hydrolases and related enzymes. Biochem J 280:51-55
22. Svensson B, Janecek S (2013) Glycoside hydrolase family 13. CAZypedia. http://www.cazypedia.org/. Accessed 18 Mar 2013
23. Janecek S, Svensson B, Henrissat B (1997) Domain evolution in the α-amylase family. J Mol Evol 45:322-331
24. Fort J, de la Ballina LR, Burghardt HE, Ferrer-Costa C, Turnay J, Ferrer-Orta C, Uson I, Zorzano A, Fernandez-Recio J, Orozco M, Lizarbe MA, Fita I, Palacin M (2007) The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. J Biol Chem 282:31444-31452
25. Gabrisko M, Janecek S (2009) Looking for the ancestry of the heavy-chain subunits of heteromeric amino acid transporters rBAT and 4F2hc within the GH13 α-amylase family. FEBS J 276:7265-7278
26. MacGregor EA (1993) Relationships between structure and activity in the α-amylase family of starch-metabolising enzymes. Starch/Staerke 45:232-237
27. Janecek S (1994) 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 353:119-123
28. Svensson B (1994) Protein engineering in the α-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol Biol 25:141-157
29. Kuriki T, Imanaka T (1999) The concept of the α-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng 87:557-565
30. van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, Dijkhuizen L (2002) Properties and applications of starch-converting enzymes of the α-amylase family. J Biotechnol 94:137-155
31. Matsuura Y, Kusunoki M, Harada W, Kakudo M (1984) Structure and possible catalytic residues of Taka-amylase A. J Biochem 95:697-702
32. Banner DW, Bloomer AC, Petsko GA, Phillips DC, Pogson CI, Wilson IA, Corran PH, Furth AJ, Milman JD, Offord RE, Priddle JD, Waley SG (1975) Structure of chicken muscle triose phosphate isomerase determined crystallographically at 2.5 angstrom resolution using amino acid sequence data. Nature 255:609-614
33. Farber GK, Petsko GA (1990) The evolution of α/β barrel enzymes. Trends Biochem Sci 15:228-234
34. Penninga D, van der Veen BA, Knegtel RM, van Hijum SA, Rozeboom HJ, Kalk KH, Dijkstra BW, Dijkhuizen L (1996) The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J Biol Chem 271:32777-32784
35. Abe A, Tonozuka T, Sakano Y, Kamitori S (2004) Complex structures of Thermoactinomyces vulgaris R-47 α-amylase 1 with malto-oligosaccharides demonstrate the role of domain N acting as a starch-binding domain. J Mol Biol 335:811-822
36. Boraston AB, Healey M, Klassen J, Ficko-Blean E, Lammerts van Bueren A, Law V (2006) A structural and functional analysis of α-glucan recognition by family 25 and 26 carbohydrate-binding modules reveals a conserved mode of starch recognition. J Biol Chem 281:587-598
37. van Bueren AL, Boraston AB (2007) The structural basis of α-glucan recognition by a family 41 carbohydrate-binding module from Thermotoga maritima. J Mol Biol 365:555-560
38. Koropatkin NM, Smith TJ (2010) SusG: a unique cell-membrane-associated α-amylase from a prominent human gut symbiont targets complex starch molecules. Structure 18:200-215
39. Svensson B, Jespersen H, Sierks MR, MacGregor EA (1989) Sequence homology between putative raw-starch binding domains from different starch-degrading enzymes. Biochem J 264:309-311
40. Janecek S, Sevcik J (1999) The evolution of starch-binding domain. FEBS Lett 456:119-125
41. Janecek S, Svensson B, MacGregor EA (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
42. Rodriguez-Sanoja R, Oviedo N, Sanchez S (2005) Microbial starch-binding domain. Curr Opin Microbiol 8:260-267
43. Machovic M, Janecek S (2006) Starch-binding domains in the post-genome era. Cell Mol Life Sci 63:2710-2724
44. Christiansen C, Abou Hachem M, Janecek S, Viksø-Nielsen A, Blennow A, Svensson B (2009) The carbohydrate-binding module family 20 - diversity, structure, and function. FEBS J 276:5006-5029
45. Janecek S, Svensson B, MacGregor EA (2011) Structural and evolutionary aspects of two families of non-catalytic domains present in starch and glycogen binding proteins from microbes, plants and animals. Enzyme Microb Technol 49:429-440
46. Janecek S (2002) How many conserved sequence regions are there in the α-amylase family? Biologia 57(Suppl 11):29-41
47. Takata H, Kuriki T, Okada S, Takesada Y, Iizuka M, Minamiura N, Imanaka T (1992) Action of neopullulanase. Neopullulanase catalyzes both hydrolysis and transglycosylation at α-(1,4)- and α-(1,6)-glucosidic linkages. J Biol Chem 267:18447-18452
48. Nakajima R, Imanaka T, Aiba S (1986) Comparison of amino acid sequences of eleven different α-amylases. Appl Microbiol Biotechnol 23:355-360
49. Toda H, Kondo K, Narita K (1982) The complete amino acid sequence of Taka-amylase A. Proc Jpn Acad B58:208-212
50. Friedberg F (1983) On the primary structure of amylases. FEBS Lett 152:139-140
51. Rogers JC (1985) Conserved amino acid sequence domains in α-amylases from plants, mammals, and bacteria. Biochem Biophys Res Commun 128:470-476
52. 8-barrel domains. Biochem J 288:1069-1070
53. Janecek S (1994) Sequence similarities and evolutionary relationships of microbial, plant and animal α-amylases. Eur J Biochem 224:519-524
54. MacGregor EA, Jespersen HM, Svensson B (1996) A circularly permuted α-amylase-type α/β-barrel structure in glucan-synthesizing glucosyltransferases. FEBS Lett 378:263-266
55. Vujicic-Zagar A, Pijning T, Kralj S, Lopez CA, Eeuwema W, Dijkhuizen L, Dijkstra BW (2010) Crystal structure of a 117-kDa glucansucrase fragment provides insight into evolution and product specificity of GH70 enzymes. Proc Natl Acad Sci USA 107:21406-21411
56. Ito K, Ito S, Shimamura T, Weyand S, Kawarasaki Y, Misaka T, Abe K, Kobayashi T, Cameron AD, Iwata S (2011) Crystal structure of glucansucrase from the dental caries pathogen Streptococcus mutans. J Mol Biol 408:177-186
