Structure and molecular model refinement of <i>Aspergillus oryzae</i> (TAKA) α-amylase: an application of the simulated-annealing method

Swift, H. J.; Brady, Leo; Derewenda, Zygmunt S.; Dodson, E.J.; Dodson, Guy; Turkenburg, J.P.; Wilkinson, Anthony J.

doi:10.1107/s0108768191001970

Cited by 102 publications

(69 citation statements)

References 13 publications

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“…At the opposite end of the active site we observe a phenylalanine in AHA (Phe 223) as well as in mammalian (Buisson et al, 1987;Qian et al, 1993;Larson et al, 1994;Brayer et al, 1995;Ramasubbu et al, 1996), and plant (isozyme 2 from barley malt) (Kadziola, 1993;Kadziola et al, 1994) a-amylases, whereas this phenylalanine has been replaced by a tyrosine in TAKA (Matsuura et al, 1984;Swift et al, 1991) and acid (Boel et al, 1990;Brady et al, 1991) a-amylases. Finally, two consecutive tryptophans (46 and 47) are found next to 50.…”

Section: N Aghujan Et Almentioning

confidence: 86%

“…Only subtle structural adjustments were expected to affect either the substrate binding-and active sites or the overall molecular architecture leading to a flexible ( a s judged from physico-chemical data) conformation of these enzymes. The wide range of known three-dimensional structures of a-amylases from Aspergillus oryzae (Matsuura et al, 1984;Swift et al, 1991), Aspergillus niger (Boel et al, 1990;Brady et al, 1991), porcine pancreas (Buisson et al, 1987;Qian et al, 1993;Larson et al. 1994), barley seeds (Kadziola et al, 1994), Bacillus lichenifomis (Machius et al, 1995), human pancreas (Brayer et al, 1995), and human salivary (Ramasubbu et al, 1996) constitute an ideal system for studies of adaptation of enzymes to extreme conditions on a molecular level.…”

Section: Activity At Low Temperaturementioning

confidence: 99%

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Crystal structures of the psychrophilic α‐amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor

et al. 1998

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Alteromonas haloplanctis is a bacterium that flourishes in Antarctic sea-water and it is considered as an extreme psychrophile. We have determined the crystal structures of the a-amylase (AHA) secreted by this bacterium, in its native state to 2.0 8, resolution as well as in complex with Tris to 1.85 8, resolution. The structure of AHA, which is the first experimentally determined three-dimensional structure of a psychrophilic enzyme, resembles those of other known a-amylases of various origins with a surprisingly greatest similarity to mammalian a-amylases. AHA contains a chloride ion which activates the hydrolytic cleavage of substrate a-1,4-glycosidic bonds. The chloride binding site is situated -5 8, from the active site which is characterized by a triad of acid residues (Asp 174, Glu 200, Asp 264). These are all involved in firm binding of the Tris moiety. A reaction mechanism for substrate hydrolysis is proposed on the basis of the Tris inhibitor binding and the chloride activation. A trio of residues (Ser 303, His 337, Glu 19) having a striking spatial resemblance with serine-protease like catalytic triads was found -22 A from the active site. We found that this triad is equally present in other chloride dependent a-amylases, and suggest that it could be responsible for autoproteolytic events observed in solution for this cold adapted a-amylase.Keywords: allosteric activation; cold adaptation; crystal structure; glycosyl hydrolases; inhibition; psychrophilic a-Amylases a-1,4-glucan-4-glucanohydrolase, EC 3.2.1.1 are endoglucanases widely distributed in bacteria, fungi, animals, and plants. They catalyze the hydrolysis of starch, glycogen, and related polysaccharides by cleaving internal a-1,Cglycosidic bonds. In addition to their biochemical interest, a-amylases have a number of important biotechnological applications in food and starch processing industries (Vihinen & Mantsala, 1989).Alteromonas haloplanctis is a gram negative bacterium collected in Antarctica and secreting a calcium-and chloride-dependent a-amylase. It grows at sub-zero temperatures in its natural environment and can be considered as an extreme psychrophile (Feller et al., 1992). The psychrophilic a-amylase is characterized by a high catalytic efficiency which compensates for the reduction of chemical reaction rates inherent to low temperatures. In addition, all biophysical parameters recorded suggest a flexible conformation of this heat-labile a-amylase. The two crystal structures reported here are the first three-dimensional structures of a psy- chrophilic enzyme; moreover, they provide a number of significant features related to various aspects of biochemistry and microbiology. The structure of A. haloplanctis a-amylase cornplexed with Tris allows to understand the molecular basis of glycosidase inhibition by this cation which is a widely used compound in biochemistry. This bacterial a-amylase requires a chloride ion for its activity, a property previously considered as specific to mammalian a-amylases (Brayer et al., 1995). ...

