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Glycoside Hydrolase Family 13

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Glycoside Hydrolase Family GH13
Clan GH-H
Mechanism retaining
Active site residues known
CAZy DB link
http://www.cazy.org/GH13.html


Contents

Substrate specificities

Family GH13 is the major glycoside hydrolase family acting on substrates containing α-glucoside linkages. A number of reviews are concerned with α-amylases [1, 2, 3, 4, 5]. GH13 contains hydrolases, transglycosidases and isomerases [4]; noticeably animal amino acid transporters [6], which have no glycosidase activity [7], are also GH13 members. The enzymes are found in a very wide range of organisms from all kingdoms. While known specificities are indicated by the enzyme named as listed below, for several of these numerous enzymes are characterized representing subspecificities defined by structural requirements for preferred substrates or the structure of the predominant product(s).

Described enzymes include: α-amylase (EC 3.2.1.1); oligo-1,6-glucosidase (EC 3.2.1.10); α-glucosidase (EC 3.2.1.20); pullulanase (EC 3.2.1.41); cyclomaltodextrinase (EC 3.2.1.54); maltotetraose-forming α-amylase (EC 3.2.1.60); isoamylase (EC 3.2.1.68); dextran glucosidase (EC 3.2.1.70); trehalose-6-phosphate hydrolase (EC 3.2.1.93); maltohexaose-forming α-amylase (EC 3.2.1.98); maltotriose-forming α-amylase (EC 3.2.1.116); maltogenic amylase (EC 3.2.1.133); neopullulanase (EC 3.2.1.135); malto-oligosyltrehalose trehalohydrolase (EC 3.2.1.141); limit dextrinase (EC 3.2.1.142); maltopentaose-forming α-amylase (EC 3.2.1.-); amylosucrase (EC 2.4.1.4); sucrose phosphorylase (EC 2.4.1.7); branching enzyme (EC 2.4.1.18); cyclomaltodextrin glucanotransferase (CGTase) (EC 2.4.1.19); 4-α-glucanotransferase (EC 2.4.1.25); isomaltulose synthase (EC 5.4.99.11); trehalose synthase (EC 5.4.99.16).

As mentioned above, heavy-chains of heteromeric amino acid transporters belong to the GH13 [6, 8]. Among thousands of sequences and ~30 different enzymes specificities [9] many are closely related to each other, GH13 therefore has officially been subdivided into almost 40 subfamilies [10]; several subfamilies, e.g., the oligo-1,6-glucosidase and neopullulanase subfamilies were described earlier [11]. Notably, a considerable number of GH13 members contain carbohydrate binding modules (CBMs) referred to as starch binding domains belonging to CBM20, CBM21, CBM25, CBM26, CBM34, CBM41, CBM45, CBM48, CBM53, and CBM58 [12, 13, 14, 15, 16].

The GH13 enzymes have a wide range of different preferred substrates and products. For example, the α-amylases prefer polysaccharides of the α-1,4-glucan type, such as amylose and amylopectin, but are also able to attack the supramolecular structures represented by starch granules and glycogen particles. Besides they have some significant albeit slower turn-over of maltooligosaccharides of a certain degree of polymerization. These typical substrate profiles can be manipulated through protein engineering.

The α-amylase family was defined in 1991 as family GH13 when the sequence-based classification of glycoside hydrolases was created [17]. The α-amylase family as an enzyme family, however, was established based on results of several independent findings focused on starch hydrolases and related enzymes [18, 19, 20, 21]. These enzymes were shown to exhibit sequence similarities and, at that time, a predicted (β/α)8-barrel (i.e. TIM-barrel) fold. The basic criteria for a protein to be a member of the α-amylase family were as follows [21]: the enzyme should (i) act on the α-glucosidic linkages; (ii) hydrolyse or form by transglycosylation the α-glucosidic linkages; (iii) contain the four conserved sequence regions in its amino acid sequence; and (iv) possess the catalytic triad formed by the three residues corresponding to Asp206, Glu230 and Asp297 of Taka-amylase A (the α-amylase from Aspergillus oryzae). A dramatic increase of the number of GH13 members to several thousands [9] offered a greater variety in both substrate and product specificities and sequence diversity so that the above criteria had to be updated. For example, also enzymes active on α-1,1-, α-1,2-, α-1,3- and α-1,5-glucosidic linkages belong to the α-amylase family [4] and the four best known and well-accepted conserved sequence regions, defined first for eleven α-amylases [22], were completed by the additional three regions [23, 24] which can often help to assign the correct enzyme specificity of α-amylase family members (for a review, see [25]). Of note may be the enzyme neopullulanase [26] that was found to catalyze both the hydrolysis of α-1,4- and α-1,6-glucosidic bonds as well as the transglycosylation to form these two types of glucosidic bonds.

The α-amylase family represents a clan GH-H of three glycoside hydrolase families GH13, GH70 and GH77 [4], and should be distinguished from the second smaller α-amylase family GH57 [27]. A remote homology to the family GH31 has also been discussed [28]. The evolutionary relationships were described for the entire GH13 family [2, 10, 20, 29] and some closely related specificities, i.e. subfamilies [11, 30], as well as many examples of close evolutionary relatedness were reported for the individual groups of α-amylases, e.g., those from animals and actinomycetes [24], plants and archaeons [31, 32], insects [33], and fungi [34, 35].