57. Brison Y, Pijning T, Malbert Y, Fabre E, Mourey L, Morel S, Potocki-Veronese G, Monsan P, Tranier S, Remaud-Simeon M, Dijkstra BW (2012) Functional and structural characterization of α-(1,2) branching sucrase derived from DSR-E glucansucrase. J Biol Chem 287:7915-7924
58. Pijning T, Vujicic-Zagar A, Kralj S, Dijkhuizen L, Dijkstra BW (2012) Structure of the α-1,6/α-1,4-specific glucansucrase GTFA from Lactobacillus reuteri 121. Acta Crystallogr Sect F Struct Biol Cryst Commun 68:1448-1454
59. Przylas I, Tomoo K, Terada Y, Takaha T, Fujii K, Saenger W, Sträter N (2000) Crystal structure of amylomaltase from Thermus aquaticus, a glycosyltransferase catalysing the production of large cyclic glucans. J Mol Biol 296:873-886
60. Barends TR, Bultema JB, Kaper T, van der Maarel MJ, Dijkhuizen L, Dijkstra BW (2007) Three-way stabilization of the covalent intermediate in amylomaltase, an α-amylase-like transglycosylase. J Biol Chem 282:17242-17249
61. Jung JH, Jung TY, Seo DH, Yoon SM, Choi HC, Park BC, Park CS, Woo EJ (2011) Structural and functional analysis of substrate recognition by the 250s loop in amylomaltase from Thermus brockianus. Proteins 79:633-644
62. Godany A, Vidova B, Janecek S (2008) The unique glycoside hydrolase family 77 amylomaltase from Borrelia burgdorferi with only catalytic triad conserved. FEMS Microbiol Lett 284:84-91
63. Machovic M, Janecek S (2003) The invariant residues in the α-amylase family: just the catalytic triad. Biologia 58:1127-1132
64. 8-barrel domain and evolutionary relationship to other amylolytic enzymes. J Protein Chem 12:791-805
65. Janecek S (1997) α-Amylase family: molecular biology and evolution. Prog Biophys Mol Biol 67:67-97
66. Janecek S, Svensson B, MacGregor EA (2007) A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31. FEBS Lett 581:1261-1268
67. Oslancova A, Janecek S (2002) Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the α-amylase family defined by the fifth conserved sequence region. Cell Mol Life Sci 59:1945-1959
68. Aghajari N, Feller G, Gerday C, Haser R (1998) Crystal structures of the psychrophilic α-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci 7:564-572
69. Aghajari N, Feller G, Gerday C, Haser R (1998) Structures of the psychrophilic Alteromonas haloplanctis α-amylase give insights into cold adaptation at a molecular level. Structure 6:1503-1516
70. Tan TC, Mijts BN, Swaminathan K, Patel BK, Divne C (2008) Crystal structure of the polyextremophilic α-amylase AmyB from Halothermothrix orenii: details of a productive enzyme-substrate complex and an N domain with a role in binding raw starch. J Mol Biol 378:852-870
71. Puspasari F, Radjasa OK, Noer AS, Nurachman Z, Syah YM, van der Maarel M, Dijkhuizen L, Janecek S, Natalia D (2013) Raw starch-degrading α-amylase from Bacillus aquimaris MKSC 6.2: isolation and expression of the gene, bioinformatics and biochemical characterization of the recombinant enzyme. J Appl Microbiol 114:108-120
72. Boel E, Brady L, Brzozowski AM, Derewenda Z, Dodson GG, Jensen VJ, Petersen SB, Swift H, Thim L, Woldike HF (1990) Calcium binding in α-amylases: an X-ray diffraction study at 2.1-Å resolution of two enzymes from Aspergillus. Biochemistry 29:6244-6249
73. Vujicic-Zagar A, Dijkstra BW (2006) Monoclinic crystal form of Aspergillus niger α-amylase in complex with maltose at 1.8 Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 62:716-721
74. Siddiqui KS, Poljak A, De Francisci D, Guerriero G, Pilak O, Burg D, Raftery MJ, Parkin DM, Trewhella J, Cavicchioli R (2010) A chemically modified α-amylase with a molten-globule state has entropically driven enhanced thermal stability. Protein Eng Des Sel 23:769-780
75. Sugahara M, Takehira M, Yutani K (2013) Effect of heavy atoms on the thermal stability of α-amylase from Aspergillus oryzae. PLoS ONE 8:e57432
76. Iefuji H, Chino M, Kato M, Iimura Y (1996) Raw-starch-digesting and thermostable α-amylase from the yeast Cryptococcus sp. S-2: purification, characterization, cloning and sequencing. Biochem J 318:989-996
77. Galdino AS, Ulhoa CJ, Moraes LM, Prates MV, Bloch C Jr, Torres FA (2008) Cloning, molecular characterization and heterologous expression of AMY1, an α-amylase gene from Cryptococcus flavus. FEMS Microbiol Lett 280:189-194
78. Steyn AJ, Marmur J, Pretorius IS (1995) Cloning, sequence analysis and expression in yeasts of a cDNA containing a Lipomyces kononenkoae α-amylase-encoding gene. Gene 166:65-71
79. Kang HK, Lee JH, Kim D, Day DF, Robyt JF, Park KH, Moon TW (2004) Cloning and expression of Lipomyces starkeyi α-amylase in Escherichia coli and determination of some of its properties. FEMS Microbiol Lett 233:53-64
80. Hostinova E, Janecek S, Gasperik J (2010) Gene sequence, bioinformatics and enzymatic characterization of α-amylase from Saccharomycopsis fibuligera KZ. Protein J 29:355-364
81. Cuyvers S, Dornez E, Delcour JA, Courtin CM (2012) Occurrence and functional significance of secondary carbohydrate binding sites in glycoside hydrolases. Crit Rev Biotechnol 32:93-107
82. Cockburn D, Svensson B (2013) Surface binding sites in carbohydrate active enzymes: an emerging picture of structural and functional diversity. In: Lindhorst TK, Rauter AP (eds) SPR carbohydrate chemistry - chemical and biological approaches, vol 39. Royal Society of Chemistry, Cambridge. doi: 10.1039/9781849737173-00204
83. Møller MS, Cockburn D, Nielsen JW, Jensen JM, Vester-Christensen MB, Nielsen MM, Andersen JM, Wilkens C, Rannes J, Hägglund P, Henriksen A, Abou Hachem M, Willemoës M, Svensson B (2013) Surface binding sites (SBSs), mechanism and regulation of enzymes degrading amylopectin and α-limit dextrins. J Appl Glycosci. doi: 10.5458/jag.jag.JAG-2012-023