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Section: N Aghujan Et Almentioning

confidence: 86%

Section: Activity At Low Temperaturementioning

confidence: 99%

Crystal structures of the psychrophilic α‐amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor

et al. 1998

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“…This favourable degree of identity allowed the building of a model of the three-dimensional structure of the psychrophilic a-amylase. The predicted molecular architecture follows the pattern of known a-amylase structures (Swift et al, 1991;Qian et al, 1993). The enzyme is made of a central barrel (domain A), a P-pleated domain B and a globular C-terminal domain C. Amino acids with their side chain directed towards the active site, amongst which Glu233, Asp300 and Asp197 are the main catalytic residues, are conserved suggesting a very close reaction mechanism in both enzymes.…”

Section: A Haloplanctis A-amylase Structural Model Analysismentioning

confidence: 99%

“…The disulfide bond Cys70-CysllS is absent in A. haloplanctis a-amylase. However, mesophilic a-amylases from Aspergillus oryzae (Swift et al, 1991) and Streptomyces limosus (Long et al, 1987) are also devoid of this disulfide linkage which does not seem of crucial importance for stability. Negatively charged side chains at the N-terminal first turn of a helices and positively charged side chains at the C-terminal last turn of a helices are considered as stabilizing factors (Shoemaker et al, 1987;Rentier-Delrue et al, 1993).…”

Section: Conformational Stability Of the Psychrophilic Enzymementioning

confidence: 99%

Stability and structural analysis of α‐amylase from the antarctic psychrophile Alteromonas haloplanctis A23

Feller

Payan

Theys

et al. 1994

European Journal of Biochemistry

201

129

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The a-amylase secreted by the antarctic bacterium Alteromonas haloplanctis displays 66% amino acid sequence similarity with porcine pancreatic a-amylase. The psychrophilic a-amylase is however characterized by a sevenfold higher k,,, and k,,/K,,, values at 4°C and a lower conformational stability estimated as 10 kJ . mol-' with respect to the porcine enzyme. It is proposed that both properties arise from an increase in molecular flexibility required to compensate for the reduction of reaction rates at low temperatures. This is supported by the fast denaturation rates induced by temperature, urea or guanidinium chloride and by the shift towards low temperatures of the apparent optimal temperature of activity.When compared with the known three-dimensional structure of porcine pancreatic a-amylase, homology modelling of the psychrophilic a-amylase reveals several features which may be assumed to be responsible for a more flexible, heat-labile conformation: the lack of several surface salt bridges in the @/a)* domain, the reduction of the number of weakly polar interactions involving an aromatic side chain, a lower hydrophobicity associated with the increased flexibility index of amino acids forming the hydrophobic clusters and by substitutions of proline for alanine residues in loops connecting secondary structures. The weaker affinity of the enzyme for Ca2+ (Kd = 44 nM) and for C1F (Kd = 1.2 mM at 4°C) can result from single amino acid substitutions in the Ca2+-binding and CIF-binding sites and can also affect the compactness of a-amylase.

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“…A different crystalline form of this enzyme structure was also solved recently with the same resolution (Larson et al, 1994). Two fungal a-amylase structures were refined at high resolution; Aspergillus niger acid amylase (Boel et al, 1990;Brady et al, 1991) and Aspergillus oryzae Taka amylase (Swift et al, 1991). The structure of cereal a-amylase from barley was also recently solved (Kadziola et al, 1994).…”

mentioning

confidence: 99%

Molecular Modelling of the Interaction Between the Catalytic Site of Pig Pancreatic α‐Amylase and Amylose Fragments

Casset¹,

Imberty

Haser

et al. 1995

European Journal of Biochemistry

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A stereo chemical refinement of the crystalline complex between porcine pancreatic a-amylase and a pseudopentasaccharide from the amylostatin family has been performed through molecular mechanics calculations, using a set of parameters appropriate for protein and protein-carbohydrate interactions. The refinement provided a starting point for docking a maltopentaose moiety within the catalytic site, in the absence of water. A thorough exploration of the different orientations and conformations of maltopentaose established the sense of binding of the amylosic substrate in the amylase cleft. After optimising the geometry of the binding site, the conformations adopted by the four contiguous linkages could be rationalised by considering the environment, either hydrophobic or hydrophilic, of the different glucose moieties. Seemingly, details of the non-bonded interactions (hydrogen bonds, van der Waals and stacking interactions) that underlie this molecular recognition have been established. In particular, it was confirmed that the three acidic amino acids of the catalytic site (Asp197, Asp300 and Glu233) are close to their glucosidic target, and that there is no steric reason to propose an alteration of the 4C, conformation of the glucose residue prior to hydrolysis. However, in the absence of water molecules, it is difficult to elucidate the details of the catalysis. Additional macroscopic information has been gained, such as the impossibility to fit a double-helical arrangement of amylose chains in the amylasic cleft. This explains why some native starches containing such motifs resist amylolytic enzymes. Tentative models involving longer amylosic chains have been elaborated, which extend our knowledge of the interaction and orientation of starch fragments in the vicinity of the hydrolytic sites.

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Structure and molecular model refinement of Aspergillus oryzae (TAKA) α-amylase: an application of the simulated-annealing method

Cited by 102 publications

References 13 publications

Crystal structures of the psychrophilic α‐amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor

Crystal structures of the psychrophilic α‐amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor

Stability and structural analysis of α‐amylase from the antarctic psychrophile Alteromonas haloplanctis A23

Molecular Modelling of the Interaction Between the Catalytic Site of Pig Pancreatic α‐Amylase and Amylose Fragments

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