Exogenous and endogenous inhibitory proteins have also been reported from microorganisms and plants [36] directed towards α-amylases [37] and limit dextrinases [38, 39, 40].

Kinetics and Mechanism

GH13 enzymes employ the retaining mechanism. This was first demonstrated by quantitative gas liquid chromatographic analysis of formation of α-maltose from different maltosides [41] and further supported by the NMR analysis of the release of α-maltose from similar substrates [42]. It was also demonstrated for a number of different α-amylases that they follow the classical Koshland double-displacement mechanism. This has moreover been supported by covalent labelling using 4-deoxy-maltotriose-fluoride trapping the catalytic nucleophile [43], numerous three-dimensional structures, and site-directed mutational substitution of the catalytic site residues [44, 45]. Some of the GH13 members use a multiple attack or processive mechanism [46, 47, 48] involving several glycoside bond cleavages to be executed in the same enzyme-substrate encounter. In several cases the binding energies have been determined by using subsite mapping [49, 50, 51, 52], which gives a subsite binding energy profile characteristic for individual enzymes. Several α-amylases have been reported to interact with polymeric substrates at surface sites situated as a certain distance of the active site [53, 54, 55, 56]. Finally interaction with insoluble substrates, such as starch granules or glycogen can occur both at these sites [54, 55, 57] as well as by the involvement of separate binding modules referred to as starch binding domains [58, 59, 60, 61].

Catalytic Residues

The catalytic residues have been identified from early crystal structures [62, 63]. In fact throughout the family GH13 only the catalytic triad plus an arginine residue are totally conserved; the catalytic site includes an aspartate as catalytic nucleophile, a glutamate as general acid/base, and an aspartate that participates critically in stabilizing the transition state [43]. The fourth invariantly conserved GH13 residue, the arginine, is positioned two residues preceding the catalytic nucleophile [4]. This conservation does not apply for the enzymatically inactive heavy-chains (rBAT proteins and 4F2hc antigens) of the amino acid transporters [8]. Numerous mutational analyses have been performed to confirm the essential roles of the three residues in catalysis, and normally the loss in activity is four to five orders of magnitude.

Three-dimensional structures

Numerous GH13 subfamilies contain members for which a three-dimensional structure has been determined. In general, the GH13 members are multidomain proteins with catalytic (β/α)8-barrel (i.e. TIM-barrel) domain (called domain A) having a small domain B (usually varying in length and of irregular structure) [6] inserted in the loop between the β3-strand and α3-helix of the barrel, and succeeded by the C-terminal antiparallel β-sandwich domain, called domain C. The catalytic site formed by the C-terminal extensions of strands β4, β5 and β7, carrying the catalytic triad of aspartate, glutamate and aspartate, respectively [62, 64, 65], but also other loops contribute to the overall architecture of the active site.

The first crystals for barley α-amylase were reported in the mid-forties, however the first crystal structures were those of TAKA-amylase A [62, 66] (PDB ID 2taa 7taa) and porcine pancreatic α-amylase [63, 64] (PDB ID 1ppi). This was followed by structures of other α-amylases from bacteria [67, 68, 69] (PDB ID 1bpl 1bpl 1e43)and from higher plants [65, 70] (PDB ID 1amy 1ht6); the industrially important cyclodextrin glucanotransferase [71, 72, 73] (PDB ID 1cgt 1cdg 1pez) and the closely related maltogenic α-amylase [74] (PDB ID 1qhp). Later on the structures of the amylopectin debranching isoamylase [75] (PDB ID 1bf2) and the related pullulanase [76] (PDB ID 2fhf) and limit dextrinase [77] (PDB ID 2y5e) were determined. Furthermore the oligo-1,6-glucosidase [78] (PDB ID 1uok) and the related dextran glucosidase [79] (PDB ID 2zic), as well as maltogenic amylase [80] (PDB ID 1sma), cyclomaltodextrinase [81] (PDB ID 1ea9) and neopullulanase [82] (PDB ID 1j0h) - nearly indistinguishable from each other - together with the neopullulanase-like “α-amylases” TVA I [83] (PDB ID 1ji1) and TVA II [84] (PDB ID 1bvz), and the amylosucrase [85] (PDB ID 1g5a), sucrose phosphorylase [86] (PDB ID 1r7a), sucrose hydrolase [87] (PDB ID 1cze) and sucrose isomerase [88, 89] (PDB ID 1m53 1zja), were solved. Finally structures have been solved of glycogen branching [90] (PDB ID 1m7x) and debranching [91] (PDB ID 2vnc) enzymes.

Among the solved structures are numerous site-directed-mutant and ligand-complexed forms. However, although there are structures available for most of the GH13 specificities, some still remain to be determined. Noticeably crystal structures are available of several α-amylase/proteinaceous inhibitor complexes (for reviews, see [37, 92]).

For a complete list of all currently available three-dimensional structures, please see the GH13 page in CAZy database, which is continuously updated.

Family Firsts

First sterochemistry determination

α-Maltose was released from different α-maltosides by Bacillus subtilis saccharifying α-amylase, Taka-amylase A, and porcine pancreas α-amylase, as determined by quantitative gas liquid chromatography [41]. This was as well demonstrated by NMR analysis of the anomeric configuration of the released product [42].