84. Kaneko A, Sudo S, Sakamoto Y, Tamura G, Ishikawa T, Ohba T (1996) Molecular-cloning and determination of the nucleotide-sequence of a gene encoding an acid-stable α-amylase from Aspergillus-kawachii. J Ferment Bioeng 81:292-298
85. Machovic M, Janecek S (2006) The evolution of putative starch-binding domains. FEBS Lett 580:6349-6356
86. Klein C, Schulz GE (1991) Structure of cyclodextrin glycosyltransferase refined at 2.0 Å resolution. J Mol Biol 217:737-750
87. Uitdehaag JC, Mosi R, Kalk KH, van der Veen BA, Dijkhuizen L, Withers SG, Dijkstra BW (1999) X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the α-amylase family. Nat Struct Biol 6:432-436
88. Watanabe K, Hata Y, Kizaki H, Katsube Y, Suzuki Y (1997) The refined crystal structure of Bacillus cereus oligo-1,6-glucosidase at 2.0 Å resolution: structural characterization of proline-substitution sites for protein thermostabilization. J Mol Biol 269:142-153
89. Yamamoto K, Miyake H, Kusunoki M, Osaki S (2010) Crystal structures of isomaltase from Saccharomyces cerevisiae and in complex with its competitive inhibitor maltose. FEBS J 277:4205-4214
90. Shirai T, Hung VS, Morinaka K, Kobayashi T, Ito S (2008) Crystal structure of GH13 α-glucosidase GSJ from one of the deepest sea bacteria. Proteins 73:126-133
91. Hondoh H, Saburi W, Mori H, Okuyama M, Nakada T, Matsuura Y, Kimura A (2008) Substrate recognition mechanism of α-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans. J Mol Biol 378:913-922
92. Møller MS, Fredslund F, Majumder A, Nakai H, Poulsen JC, Lo Leggio L, Svensson B, Abou Hachem M (2012) Enzymology and structure of the GH13-31 glucan 1,6-α-glucosidase that confers isomaltooligosaccharide utilization in the probiotic Lactobacillus acidophilus NCFM. J Bacteriol 194:4249-4259
93. Zhang D, Li N, Lok SM, Zhang LH, Swaminathan K (2003) Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism. J Biol Chem 278:35428-35434
94. Ravaud S, Robert X, Watzlawick H, Haser R, Mattes R, Aghajari N (2007) Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization. J Biol Chem 282:28126-28136
95. Ravaud S, Robert X, Watzlawick H, Haser R, Mattes R, Aghajari N (2009) Structural determinants of product specificity of sucrose isomerases. FEBS Lett 583:1964-1968
96. Machius M, Wiegand G, Huber R (1995) Crystal structure of calcium-depleted Bacillus licheniformis α-amylase at 2.2 Å resolution. J Mol Biol 246:545-559
97. Hwang KY, Song HK, Chang C, Lee J, Lee SY, Kim KK, Choe S, Sweet RM, Suh SW (1997) Crystal structure of thermostable α-amylase from Bacillus licheniformis refined at 1.7 Å resolution. Mol Cells 7:251-258
98. Suvd D, Fujimoto Z, Takase K, Matsumura M, Mizuno H (2001) Crystal structure of Bacillus stearothermophilus α-amylase: possible factors determining the thermostability. J Biochem 129:461-468
99. Alikhajeh J, Khajeh K, Ranjbar B, Naderi-Manesh H, Lin YH, Liu E, Guan HH, Hsieh YC, Chuankhayan P, Huang YC, Jeyaraman J, Liu MY, Chen CJ (2010) Structure of Bacillus amyloliquefaciens α-amylase at high resolution: implications for thermal stability. Acta Crystallogr Sect F Struct Biol Cryst Commun 66:121-129
100. Fujimoto Z, Takase K, Doui N, Momma M, Matsumoto T, Mizuno H (1998) Crystal structure of a catalytic-site mutant α-amylase from Bacillus subtilis complexed with maltopentaose. J Mol Biol 277:393-407
101. Davies GJ, Brzozowski AM, Dauter Z, Rasmussen MD, Borchert TV, Wilson KS (2005) Structure of a Bacillus halmapalus family 13 α-amylase, BHA, in complex with an acarbose-derived nonasaccharide at 2.1 Å resolution. Acta Crystallogr D Biol Crystallogr 61:190-193
102. Lyhne-Iversen L, Hobley TJ, Kaasgaard SG, Harris P (2006) Structure of Bacillus halmapalus α-amylase crystallized with and without the substrate analogue acarbose and maltose. Acta Crystallogr Sect F Struct Biol Cryst Commun 62:849-854
103. Nonaka T, Fujihashi M, Kita A, Hagihara H, Ozaki K, Ito S, Miki K (2003) Crystal structure of calcium-free α-amylase from Bacillus sp. strain KSM-K38 (AmyK38) and its sodium ion binding sites. J Biol Chem 278:24818-24824
104. Shirai T, Igarashi K, Ozawa T, Hagihara H, Kobayashi T, Ozaki K, Ito S (2007) Ancestral sequence evolutionary trace and crystal structure analyses of alkaline α-amylase from Bacillus sp. KSM-1378 to clarify the alkaline adaptation process of proteins. Proteins 66:600-610
105. Kanai R, Haga K, Akiba T, Yamane K, Harata K (2004) Biochemical and crystallographic analyses of maltohexaose-producing amylase from alkalophilic Bacillus sp. 707. Biochemistry 43:14047-14056
106. Tsukamoto A, Kimura K, Ishii Y, Takano T, Yamane K (1988) Nucleotide sequence of the maltohexaose-producing amylase gene from an alkalophilic Bacillus sp. #707 and structural similarity to liquefying type α-amylases. Biochem Biophys Res Commun 151:25-31
107. van der Kaaij RM, Janecek S, van der Maarel MJ, Dijkhuizen L (2007) Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal α-amylase enzymes. Microbiology 153:4003-4015
108. Marion CL, Rappleye CA, Engle JT, Goldman WE (2006) An α-(1,4)-amylase is essential for α-(1,3)-glucan production and virulence in Histoplasma capsulatum. Mol Microbiol 62:970-983
109. Camacho E, Sepulveda VE, Goldman WE, San-Blas G, Nino-Vega GA (2012) Expression of Paracoccidioides brasiliensis AMY1 in a Histoplasma capsulatum amy1 mutant, relates an α-(1,4)-amylase to cell wall α-(1,3)-glucan synthesis. PLoS ONE 7:e50201
110. Rodriguez Sanoja R, Morlon-Guyot J, Jore J, Pintado J, Juge N, Guyot JP (2000) Comparative characterization of complete and truncated forms of Lactobacillus amylovorus α-amylase and role of the C-terminal direct repeats in raw-starch binding. Appl Environ Microbiol 66:3350-3356
111. Rodriguez-Sanoja R, Ruiz B, Guyot JP, Sanchez S (2005) Starch-binding domain affects catalysis in two Lactobacillus α-amylases. Appl Environ Microbiol 71:297-302
112. Guillen D, Santiago M, Linares L, Perez R, Morlon J, Ruiz B, Sanchez S, Rodriguez-Sanoja R (2007) α-Amylase starch binding domains: cooperative effects of binding to starch granules of multiple tandemly arranged domains. Appl Environ Microbiol 73:3833-3837
113. Rodriguez-Sanoja R, Oviedo N, Escalante L, Ruiz B, Sanchez S (2009) A single residue mutation abolishes attachment of the CBM26 starch-binding domain from Lactobacillus amylovorus α-amylase. J Ind Microbiol Biotechnol 36:341-346
114. Janecek S, Leveque E, Belarbi A, Haye B (1999) Close evolutionary relatedness of α-amylases from Archaea and plants. J Mol Evol 48:421-426
115. Da Lage JL, Feller G, Janecek S (2004) Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the α-amylase model. Cell Mol Life Sci 61:97-109
116. Jones RA, Jermiin LS, Easteal S, Patel BK, Beacham IR (1999) Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium. J Appl Microbiol 86:93-107
117. Leveque E, Janecek S, Belarbi A, Haye B (2000) Thermophilic archaeal amylolytic enzymes. Enzyme Microb Technol 26:2-13
118. Leveque E, Haye B, Belarbi A (2000) 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 186:67-71
119. Lim JK, Lee HS, Kim YJ, Bae SS, Jeon JH, Kang SG, Lee JH (2007) Critical factors to high thermostability of an α-amylase from hyperthermophilic archaeon Thermococcus onnurineus NA1. J Microbiol Biotechnol 17:1242-1248
120. Dong G, Vieille C, Savchenko A, Zeikus JG (1997) Cloning, sequencing, and expression of the gene encoding extracellular α-amylase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microbiol 63:3569-3576
121. Jorgensen S, Vorgias CE, Antranikian G (1997) Cloning, sequencing, characterization, and expression of an extracellular α-amylase from the hyperthermophilic archaeon Pyrococcus furiosus in Escherichia coli and Bacillus subtilis. J Biol Chem 272:16335-16342
122. Frillingos S, Linden A, Niehaus F, Vargas C, Nieto JJ, Ventosa A, Antranikian G, Drainas C (2000) Cloning and expression of α-amylase from the hyperthermophilic archaeon Pyrococcus woesei in the moderately halophilic bacterium Halomonas elongata. J Appl Microbiol 88:495-503
123. Linden A, Mayans O, Meyer-Klaucke W, Antranikian G, Wilmanns M (2003) Differential regulation of a hyperthermophilic α-amylase with a novel (Ca,Zn) two-metal center by zinc. J Biol Chem 278:9875-9884
124. Linden A, Wilmanns M (2004) Adaptation of class-13 α-amylases to diverse living conditions. ChemBioChem 5:231-239
125. Rogers JC, Milliman C (1983) Isolation and sequence analysis of a barley α-amylase cDNA clone. J Biol Chem 258:8169-8174
126. Rogers JC (1985) Two barley α-amylase gene families are regulated differently in aleurone cells. J Biol Chem 260:3731-3738
127. Kadziola A, Abe J, Svensson B, Haser R (1994) Crystal and molecular structure of barley α-amylase. J Mol Biol 239:104-121
128. Kadziola A, Søgaard M, Svensson B, Haser R (1998) Molecular structure of a barley α-amylase-inhibitor complex: implications for starch binding and catalysis. J Mol Biol 278:205-217
129. Robert X, Haser R, Gottschalk TE, Ratajczak F, Driguez H, Svensson B, Aghajari N (2003) The structure of barley α-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs. Structure 11:973-984
130. Robert X, Haser R, Mori H, Svensson B, Aghajari N (2005) Oligosaccharide binding to barley α-amylase 1. J Biol Chem 280:32968-32978
131. Baulcombe DC, Huttly AK, Martienssen RA, Barker RF, Jarvis MG (1987) A novel wheat α-amylase gene (α-Amy3). Mol Gen Genet 209:33-40
132. Huang N, Sutliff TD, Litts JC, Rodriguez RL (1990) Classification and characterization of the rice α-amylase multigene family. Plant Mol Biol 14:655-668
133. Young TE, DeMason DA, Close TJ (1994) Cloning of an α-amylase cDNA from aleurone tissue of germinating maize seed. Plant Physiol 105:759-760
134. Mori H, Kobayashi T, Tonokawa T, Tatematsu A, Matsui H, Kimura A, Chiba S (1997) Molecular cloning of an α-amylase cDNA from germinating cotyledons of kidney bean (Phaseolus vulgaris L. cv. Toramame). J Appl Glycosci 45:261-267
135. Wegrzyn T, Reilly K, Cipriani G, Murphy P, Newcomb R, Gardner R, MacRae E (2000) A novel α-amylase gene is transiently upregulated during low temperature exposure in apple fruit. Eur J Biochem 267:1313-1322
136. Stanley D, Fitzgerald AM, Farnden KJA, MacRae EA (2002) Characterisation of putative α-amylases from apple (Malus domestica) and Arabidopsis thaliana. Biologia 57(Suppl 11):137-148
137. Junior AV, do Nascimento JR, Lajolo FM (2006) Molecular cloning and characterization of an α-amylase occurring in the pulp of ripening bananas and its expression in Pichia pastoris. J Agric Food Chem 54:8222-8228
138. Bozonnet S, Jensen MT, Nielsen MM, Aghajari N, Jensen MH, Kramhøft B, Willemoës M, Tranier S, Haser R, Svensson B (2007) The 'pair of sugar tongs' site on the non-catalytic domain C of barley α-amylase participates in substrate binding and activity. FEBS J 274:5055-5067
139. Nielsen MM, Bozonnet S, Seo ES, Motyan JA, Andersen JM, Dilokpimol A, Abou Hachem M, Gyemant G, Naested H, Kandra L, Sigurskjold BW, Svensson B (2009) Two secondary carbohydrate binding sites on the surface of barley α-amylase 1 have distinct functions and display synergy in hydrolysis of starch granules. Biochemistry 48:7686-7697
140. Nielsen JW, Kramhøft B, Bozonnet S, Abou Hachem M, Stipp SL, Svensson B, Willemoës M (2012) Degradation of the starch components amylopectin and amylose by barley α-amylase 1: role of surface binding site 2. Arch Biochem Biophys 528:1-6
141. Tranier S, Deville K, Robert X, Bozonnet S, Haser R, Svensson B, Aghajari N (2005) Insights into the "pair of sugar tongs" surface binding site in barley α-amylase isozymes and crystallization of appropriate sugar tongs mutants. Biologia 60(Suppl 16):37-46
142. 8 scaffold. Mol Biol Evol 18:38-54