First catalytic nucleophile

A glycosidic covalent bond was formed in the intermediate of the mechanism between the catalytic nucleophile (D229) of Bacillus circulans 251 CGTase and a maltotriosyl moiety [43] (PDB ID 1cxl). Mutational analysis of human pancreatic α-amylase provided strong support for D197 being the catalytic nucleophile as demonstrated by kinetics analysis [93] (PDB ID 1kbb).

First general acid/base

Mutational analysis of human pancreatic α-amylase using enzymatic kinetics and structural analysis provided strong support for E233 playing the role of the catalytic acid/base [93] (PDB ID 1kbb).

First 3-D structure

The first high-resolution three-dimensional structure was determined for Taka-amylase A [62] (PDB ID 2taa).

References

  1. Svensson B. Protein engineering in the alpha-amylase family: catalytic mechanism, substrate specificity, and stability. Plant Mol Biol. 1994 May;25(2):141-57. PubMed ID:8018865 | HubMed [Svensson1994]
  2. Janecek S. alpha-Amylase family: molecular biology and evolution. Prog Biophys Mol Biol. 1997;67(1):67-97. PubMed ID:9401418 | HubMed [Janecek1997a]
  3. Kuriki T and Imanaka T. The concept of the alpha-amylase family: structural similarity and common catalytic mechanism. J Biosci Bioeng. 1999;87(5):557-65. PubMed ID:16232518 | HubMed [Kuriki1999]
  4. MacGregor EA, Janecek S, and Svensson B. Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes. Biochim Biophys Acta. 2001 Mar 9;1546(1):1-20. PubMed ID:11257505 | HubMed [MacGregor2001]
  5. van der Maarel MJ, van der Veen B, Uitdehaag JC, Leemhuis H, and Dijkhuizen L. Properties and applications of starch-converting enzymes of the alpha-amylase family. J Biotechnol. 2002 Mar 28;94(2):137-55. PubMed ID:11796168 | HubMed [vanderMaarel2002]
  6. Janecek S, Svensson B, and Henrissat B. Domain evolution in the alpha-amylase family. J Mol Evol. 1997 Sep;45(3):322-31. PubMed ID:9302327 | HubMed [Janecek1997b]
  7. Fort J, de la Ballina LR, Burghardt HE, Ferrer-Costa C, Turnay J, Ferrer-Orta C, Usón I, Zorzano A, Fernández-Recio J, Orozco M, Lizarbe MA, Fita I, and Palacín M. The structure of human 4F2hc ectodomain provides a model for homodimerization and electrostatic interaction with plasma membrane. J Biol Chem. 2007 Oct 26;282(43):31444-52. DOI:10.1074/jbc.M704524200 | PubMed ID:17724034 | HubMed [Fort2007]
  8. Gabrisko M and Janecek S. Looking for the ancestry of the heavy-chain subunits of heteromeric amino acid transporters rBAT and 4F2hc within the GH13 alpha-amylase family. FEBS J. 2009 Dec;276(24):7265-78. DOI:10.1111/j.1742-4658.2009.07434.x | PubMed ID:19878315 | HubMed [Gabrisko2009]
  9. Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, and Henrissat B. The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res. 2009 Jan;37(Database issue):D233-8. DOI:10.1093/nar/gkn663 | PubMed ID:18838391 | HubMed [Cantarel2009]
  10. Stam MR, Danchin EG, Rancurel C, Coutinho PM, and Henrissat B. Dividing the large glycoside hydrolase family 13 into subfamilies: towards improved functional annotations of alpha-amylase-related proteins. Protein Eng Des Sel. 2006 Dec;19(12):555-62. DOI:10.1093/protein/gzl044 | PubMed ID:17085431 | HubMed [Stam2006]
  11. Oslancová A and Janecek S. Oligo-1,6-glucosidase and neopullulanase enzyme subfamilies from the alpha-amylase family defined by the fifth conserved sequence region. Cell Mol Life Sci. 2002 Nov;59(11):1945-59. PubMed ID:12530525 | HubMed [Oslancova2002]
  12. Svensson B, Jespersen H, Sierks MR, and MacGregor EA. Sequence homology between putative raw-starch binding domains from different starch-degrading enzymes. Biochem J. 1989 Nov 15;264(1):309-11. PubMed ID:2481445 | HubMed [Svensson1989]
  13. Janecek S and Sevcík J. The evolution of starch-binding domain. FEBS Lett. 1999 Jul 30;456(1):119-25. PubMed ID:10452542 | HubMed [Janecek1999a]
  14. Rodríguez-Sanoja R, Oviedo N, and Sánchez S. Microbial starch-binding domain. Curr Opin Microbiol. 2005 Jun;8(3):260-7. DOI:10.1016/j.mib.2005.04.013 | PubMed ID:15939348 | HubMed [Rodriguez-Sanoja2005]
  15. Machovic M and Janecek S. Starch-binding domains in the post-genome era. Cell Mol Life Sci. 2006 Dec;63(23):2710-24. DOI:10.1007/s00018-006-6246-9 | PubMed ID:17013558 | HubMed [Machovic2006]