143. Godany A, Majzlova K, Horvathova V, Vidova B, Janecek S (2010) Tyrosine 39 of GH13 α-amylase from Thermococcus hydrothermalis contributes to its thermostability. Biologia 65:408-415
144. Da Lage JL, Danchin EG, Casane D (2007) Where do animal α-amylases come from? An interkingdom trip. FEBS Lett 581:3927-3935
145. Feller G, Lonhienne T, Deroanne C, Libioulle C, Van Beeumen J, Gerday C (1992) Purification, characterization, and nucleotide sequence of the thermolabile α-amylase from the Antarctic psychrotroph Alteromonas haloplanctis A23. J Biol Chem 267:5217-5221
146. Feller G, Payan F, Theys F, Qian M, Haser R, Gerday C (1994) Stability and structural analysis of α-amylase from the Antarctic psychrophile Alteromonas haloplanctis A23. Eur J Biochem 222:441-447
147. D'Amico S, Gerday C, Feller G (2000) Structural similarities and evolutionary relationships in chloride-dependent α-amylases. Gene 253:95-105
148. Aghajari N, Feller G, Gerday C, Haser R (2002) Structural basis of α-amylase activation by chloride. Protein Sci 11:1435-1441
149. Cipolla A, Delbrassine F, Da Lage JL, Feller G (2012) Temperature adaptations in psychrophilic, mesophilic and thermophilic chloride-dependent α-amylases. Biochimie 94:1943-1950
150. Boer PH, Hickey DA (1986) The α-amylase gene in Drosophila melanogaster: nucleotide sequence, gene structure and expression motifs. Nucleic Acids Res 14:8399-8411
151. Da Lage JL, Wegnez M, Cariou ML (1996) Distribution and evolution of introns in Drosophila amylase genes. J Mol Evol 43:334-347
152. Da Lage JL, Renard E, Chartois F, Lemeunier F, Cariou ML (1998) Amyrel, a paralogous gene of the amylase gene family in Drosophila melanogaster and the Sophophora subgenus. Proc Natl Acad Sci USA 95:6848-6853
153. Da Lage JL, Maisonhaute C, Maczkowiak F, Cariou ML (2003) A nested α-amylase gene in Drosophila ananassae. J Mol Evol 57:355-362
154. Strobl S, Gomis-Ruth FX, Maskos K, Frank G, Huber R, Glockshuber R (1997) The α-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis. FEBS Lett 409:109-114
155. Strobl S, Maskos K, Betz M, Wiegand G, Huber R, Gomis-Ruth FX, Glockshuber R (1998) Crystal structure of yellow meal worm α-amylase at 1.64 Å resolution. J Mol Biol 278:617-628
156. Le Moine S, Sellos D, Moal J, Daniel JY, San Juan Serrano F, Samain JF, Van Wormhoudt A (1997) Amylase on Pecten maximus (Mollusca, bivalves): protein and cDNA characterization; quantification of the expression in the digestive gland. Mol Mar Biol Biotechnol 6:228-237
157. Nikapitiya C, Oh C, Whang I, Kim CG, Lee YH, Kim SJ, Lee J (2009) Molecular characterization, gene expression analysis and biochemical properties of α-amylase from the disk abalone, Haliotis discus discus. Comp Biochem Physiol B Biochem Mol Biol 152:271-281
158. Van Wormhoudt A, Sellos D (1996) Cloning and sequencing analysis of three amylase cDNAs in the shrimp Penaeus vannamei (Crustacea decapoda): evolutionary aspects. J Mol Evol 42:543-551
159. Da Lage JL, Maczkowiak F, Cariou ML (2011) Phylogenetic distribution of intron positions in α-amylase genes of bilateria suggests numerous gains and losses. PLoS ONE 6:e19673
160. Buisson G, Duee E, Haser R, Payan F (1987) Three-dimensional structure of porcine pancreatic α-amylase at 2.9 Å resolution. Role of calcium in structure and activity. EMBO J 6:3909-3916
161. Qian M, Haser R, Payan F (1993) Structure and molecular model refinement of pig pancreatic α-amylase at 2.1 Å resolution. J Mol Biol 231:785-799
162. Qian M, Haser R, Buisson G, Duee E, Payan F (1994) The active center of a mammalian α-amylase. Structure of the complex of a pancreatic α-amylase with a carbohydrate inhibitor refined to 2.2-Å resolution. Biochemistry 33:6284-6294
163. Gilles C, Astier JP, Marchis-Mouren G, Cambillau C, Payan F (1996) Crystal structure of pig pancreatic α-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose. Eur J Biochem 238:561-569
164. Ramasubbu N, Paloth V, Luo Y, Brayer GD, Levine MJ (1996) Structure of human salivary α-amylase at 1.6 Angstrom resolution: implications for its role in the oral cavity. Acta Crystallogr D 52:435-446
165. Brayer GD, Luo Y, Withers SG (1995) The structure of human pancreatic α-amylase at 1.8 Å resolution and comparisons with related enzymes. Protein Sci 4:1730-1742
166. Mizutani K, Toyoda M, Otake Y, Yoshioka S, Takahashi N, Mikami B (2012) Structural and functional characterization of recombinant medaka fish α-amylase expressed in yeast Pichia pastoris. Biochim Biophys Acta 1824:954-962
167. Machius M, Vertesy L, Huber R, Wiegand G (1996) Carbohydrate and protein-based inhibitors of porcine pancreatic α-amylase: structure analysis and comparison of their binding characteristics. J Mol Biol 260:409-421
168. Payan F, Qian M (2003) Crystal structure of the pig pancreatic α-amylase complexed with malto-oligosaccharides. J Protein Chem 22:275-284
169. Larson SB, Day JS, McPherson A (2010) X-ray crystallographic analyses of pig pancreatic α-amylase with limit dextrin, oligosaccharide, and α-cyclodextrin. Biochemistry 49:3101-3115
170. Qin X, Ren L, Yang X, Bai F, Wang L, Geng P, Bai G, Shen Y (2011) Structures of human pancreatic α-amylase in complex with acarviostatins: implications for drug design against type II diabetes. J Struct Biol 174:196-202
171. Yang CH, Liu WH (2007) Cloning and characterization of a maltotriose-producing α-amylase gene from Thermobifida fusca. J Ind Microbiol Biotechnol 34:325-330
172. Doukyu N, Yamagishi W, Kuwahara H, Ogino H (2008) A maltooligosaccharide-forming amylase gene from Brachybacterium sp. strain LB25: cloning and expression in Escherichia coli. Biosci Biotechnol Biochem 72:2444-2447
173. Yamaguchi R, Tokunaga H, Ishibashi M, Arakawa T, Tokunaga M (2011) Salt-dependent thermo-reversible α-amylase: cloning and characterization of halophilic α-amylase from moderately halophilic bacterium, Kocuria varians. Appl Microbiol Biotechnol 89:673-684
174. Yamaguchi R, Arakawa T, Tokunaga H, Ishibashi M, Tokunaga M (2012) Distinct characteristics of single starch-binding domain SBD1 derived from tandem domains SBD1-SBD2 of halophilic Kocuria varians α-amylase. Protein J 31:250-258
175. Yamaguchi R, Inoue Y, Tokunaga H, Ishibashi M, Arakawa T, Sumitani J, Kawaguchi T, Tokunaga M (2012) Halophilic characterization of starch-binding domain from Kocuria varians α-amylase. Int J Biol Macromol 50:95-102
176. Sumitani J, Tottori T, Kawaguchi T, Arai M (2000) New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 α-amylase contributes to starch binding and raw starch degrading. Biochem J 350:477-484
177. Virolle MJ, Long CM, Chang S, Bibb MJ (1988) Cloning, characterisation and regulation of an α-amylase gene from Streptomyces venezuelae. Gene 74:321-334
178. Vigal T, Gil JA, Daza A, Garcia-Gonzalez MD, Martin JF (1991) Cloning, characterization and expression of an α-amylase gene from Streptomyces griseus IMRU3570. Mol Gen Genet 225:278-288
179. Da Lage JL, Binder M, Hua-Van A, Janecek S, Casane D (2013) Gene make-up: rapid and massive intron gains after horizontal transfer of a bacterial α-amylase gene to Basidiomycetes. BMC Evol Biol 13:40
180. Chen W, Xie T, Shao Y, Chen F (2012) Phylogenomic relationships between amylolytic enzymes from 85 strains of fungi. PLoS ONE 7:e49679
181. Hu NT, Hung MN, Huang AM, Tsai HF, Yang BY, Chow TY, Tseng YH (1992) Molecular cloning, characterization and nucleotide sequence of the gene for secreted α-amylase from Xanthomonas campestris pv. campestris. J Gen Microbiol 138:1647-1655
182. Gobius KS, Pemberton JM (1988) Molecular cloning, characterization, and nucleotide sequence of an extracellular amylase gene from Aeromonas hydrophila. J Bacteriol 170:1325-1332
183. Na HK, Kim ES, Lee HH, Yoo OJ, Jhon DY (1996) Cloning and nucleotide sequence of the α-amylase gene from alkalophilic Pseudomonas sp. KFCC 10818. Mol Cells 2:203-208
184. Kang EJ, Kim ES, Lee JE, Jhon DY (2001) Cloning, sequencing, characterization, and expression of a new α-amylase isozyme gene (amy3) from Pseudomonas sp. Biotechnol Lett 23:811-816
185. Majzlova K, Pukajova Z, Janecek S (2013) Tracing the evolution of the α-amylase subfamily GH13-36 covering the amylolytic enzymes intermediate between oligo-1,6-glucosidases and neopullulanases. Carbohydr Res 367:48-57
186. Horinouchi S, Fukusumi S, Ohshima T, Beppu T (1988) Cloning and expression in Escherichia coli of two additional amylase genes of a strictly anaerobic thermophile, Dictyoglomus thermophilum, and their nucleotide sequences with extremely low guanine-plus-cytosine contents. Eur J Biochem 176:243-253
187. Metz RJ, Allen LN, Cao TM, Zeman NW (1988) Nucleotide sequence of an amylase gene from Bacillus megaterium. Nucleic Acids Res 16:5203
188. Brumm PJ, Hebeda RE, Teague WM (1991) Purification and characterization of the commercialized, cloned Bacillus megaterium α-amylase. Part I: purification and hydrolytic properties. Starch/Staerke 43:315-319
189. Brumm PJ, Hebeda RE, Teague WM (1991) Purification and characterization of the commercialized, cloned Bacillus megaterium α-amylase. Part II: transferase properties. Starch/Staerke 43:319-323
190. Abe J, Shibata Y, Fujisue M, Hizukuri S (1996) Expression of periplasmic α-amylase of Xanthomonas campestris K-11151 in Escherichia coli and its action on maltose. Microbiology 142:1505-1512
191. Yebra MJ, Arroyo J, Sanz P, Priet JA (1997) Characterization of novel neopullulanase from Bacillus polymyxa. Appl Biochem Biotechnol 68:113-120
192. Yebra MJ, Blasco A, Sanz P (1999) Expression and secretion of Bacillus polymyxa neopullulanase in Saccharomyces cerevisiae. FEMS Microbiol Lett 170:41-49
193. Nakagawa Y, Saburi W, Takada M, Hatada Y, Horikoshi K (2008) Gene cloning and enzymatic characteristics of a novel γ-cyclodextrin-specific cyclodextrinase from alkalophilic Bacillus clarkii 7364. Biochim Biophys Acta 1784:2004-2011
194. Ballschmiter M, Armbrecht M, Ivanova K, Antranikian G, Liebl W (2005) AmyA, an α-amylase with β-cyclodextrin-forming activity, and AmyB from the thermoalkaliphilic organism Anaerobranca gottschalkii: two α-amylases adapted to their different cellular localizations. Appl Environ Microbiol 71:3709-3715
195. Liebl W, Stemplinger I, Ruile P (1997) Properties and gene structure of the Thermotoga maritima α-amylase AmyA, a putative lipoprotein of a hyperthermophilic bacterium. J Bacteriol 179:941-948
196. Mijts BN, Patel BK (2002) Cloning, sequencing and expression of an α-amylase gene, amyA, from the thermophilic halophile Halothermothrix orenii and purification and biochemical characterization of the recombinant enzyme. Microbiology 148:2343-2349
197. Sivakumar N, Li N, Tang JW, Patel BK, Swaminathan K (2006) Crystal structure of AmyA lacks acidic surface and provide insights into protein stability at poly-extreme condition. FEBS Lett 580:2646-2652
198. Liu Y, Lei Y, Zhang X, Gao Y, Xiao Y, Peng H (2012) Identification and phylogenetic characterization of a new subfamily of α-amylase enzymes from marine microorganisms. Mar Biotechnol 14:253-260
199. Lei Y, Peng H, Wang Y, Liu Y, Han F, Xiao Y, Gao Y (2012) Preferential and rapid degradation of raw rice starch by an α-amylase of glycoside hydrolase subfamily GH13-37. Appl Microbiol Biotechnol 94:1577-1584
200. Yu J, Wang C, Hu Y, Dong Y, Wang Y, Tu X, Peng H, Zhang X (2013) Purification, crystallization and preliminary crystallographic analysis of the marine α-amylase AmyP. Acta Crystallogr Sect F Struct Biol Cryst Commun 69:263-266