  16. Christiansen C, Abou Hachem M, Janecek S, Viksø-Nielsen A, Blennow A, and Svensson B. The carbohydrate-binding module family 20--diversity, structure, and function. FEBS J. 2009 Sep;276(18):5006-29. DOI:10.1111/j.1742-4658.2009.07221.x | PubMed ID:19682075 | HubMed [Christiansen2009]
  17. Henrissat B. A classification of glycosyl hydrolases based on amino acid sequence similarities. Biochem J. 1991 Dec 1;280 ( Pt 2):309-16. PubMed ID:1747104 | HubMed [Henrissat1991]
  18. MacGregor EA and Svensson B. A super-secondary structure predicted to be common to several alpha-1,4-D-glucan-cleaving enzymes. Biochem J. 1989 Apr 1;259(1):145-52. PubMed ID:2524186 | HubMed [MacGregor1989]
  19. Jespersen HM, MacGregor EA, Sierks MR, and Svensson B. Comparison of the domain-level organization of starch hydrolases and related enzymes. Biochem J. 1991 Nov 15;280 ( Pt 1):51-5. PubMed ID:1741756 | HubMed [Jespersen1991]
  20. Jespersen HM, MacGregor EA, Henrissat B, Sierks MR, and Svensson B. Starch- and glycogen-debranching and branching enzymes: prediction of structural features of the catalytic (beta/alpha)8-barrel domain and evolutionary relationship to other amylolytic enzymes. J Protein Chem. 1993 Dec;12(6):791-805. PubMed ID:8136030 | HubMed [Jespersen1993]
  21. Takata H, Kuriki T, Okada S, Takesada Y, Iizuka M, Minamiura N, and Imanaka T. Action of neopullulanase. Neopullulanase catalyzes both hydrolysis and transglycosylation at alpha-(1----4)- and alpha-(1----6)-glucosidic linkages. J Biol Chem. 1992 Sep 15;267(26):18447-52. PubMed ID:1388153 | HubMed [Takata1992]
  22. Nakajima R, Imanaka T, and Aiba S. Comparison of amino acid sequences of eleven different α-amylases. Appl Microbiol Biotechnol 1986; 23(5): 355-60. (DOI: 10.1007/BF00257032) [Nakajima1986]
  23. Janecek S. New conserved amino acid region of alpha-amylases in the third loop of their (beta/alpha)8-barrel domains. Biochem J. 1992 Dec 15;288 ( Pt 3):1069-70. PubMed ID:1471979 | HubMed [Janecek1992]
  24. Janecek S. Sequence similarities and evolutionary relationships of microbial, plant and animal alpha-amylases. Eur J Biochem. 1994 Sep 1;224(2):519-24. PubMed ID:7925367 | HubMed [Janecek1994a]
  25. Janecek S. How many conserved sequence regions are there in the α-amylase family? Biologia 2002; 57(Suppl. 11): 29-41. (PDF) [Janecek2002]
  26. Kuriki T, Takata H, Okada S, and Imanaka T. Analysis of the active center of Bacillus stearothermophilus neopullulanase. J Bacteriol. 1991 Oct;173(19):6147-52. PubMed ID:1917847 | HubMed [Kuriki1991]
  27. Janecek S Amylolytic families of glycoside hydrolases: focus on the family GH-57. Biologia 2005; 60(Suppl. 16): 177-84. (PDF) [Janecek2005]
  28. Janecek S, Svensson B, and MacGregor EA. A remote but significant sequence homology between glycoside hydrolase clan GH-H and family GH31. FEBS Lett. 2007 Apr 3;581(7):1261-8. DOI:10.1016/j.febslet.2007.02.036 | PubMed ID:17349635 | HubMed [Janecek2007]
  29. Janecek S. Parallel beta/alpha-barrels of alpha-amylase, cyclodextrin glycosyltransferase and oligo-1,6-glucosidase versus the barrel of beta-amylase: evolutionary distance is a reflection of unrelated sequences. FEBS Lett. 1994 Oct 17;353(2):119-23. PubMed ID:7926034 | HubMed [Janecek1994b]
  30. Park KH, Kim TJ, Cheong TK, Kim JW, Oh BH, and Svensson B. Structure, specificity and function of cyclomaltodextrinase, a multispecific enzyme of the alpha-amylase family. Biochim Biophys Acta. 2000 May 23;1478(2):165-85. PubMed ID:10825529 | HubMed [Park2000]
  31. Janecek S, Lévêque E, Belarbi A, and Haye B. Close evolutionary relatedness of alpha-amylases from Archaea and plants. J Mol Evol. 1999 Apr;48(4):421-6. PubMed ID:10079280 | HubMed [Janecek1999b]
  32. Jones RA, Jermiin LS, Easteal S, Patel BK, and Beacham IR. Amylase and 16S rRNA genes from a hyperthermophilic archaebacterium. J Appl Microbiol. 1999 Jan;86(1):93-107. PubMed ID:10030014 | HubMed [Jones1999]
  33. Da Lage JL, Feller G, and Janecek S. Horizontal gene transfer from Eukarya to bacteria and domain shuffling: the alpha-amylase model. Cell Mol Life Sci. 2004 Jan;61(1):97-109. DOI:10.1007/s00018-003-3334-y | PubMed ID:14704857 | HubMed [DaLage2004]
  34. van der Kaaij RM, Janecek S, van der Maarel MJ, and Dijkhuizen L. Phylogenetic and biochemical characterization of a novel cluster of intracellular fungal alpha-amylase enzymes. Microbiology. 2007 Dec;153(Pt 12):4003-15. DOI:10.1099/mic.0.2007/008607-0 | PubMed ID:18048915 | HubMed [vanderKaaij2007]
  35. Hostinová E, Janecek S, and Gasperík J. Gene sequence, bioinformatics and enzymatic characterization of alpha-amylase from Saccharomycopsis fibuligera KZ. Protein J. 2010 Jul;29(5):355-64. DOI:10.1007/s10930-010-9260-6 | PubMed ID:20552260 | HubMed [Hostinova2010]
  36. Bowman DE. AMYLASE INHIBITOR OF NAVY BEANS. Science. 1945 Oct 5;102(2649):358-9. DOI:10.1126/science.102.2649.358 | PubMed ID:17730484 | HubMed [Bowman1945]
  37. Svensson B, Fukuda K, Nielsen PK, and Bønsager BC. Proteinaceous alpha-amylase inhibitors. Biochim Biophys Acta. 2004 Feb 12;1696(2):145-56. DOI:10.1016/j.bbapap.2003.07.004 | PubMed ID:14871655 | HubMed [Svensson2004]
  38. Macri LJ, MacGregor AW, Schroeder SW, and Bazin SL. Detection of a limit dextrinase inhibitor in barley. J Cereal Sci 1993; 18(2): 103-6. (DOI: 10.1006/jcrs.1993.1038) [Macri1993]
  39. MacGregor AW, Donald LJ, MacGregor EA, and Duckworth HW. Stoichiometry of the complex formed by barley limit dextrinase with its endogenous inhibitor. Determination by electrospray time-of-flight mass spectrometry. J Cereal Sci 2003; 37(3) 357-62. (DOI: 10.1006/jcrs.2002.0500) [MacGregor2003]
  40. MacGregor EA. The proteinaceous inhibitor of limit dextrinase in barley and malt. Biochim Biophys Acta. 2004 Feb 12;1696(2):165-70. DOI:10.1016/j.bbapap.2003.09.018 | PubMed ID:14871657 | HubMed [MacGregor2004]
  41. Kimura A, and Chiba S. Quantitative study of anomeric forms of maltose produced by α- and β-amylases. Agric Biol Chem 1983; 47(8): 1747-53. (Link) [Kimura1983]
  42. Isoda Y, Shimizu Y, Hashimoto A, Fujiwara H, Nitta Y, and Kagemoto A. Mechanism of hydrolyses of phenyl alpha-maltosides catalyzed by taka-amylase A. J Biochem. 1992 Feb;111(2):204-9. PubMed ID:1569044 | HubMed [Isoda1992]
  43. Uitdehaag JC, Mosi R, Kalk KH, van der Veen BA, Dijkhuizen L, Withers SG, and Dijkstra BW. X-ray structures along the reaction pathway of cyclodextrin glycosyltransferase elucidate catalysis in the alpha-amylase family. Nat Struct Biol. 1999 May;6(5):432-6. DOI:10.1038/8235 | PubMed ID:10331869 | HubMed [Uitdehaag1999]
  44. Kelly RM, Leemhuis H, and Dijkhuizen L. Conversion of a cyclodextrin glucanotransferase into an alpha-amylase: assessment of directed evolution strategies. Biochemistry. 2007 Oct 2;46(39):11216-22. DOI:10.1021/bi701160h | PubMed ID:17824673 | HubMed [Kelly2007]
  45. Yang SJ, Min BC, Kim YW, Jang SM, Lee BH, and Park KH. Changes in the catalytic properties of Pyrococcus furiosus thermostable amylase by mutagenesis of the substrate binding sites. Appl Environ Microbiol. 2007 Sep;73(17):5607-12. DOI:10.1128/AEM.00499-07 | PubMed ID:17630303 | HubMed [Yang2007]
  46. Robyt JF and French D. Multiple attach hypothesis of alpha-amylase action: action of porcine pancreatic, human salivary, and Aspergillus oryzae alpha-amylases. Arch Biochem Biophys. 1967 Oct;122(1):8-16. PubMed ID:6076229 | HubMed [Robyt1967]
  47. Mazur AK and Nakatani H. Multiple attack mechanism in the porcine pancreatic alpha-amylase hydrolysis of amylose and amylopectin. Arch Biochem Biophys. 1993 Oct;306(1):29-38. DOI:10.1006/abbi.1993.1476 | PubMed ID:8215418 | HubMed [Mazur1993]
  48. Kramhøft B, Bak-Jensen KS, Mori H, Juge N, Nøhr J, and Svensson B. Involvement of individual subsites and secondary substrate binding sites in multiple attack on amylose by barley alpha-amylase. Biochemistry. 2005 Feb 15;44(6):1824-32. DOI:10.1021/bi048100v | PubMed ID:15697208 | HubMed [Kramhoft2005]
  49. Prodanov E, Seigner C, and Marchis-Mouren G. Subsite profile of the active center of porcine pancreatic alpha-amylase. Kinetic studies using maltooligosaccharides as substrates. Biochem Biophys Res Commun. 1984 Jul 18;122(1):75-81. PubMed ID:6611158 | HubMed [Prodanov1984]