201. Puspasari F, Nurachman Z, Noer AS, Radjasa OK, van der Maarel MJEC, Natalia D (2011) Characteristics of raw starch degrading α-amylase from Bacillus aquimaris MKSC 6.2 associated with soft coral Sinularia sp. Starch/Staerke 63:461-467
202. Finore I, Kasavi C, Poli A, Romano I, Toksoy Oner E, Kirdar B, Dipasquale L, Nicolaus B, Lama L (2011) Purification, biochemical characterization and gene sequencing of a thermostable raw starch digesting α-amylase from Geobacillus thermoleovorans subsp. stromboliensis subsp. nov. World J Microbiol Biotechnol 27:2425-2433
203. Chai YY, Rahman RN, Illias RM, Goh KM (2012) Cloning and characterization of two new thermostable and alkalitolerant α-amylases from the Anoxybacillus species that produce high levels of maltose. J Ind Microbiol Biotechnol 39:731-741
204. Mok SC, Teh AH, Saito JA, Najimudin N, Alam M (2013) Crystal structure of a compact α-amylase from Geobacillus thermoleovorans. Enzyme Microb Technol 53:46-54
205. Buedenbender S, Schulz GE (2009) Structural base for enzymatic cyclodextrin hydrolysis. J Mol Biol 385:606-617
206. Shipman JA, Cho KH, Siegel HA, Salyers AA (1999) Physiological characterization of SusG, an outer membrane protein essential for starch utilization by Bacteroides thetaiotaomicron. J Bacteriol 181:7206-7211
207. Martens EC, Koropatkin NM, Smith TJ, Gordon JI (2009) Complex glycan catabolism by the human gut microbiota: the Bacteroidetes Sus-like paradigm. J Biol Chem 284:24673-24677
208. Cameron EA, Maynard MA, Smith CJ, Smith TJ, Koropatkin NM, Martens EC (2012) Multidomain carbohydrate-binding proteins involved in Bacteroides thetaiotaomicron starch metabolism. J Biol Chem 287:34614-34625
209. Fukusumi S, Kamizono A, Horinouchi S, Beppu T (1988) Cloning and nucleotide sequence of a heat-stable amylase gene from an anaerobic thermophile, Dictyoglomus thermophilum. Eur J Biochem 174:15-21
210. Laderman KA, Asada K, Uemori T, Mukai H, Taguchi Y, Kato I, Anfinsen CB (1993) α-Amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. Cloning and sequencing of the gene and expression in Escherichia coli. J Biol Chem 268:24402-24407
211. Janecek S (1998) Sequence of archaeal Methanococcus jannaschii α-amylase contains features of families 13 and 57 of glycosyl hydrolases: a trace of their common ancestor? Folia Microbiol 43:123-128
212. Imamura H, Fushinobu S, Yamamoto M, Kumasaka T, Jeon BS, Wakagi T, Matsuzawa H (2003) Crystal structures of 4-α-glucanotransferase from Thermococcus litoralis and its complex with an inhibitor. J Biol Chem 278:19378-19386
213. Janecek S (2005) Amylolytic families of glycoside hydrolases: focus on the family GH-57. Biologia 60(Suppl 16):177-184
214. Nakajima M, Imamura H, Shoun H, Horinouchi S, Wakagi T (2004) Transglycosylation activity of Dictyoglomus thermophilum amylase A. Biosci Biotechnol Biochem 68:2369-2373
215. Laderman KA, Davis BR, Krutzsch HC, Lewis MS, Griko YV, Privalov PL, Anfinsen CB (1993) The purification and characterization of an extremely thermostable α-amylase from the hyperthermophilic archaebacterium Pyrococcus furiosus. J Biol Chem 268:24394-24401
216. Janecek S, Blesak K (2011) Sequence-structural features and evolutionary relationships of family GH57 α-amylases and their putative α-amylase-like homologues. Protein J 30:429-435
217. Blesak K, Janecek S (2012) Sequence fingerprints of enzyme specificities from the glycoside hydrolase family GH57. Extremophiles 16:497-506
218. Kim JW, Flowers LO, Whiteley M, Peeples TL (2001) Biochemical confirmation and characterization of the family-57-like α-amylase of Methanococcus jannaschii. Folia Microbiol 46:467-473
219. Jeon BS, Taguchi H, Sakai H, Ohshima T, Wakagi T, Matsuzawa H (1997) 4-α-Glucanotransferase from the hyperthermophilic archaeon Thermococcus litoralis. Enzyme purification and characterization, and gene cloning, sequencing and expression in Escherichia coli. Eur J Biochem 248:171-178
220. Tachibana Y, Fujiwara S, Takagi M, Imanaka T (1997) Cloning and expression of the 4-α-glucanotransferase gene from the hyperthermophilic archaeon Pyrococcus sp. KOD1, and characterization of the enzyme. J Ferment Bioeng 83:540-548
221. Labes A, Schonheit P (2007) Unusual starch degradation pathway via cyclodextrins in the hyperthermophilic sulfate-reducing archaeon Archaeoglobus fulgidus strain 7324. J Bacteriol 189:8901-8913
222. Dong G, Vieille C, Zeikus JG (1997) Cloning, sequencing, and expression of the gene encoding amylopullulanase from Pyrococcus furiosus and biochemical characterization of the recombinant enzyme. Appl Environ Microbiol 63:3577-3584
223. Erra-Pujada M, Debeire P, Duchiron F, O'Donohue MJ (1999) The type II pullulanase of Thermococcus hydrothermalis: molecular characterization of the gene and expression of the catalytic domain. J Bacteriol 181:3284-3287
224. Imamura H, Jeon BS, Wakagi T (2004) Molecular evolution of the ATPase subunit of three archaeal sugar ABC transporters. Biochem Biophys Res Commun 319:230-234
225. Jiao YL, Wang SJ, Lv MS, Xu JL, Fang YW, Liu S (2011) A GH57 family amylopullulanase from deep-sea Thermococcus siculi: expression of the gene and characterization of the recombinant enzyme. Curr Microbiol 62:222-228
226. Ballschmiter M, Fütterer O, Liebl W (2006) Identification and characterization of a novel intracellular alkaline α-amylase from the hyperthermophilic bacterium Thermotoga maritima MSB8. Appl Environ Microbiol 72:2206-2211
227. Murakami T, Kanai T, Takata H, Kuriki T, Imanaka T (2006) A novel branching enzyme of the GH-57 family in the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. J Bacteriol 188:5915-5924
228. Palomo M, Pijning T, Booiman T, Dobruchowska JM, van der Vlist J, Kralj S, Planas A, Loos K, Kamerling JP, Dijkstra BW, van der Maarel MJ, Dijkhuizen L, Leemhuis H (2011) Thermus thermophilus glycoside hydrolase family 57 branching enzyme: crystal structure, mechanism of action, and products formed. J Biol Chem 286:3520-3530