  50. Ajandouz EH, Abe J, Svensson B, and Marchis-Mouren G. Barley malt-alpha-amylase. Purification, action pattern, and subsite mapping of isozyme 1 and two members of the isozyme 2 subfamily using p-nitrophenylated maltooligosaccharide substrates. Biochim Biophys Acta. 1992 Sep 23;1159(2):193-202. PubMed ID:1390923 | HubMed [Ajandouz1992]
  51. Macgregor AW, Morgan JE, and Macgregor EA. The action of germinated barley α-amylases on linear maltodextrins. Carbohydr Res 1992; 227: 301-13. (DOI: 10.1016/0008-6215(92)85080-J) [MacGregor1992]
  52. Kandra L, Hachem MA, Gyémánt G, Kramhøft B, and Svensson B. Mapping of barley alpha-amylases and outer subsite mutants reveals dynamic high-affinity subsites and barriers in the long substrate binding cleft. FEBS Lett. 2006 Sep 18;580(21):5049-53. DOI:10.1016/j.febslet.2006.08.028 | PubMed ID:16949579 | HubMed [Kandra2006]
  53. Bozonnet S, Jensen MT, Nielsen MM, Aghajari N, Jensen MH, Kramhøft B, Willemoës M, Tranier S, Haser R, and Svensson B. The 'pair of sugar tongs' site on the non-catalytic domain C of barley alpha-amylase participates in substrate binding and activity. FEBS J. 2007 Oct;274(19):5055-67. DOI:10.1111/j.1742-4658.2007.06024.x | PubMed ID:17803687 | HubMed [Bozonnet2007]
  54. Nielsen MM, Seo ES, Bozonnet S, Aghajari N, Robert X, Haser R, and Svensson B. Multi-site substrate binding and interplay in barley alpha-amylase 1. FEBS Lett. 2008 Jul 23;582(17):2567-71. DOI:10.1016/j.febslet.2008.06.027 | PubMed ID:18588886 | HubMed [Nielsen2008]
  55. Nielsen MM, Bozonnet S, Seo ES, Mótyán JA, Andersen JM, Dilokpimol A, Abou Hachem M, Gyémánt G, Naested H, Kandra L, Sigurskjold BW, and Svensson B. Two secondary carbohydrate binding sites on the surface of barley alpha-amylase 1 have distinct functions and display synergy in hydrolysis of starch granules. Biochemistry. 2009 Aug 18;48(32):7686-97. DOI:10.1021/bi900795a | PubMed ID:19606835 | HubMed [Nielsen2009]
  56. Ragunath C, Manuel SG, Venkataraman V, Sait HB, Kasinathan C, and Ramasubbu N. Probing the role of aromatic residues at the secondary saccharide-binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding. J Mol Biol. 2008 Dec 31;384(5):1232-48. DOI:10.1016/j.jmb.2008.09.089 | PubMed ID:18951906 | HubMed [Ragunath2008]
  57. Tibbot BK, Wong DW, and Robertson GH. A functional raw starch-binding domain of barley alpha-amylase expressed in Escherichia coli. J Protein Chem. 2000 Nov;19(8):663-9. PubMed ID:11307950 | HubMed [Tibbot2000]
  58. Penninga D, van der Veen BA, Knegtel RM, van Hijum SA, Rozeboom HJ, Kalk KH, Dijkstra BW, and Dijkhuizen L. The raw starch binding domain of cyclodextrin glycosyltransferase from Bacillus circulans strain 251. J Biol Chem. 1996 Dec 20;271(51):32777-84. PubMed ID:8955113 | HubMed [Penninga1996]
  59. Rodriguez Sanoja R, Morlon-Guyot J, Jore J, Pintado J, Juge N, and Guyot JP. Comparative characterization of complete and truncated forms of Lactobacillus amylovorus alpha-amylase and role of the C-terminal direct repeats in raw-starch binding. Appl Environ Microbiol. 2000 Aug;66(8):3350-6. PubMed ID:10919790 | HubMed [Rodriguez-Sanoja2000]
  60. Sumitani J, Tottori T, Kawaguchi T, and Arai M. New type of starch-binding domain: the direct repeat motif in the C-terminal region of Bacillus sp. no. 195 alpha-amylase contributes to starch binding and raw starch degrading. Biochem J. 2000 Sep 1;350 Pt 2:477-84. PubMed ID:10947962 | HubMed [Sumitani2000]
  61. Juge N, Nøhr J, Le Gal-Coëffet MF, Kramhøft B, Furniss CS, Planchot V, Archer DB, Williamson G, and Svensson B. The activity of barley alpha-amylase on starch granules is enhanced by fusion of a starch binding domain from Aspergillus niger glucoamylase. Biochim Biophys Acta. 2006 Feb;1764(2):275-84. DOI:10.1016/j.bbapap.2005.11.008 | PubMed ID:16403494 | HubMed [Juge2006]
  62. Matsuura Y, Kusunoki M, Harada W, and Kakudo M. Structure and possible catalytic residues of Taka-amylase A. J Biochem. 1984 Mar;95(3):697-702. PubMed ID:6609921 | HubMed [Matsuura1984]
  63. Buisson G, Duée E, Haser R, and Payan F. Three dimensional structure of porcine pancreatic alpha-amylase at 2.9 A resolution. Role of calcium in structure and activity. EMBO J. 1987 Dec 20;6(13):3909-16. PubMed ID:3502087 | HubMed [Buisson1987]