229. van Lieshout JFT, Verhees CH, van der Oost J, de Vos WM, Ettema TJG, van der Sar S, Imamura H, Matsuzawa H (2003) Identification and molecular characterization of a novel type of α-galactosidase from Pyrococcus furiosus. Biocatal Biotransform 21:243-252
230. Comfort DA, Chou CJ, Conners SB, VanFossen AL, Kelly RM (2008) Functional-genomics-based identification and characterization of open reading frames encoding α-glucoside-processing enzymes in the hyperthermophilic archaeon Pyrococcus furiosus. Appl Environ Microbiol 74:1281-1283
231. Wang H, Gong Y, Xie W, Xiao W, Wang J, Zheng Y, Hu J, Liu Z (2011) Identification and characterization of a novel thermostable gh-57 gene from metagenomic fosmid library of the Juan de Fuca Ridge hydrothermal vent. Appl Biochem Biotechnol 164:1323-1338
232. Li D, Li X, Park KH (2013) An extremely thermostable amylopullulanase from Staphylothermus marinus displays both pullulan- and cyclodextrin-degrading activities. Appl Microbiol Biotechnol 97:5359-5369
233. Imamura H, Fushinobu S, Jeon BS, Wakagi T, Matsuzawa H (2001) Identification of the catalytic residue of Thermococcus litoralis 4-α-glucanotransferase through mechanism-based labeling. Biochemistry 40:12400-12406
234. Dickmanns A, Ballschmiter M, Liebl W, Ficner R (2006) Structure of the novel α-amylase AmyC from Thermotoga maritima. Acta Crystallogr D Biol Crystallogr 62:262-270
235. Santos CR, Tonoli CC, Trindade DM, Betzel C, Takata H, Kuriki T, Kanai T, Imanaka T, Arni RK, Murakami MT (2011) Structural basis for branching-enzyme activity of glycoside hydrolase family 57: structure and stability studies of a novel branching enzyme from the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1. Proteins 79:547-557
236. Zona R, Chang-Pi-Hin F, O'Donohue MJ, 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
237. Matsuura Y (2002) A possible mechanism of catalysis involving three essential residues in the enzymes of α-amylase family. Biologia 57(Suppl 11):21-27
238. Li M, Peeples TL (2004) Purification of hyperthermophilic archaeal amylolytic enzyme (MJA1) using thermoseparating aqueous two-phase systems. J Chromatogr B 807:69-74
239. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, Kerlavage AR, Dougherty BA, Tomb JF, Adams MD, Reich CI, Overbeek R, Kirkness EF, Weinstock KG, Merrick JM, Glodek A, Scott JL, Geoghagen NS, Venter JC (1996) Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science 273:1058-1073
240. Janecek S (2013) Glycoside hydrolase family 57. CAZypedia. http://www.cazypedia.org/. Accessed 18 Mar 2013
241. Watanabe H, Nishimoto T, Kubota M, Chaen H, Fukuda S (2006) Cloning, sequencing, and expression of the genes encoding an isocyclomaltooligosaccharide glucanotransferase and an α-amylase from a Bacillus circulans strain. Biosci Biotechnol Biochem 70:2690-2702
242. Janecek S, Kuchtova A (2012) In silico identification of catalytic residues and domain fold of the family GH119 sharing the catalytic machinery with the α-amylase family GH57. FEBS Lett 586:3360-3366
243. Naumoff DG (2011) Hierarchical classification of glycoside hydrolases. Biochemistry (Moscow) 76:622-635
244. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403-410
245. Kelley LA, Sternberg MJE (2009) Protein structure prediction on the Web: a case study using the Phyre server. Nat Protoc 4:363-371
246. Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T (2009) The SWISS-MODEL repository and associated resources. Nucleic Acids Res 37:D387-D392
247. Guerin DM, Lascombe MB, Costabel M, Souchon H, Lamzin V, Beguin P, Alzari PM (2002) Atomic (0.94 Å) resolution structure of an inverting glycosidase in complex with substrate. J Mol Biol 316:1061-1069
248. Guimaraes BG, Souchon H, Lytle BL, David Wu JH, Alzari PM (2002) The crystal structure and catalytic mechanism of cellobiohydrolase CelS, the major enzymatic component of the Clostridium thermocellum cellulosome. J Mol Biol 320:587-596
249. Machius M, Declerck N, Huber R, Wiegand G (1998) Activation of Bacillus licheniformis α-amylase through a disorder→order transition of the substrate-binding site mediated by a calcium-sodium-calcium metal triad. Structure 6:281-292
250. Deshpande N, Addess KJ, Bluhm WF, Merino-Ott JC, Townsend-Merino W, Zhang Q, Knezevich C, Xie L, Chen L, Feng Z, Green RK, Flippen-Anderson JL, Westbrook J, Berman HM, Bourne PE (2005) The RCSB Protein Data Bank: a redesigned query system and relational database based on the mmCIF schema. Nucleic Acids Res 3:D233-D237
251. UniProt Consortium (2013) Update on activities at the Universal Protein Resource (UniProt) in 2013. Nucleic Acids Res 41:D43-D47
252. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947-2948
253. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
254. Felsenstein J (1985) Confidence-limits on phylogenies - an approach using the bootstrap. Evolution 39:783-791
255. Page RD (1996) TreeView: an application to display phylogenetic trees on personal computers. Comput Appl Biosci 12:357-358
256. Shatsky M, Nussinov R, Wolfson HJ (2004) A method for simultaneous alignment of multiple protein structures. Proteins 56:143-156
257. Davies GJ, Wilson KS, Henrissat B (1997) Nomenclature for sugar-binding subsites in glycosyl hydrolases. Biochem J 321:557-559
258. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14:1188-1190
259. Sauer J, Sigurskjold BW, Christensen U, Frandsen TP, Mirgorodskaya E, Harrison M, Roepstorff P, Svensson B (2000) Glucoamylase: structure/function relationships, and protein engineering. Biochim Biophys Acta 1543:275-293
260. Aleshin AE, Firsov LM, Honzatko RB (1994) Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. X100 to 2.4-Å resolution. J Biol Chem 269:15631-15639