  64. Qian M, Haser R, and Payan F. Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution. J Mol Biol. 1993 Jun 5;231(3):785-99. DOI:10.1006/jmbi.1993.1326 | PubMed ID:8515451 | HubMed [Qian1993]
  65. Kadziola A, Abe J, Svensson B, and Haser R. Crystal and molecular structure of barley alpha-amylase. J Mol Biol. 1994 May 27;239(1):104-21. PubMed ID:8196040 | HubMed [Kadziola1994]
  66. Brzozowski AM and Davies GJ. Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution. Biochemistry. 1997 Sep 9;36(36):10837-45. DOI:10.1021/bi970539i | PubMed ID:9283074 | HubMed [Brzozowski1997]
  67. Machius M, Wiegand G, and Huber R. Crystal structure of calcium-depleted Bacillus licheniformis alpha-amylase at 2.2 A resolution. J Mol Biol. 1995 Mar 3;246(4):545-59. DOI:10.1006/jmbi.1994.0106 | PubMed ID:7877175 | HubMed [Machius1995]
  68. Aghajari N, Feller G, Gerday C, and Haser R. Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor. Protein Sci. 1998 Mar;7(3):564-72. DOI:10.1002/pro.5560070304 | PubMed ID:9541387 | HubMed [Aghajari1998]
  69. Brzozowski AM, Lawson DM, Turkenburg JP, Bisgaard-Frantzen H, Svendsen A, Borchert TV, Dauter Z, Wilson KS, and Davies GJ. Structural analysis of a chimeric bacterial alpha-amylase. High-resolution analysis of native and ligand complexes. Biochemistry. 2000 Aug 8;39(31):9099-107. PubMed ID:10924103 | HubMed [Brzozowski2000]
  70. Robert X, Haser R, Gottschalk TE, Ratajczak F, Driguez H, Svensson B, and Aghajari N. The structure of barley alpha-amylase isozyme 1 reveals a novel role of domain C in substrate recognition and binding: a pair of sugar tongs. Structure. 2003 Aug;11(8):973-84. PubMed ID:12906828 | HubMed [Robert2003]
  71. Hofmann BE, Bender H, and Schulz GE. Three-dimensional structure of cyclodextrin glycosyltransferase from Bacillus circulans at 3.4 A resolution. J Mol Biol. 1989 Oct 20;209(4):793-800. PubMed ID:2531228 | HubMed [Hofmann1989]
  72. Lawson CL, van Montfort R, Strokopytov B, Rozeboom HJ, Kalk KH, de Vries GE, Penninga D, Dijkhuizen L, and Dijkstra BW. Nucleotide sequence and X-ray structure of cyclodextrin glycosyltransferase from Bacillus circulans strain 251 in a maltose-dependent crystal form. J Mol Biol. 1994 Feb 18;236(2):590-600. DOI:10.1006/jmbi.1994.1168 | PubMed ID:8107143 | HubMed [Lawson1994]
  73. Leemhuis H, Rozeboom HJ, Wilbrink M, Euverink GJ, Dijkstra BW, and Dijkhuizen L. Conversion of cyclodextrin glycosyltransferase into a starch hydrolase by directed evolution: the role of alanine 230 in acceptor subsite +1. Biochemistry. 2003 Jun 24;42(24):7518-26. DOI:10.1021/bi034439q | PubMed ID:12809508 | HubMed [Leemhuis2003]
  74. Dauter Z, Dauter M, Brzozowski AM, Christensen S, Borchert TV, Beier L, Wilson KS, and Davies GJ. X-ray structure of Novamyl, the five-domain "maltogenic" alpha-amylase from Bacillus stearothermophilus: maltose and acarbose complexes at 1.7A resolution. Biochemistry. 1999 Jun 29;38(26):8385-92. DOI:10.1021/bi990256l | PubMed ID:10387084 | HubMed [Dauter1999]
  75. Katsuya Y, Mezaki Y, Kubota M, and Matsuura Y. Three-dimensional structure of Pseudomonas isoamylase at 2.2 A resolution. J Mol Biol. 1998 Sep 4;281(5):885-97. DOI:10.1006/jmbi.1998.1992 | PubMed ID:9719642 | HubMed [Katsuya1998]
  76. Mikami B, Iwamoto H, Malle D, Yoon HJ, Demirkan-Sarikaya E, Mezaki Y, and Katsuya Y. Crystal structure of pullulanase: evidence for parallel binding of oligosaccharides in the active site. J Mol Biol. 2006 Jun 9;359(3):690-707. DOI:10.1016/j.jmb.2006.03.058 | PubMed ID:16650854 | HubMed [Mikami2006]
  77. Vester-Christensen MB, Abou Hachem M, Svensson B, and Henriksen A. Crystal structure of an essential enzyme in seed starch degradation: barley limit dextrinase in complex with cyclodextrins. J Mol Biol. 2010 Nov 12;403(5):739-50. DOI:10.1016/j.jmb.2010.09.031 | PubMed ID:20863834 | HubMed [VesterChristensen2010]
  78. Kizaki H, Hata Y, Watanabe K, Katsube Y, and Suzuki Y. Polypeptide folding of Bacillus cereus ATCC7064 oligo-1,6-glucosidase revealed by 3.0 A resolution X-ray analysis. J Biochem. 1993 Jun;113(6):646-9. PubMed ID:8370659 | HubMed [Kizaki1993]
  79. Hondoh H, Saburi W, Mori H, Okuyama M, Nakada T, Matsuura Y, and Kimura A. Substrate recognition mechanism of alpha-1,6-glucosidic linkage hydrolyzing enzyme, dextran glucosidase from Streptococcus mutans. J Mol Biol. 2008 May 9;378(4):913-22. DOI:10.1016/j.jmb.2008.03.016 | PubMed ID:18395742 | HubMed [Hondoh2008]
  80. Kim JS, Cha SS, Kim HJ, Kim TJ, Ha NC, Oh ST, Cho HS, Cho MJ, Kim MJ, Lee HS, Kim JW, Choi KY, Park KH, and Oh BH. Crystal structure of a maltogenic amylase provides insights into a catalytic versatility. J Biol Chem. 1999 Sep 10;274(37):26279-86. PubMed ID:10473583 | HubMed [Kim1999]
  81. Lee HS, Kim MS, Cho HS, Kim JI, Kim TJ, Choi JH, Park C, Lee HS, Oh BH, and Park KH. Cyclomaltodextrinase, neopullulanase, and maltogenic amylase are nearly indistinguishable from each other. J Biol Chem. 2002 Jun 14;277(24):21891-7. DOI:10.1074/jbc.M201623200 | PubMed ID:11923309 | HubMed [Lee2002]
  82. Hondoh H, Kuriki T, and Matsuura Y. Three-dimensional structure and substrate binding of Bacillus stearothermophilus neopullulanase. J Mol Biol. 2003 Feb 7;326(1):177-88. PubMed ID:12547200 | HubMed [Hondoh2003]
  83. Kamitori S, Abe A, Ohtaki A, Kaji A, Tonozuka T, and Sakano Y. Crystal structures and structural comparison of Thermoactinomyces vulgaris R-47 alpha-amylase 1 (TVAI) at 1.6 A resolution and alpha-amylase 2 (TVAII) at 2.3 A resolution. J Mol Biol. 2002 Apr 26;318(2):443-53. DOI:10.1016/S0022-2836(02)00111-0 | PubMed ID:12051850 | HubMed [Kamitori2002]
  84. Kamitori S, Kondo S, Okuyama K, Yokota T, Shimura Y, Tonozuka T, and Sakano Y. Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution. J Mol Biol. 1999 Apr 16;287(5):907-21. DOI:10.1006/jmbi.1999.2647 | PubMed ID:10222200 | HubMed [Kamitori1999]
  85. Skov LK, Mirza O, Henriksen A, De Montalk GP, Remaud-Simeon M, Sarçabal P, Willemot RM, Monsan P, and Gajhede M. Amylosucrase, a glucan-synthesizing enzyme from the alpha-amylase family. J Biol Chem. 2001 Jul 6;276(27):25273-8. DOI:10.1074/jbc.M010998200 | PubMed ID:11306569 | HubMed [Skov2001]
  86. Sprogøe D, van den Broek LA, Mirza O, Kastrup JS, Voragen AG, Gajhede M, and Skov LK. Crystal structure of sucrose phosphorylase from Bifidobacterium adolescentis. Biochemistry. 2004 Feb 10;43(5):1156-62. DOI:10.1021/bi0356395 | PubMed ID:14756551 | HubMed [Sprogoe2004]
  87. Kim MI, Kim HS, Jung J, and Rhee S. Crystal structures and mutagenesis of sucrose hydrolase from Xanthomonas axonopodis pv. glycines: insight into the exclusively hydrolytic amylosucrase fold. J Mol Biol. 2008 Jul 18;380(4):636-47. DOI:10.1016/j.jmb.2008.05.046 | PubMed ID:18565544 | HubMed [Kim2008]
  88. Zhang D, Li N, Lok SM, Zhang LH, and Swaminathan K. Isomaltulose synthase (PalI) of Klebsiella sp. LX3. Crystal structure and implication of mechanism. J Biol Chem. 2003 Sep 12;278(37):35428-34. DOI:10.1074/jbc.M302616200 | PubMed ID:12819210 | HubMed [Zhang2003]
  89. Ravaud S, Robert X, Watzlawick H, Haser R, Mattes R, and Aghajari N. Trehalulose synthase native and carbohydrate complexed structures provide insights into sucrose isomerization. J Biol Chem. 2007 Sep 21;282(38):28126-36. DOI:10.1074/jbc.M704515200 | PubMed ID:17597061 | HubMed [Ravaud2007]
  90. Abad MC, Binderup K, Rios-Steiner J, Arni RK, Preiss J, and Geiger JH. The X-ray crystallographic structure of Escherichia coli branching enzyme. J Biol Chem. 2002 Nov 1;277(44):42164-70. DOI:10.1074/jbc.M205746200 | PubMed ID:12196524 | HubMed [Abad2002]
  91. Woo EJ, Lee S, Cha H, Park JT, Yoon SM, Song HN, and Park KH. Structural insight into the bifunctional mechanism of the glycogen-debranching enzyme TreX from the archaeon Sulfolobus solfataricus. J Biol Chem. 2008 Oct 17;283(42):28641-8. DOI:10.1074/jbc.M802560200 | PubMed ID:18703518 | HubMed [Woo2008]
  92. Payan F. Structural basis for the inhibition of mammalian and insect alpha-amylases by plant protein inhibitors. Biochim Biophys Acta. 2004 Feb 12;1696(2):171-80. DOI:10.1016/j.bbapap.2003.10.012 | PubMed ID:14871658 | HubMed [Payan2004]
  93. Rydberg EH, Li C, Maurus R, Overall CM, Brayer GD, and Withers SG. Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids. Biochemistry. 2002 Apr 2;41(13):4492-502. PubMed ID:11914097 | HubMed [Rydberg2002]
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