The enzyme belongs to the glycosyl hydrolase family-13. The polysaccharide substrate/product data contained in the PDB data are described from the non-reducing end to the reducing end. The Swiss-prot data are corresponding to the PDB data as follows: AMY2_HORVU;P04063: 1amy, 1ava, 1bg9 AMY_BACSU;P00691 : 1bag AMYA_ASPNG;P56271: 2aaa AMYA_ASPOR;P10529: 2taa, 6taa, 7taa AMY_ALTHA;P29957 : 1aqh, 1aqm, 1b0i AMY_TENMO;P56634 : 1clv, 1jae, 1tmq, 1viw AMYP_PIG;P00690 : 1bvn, 1dhk, 1jfh, 1ose, 1pif, 1pig, 1ppi AMYS_HUMAN;P04745: 1smd AMYP_HUMAN;P04746: 1bsi, 1cpu, 1hny Binding modes of calcium and chloride ions are various among the alpha-amylase enzymes. However, the first calcium ion binding sites can be superimposed, except for those from barley (Swiss-prot; P04063). The enzyme from barley has got the distinct binding sites for three calcium ions. Although the calcium ions are necessary for the catalytic activities, they are not involved in catalysis, and may stabilize the enzyme structures. On the other hand, in chloride-dependent alpha-amlyases, the chloride ion seems to be involved in catalysis, by raising the pKa of the catalytic glutamic acid by its electrostatic effect (see [47]). A variety of catalytic mechanisms has been proposed. In the proposed mechanisms, three acidic residues at the active site (Asp at beta-4, Glu at beta-5 and Asp at beta-7 of (alpha/beta)8 barrel structure) seemed to be involved in catalysis. Paper [22] proposed a ring-opening mechanism, in which opening of glucose ring is induced by a nucleophilic attack by a catalytic water. However, this mechanism is more complicated and unlikely than any other proposed ones, as no experimental evidence has been reported so far. On the other hand, a single displacement mechanism and a double displacement mechanism have been proposed and discussed. In both the mechanisms, an oxocarbenium ion seems to be formed either as a long-lived intermediate, or as a transition state. Papers ([4], [23], [27], [44] & [46]) proposed and supported a single displacement mechanism, in which a catalytic water would hydrolyze the glycosidic bond of the substrate directly, assisted by the acid-base catalysis. In this mechanism, the Glu resiue at the C-terminal end of beta-5 acts as a general acid, protonating the leaving oxygen atom(O4). This protonation results in the formation of oxocarbenium ion intermediate (dissociative mechanism). Next, the general base activates the catalytic water, which would make a nucleophilic attack on the C1 atom of the intermediate. On the other hand, the other papers ([9], [18], [37], [38], [43], [45], [47], [61], [62], [69], [70], [77] & [78]) supported a double displacement mechanism, in which a covalent enzyme-glycosyl intermediate would be formed prior to the hydrolysis by a catalytic water. Moreover, the papers, [18], [45], [47], [70] & [77], mentioned that protonation to the glycosidic oxygen (O4) by a general base, the Glu residue at beta-5, would occur, forming an oxocarbenium ion-like transtion state, prior to the nucleophilic attack by the Asp residue at beta-4 (suggesting a dissociative mechanism instead of an associative mechanism). After the formation of the covalent intermediate, Glu at beta-5 acts as a general base to activate a water molecule. The activated water makes a nucleophilic attack on the intermediate to complete the reaction. Considering that the anomeric configuration of the glycosidic bond is retatined, the double displacement mechanism is more compelling than the single displacement mechanism. Moreover, the papers, [9] & [37], reproted that the experimental identification of the enzyme-glycosyl intermediate could be carried out. Taken together, the double displacement mechanism seems to be supported. In this reaction mechanism, the third acidic residue, Asp at beta-7, seems to stabilize the half-chair conformation during the transition state, and raise the pKa of the catalytic acid, Glu at beta-5. However, to acts as a modulator for Glu at beta-5, Asp at beta-7 is a bit too distant.
The three-dimensional structure of [alpha]-amylase from porcine pancreas at 5 A resolution - the active-site location.
Calcium binding in alpha-amylases: an X-ray diffraction study at 2.1-A resolution of two enzymes from Aspergillus.
Structure and biosynthesis of the xylose-containing carbohydrate moiety of rice alpha-amylase.
Structure and molecular model refinement of Aspergillus oryzae (TAKA) alpha-amylase: an application of the simulated-annealing method.
Biological variation in the catalytic concentration of pancreatic alpha-amylase and triacylglycerol lipase in serum.
Alteration of bond-cleavage pattern in the hydrolysis catalyzed by Saccharomycopsis alpha-amylase altered by site-directed mutagenesis.
Site-directed mutagenesis of active site residues in Bacillus subtilis alpha-amylase.
Purification and some properties of a Haim-sensitive alpha-amylase from newly isolated Bacillus sp. No. 195.
Site-directed mutagenesis of catalytic active-site residues of Taka-amylase A.
Mechanism of hydrolyses of phenyl alpha-maltosides catalyzed by taka-amylase A.
Crystallization and preliminary X-ray crystallographic analysis of alpha-amylase from Bacillus subtilis.
Molecular structure of taka-amylase A. I. Backbone chain folding at 3 A resolution.
Crystallization and preliminary X-ray studies of wild type and catalytic-site mutant alpha-amylase from Bacillus subtilis.
Structure and molecular model refinement of pig pancreatic alpha-amylase at 2.1 A resolution.
X-RAY CRYSTALLOGRAPHY (2.1 ANGSTROMS), AND REVISIONS
The catalytic mechanism of alpha-amylases based upon enzyme crystal structures and model building calculations.
The active center of a mammalian alpha-amylase. Structure of the complex of a pancreatic alpha-amylase with a carbohydrate inhibitor refined to 2.2-A resolution.
alpha-Amylases from Thermoactinomyces vulgaris: characteristics, primary structure and structure prediction.
Crystallization and preliminary X-ray diffraction studies of the alpha-amylase inhibitor coded 0.19 from wheat kernel.
Crystal and molecular structure of barley alpha-amylase.
Refined molecular structure of pig pancreatic alpha-amylase at 2.1 A resolution.
Characterization, crystallization and preliminary X-ray crystallographic analysis of the complex between barley alpha-amylase and the bifunctional alpha-amylase/subtilisin inhibitor from barley seeds.
The crystal structure of porcine pancreatic alpha-amylase in complex with the microbial inhibitor Tendamistat.
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF COMPLEX WITH INHIBITOR
Subsite profile of the active center of porcine pancreatic alpha-amylase. Kinetic studies using maltooligosaccharides as substrates.
The structure of human pancreatic alpha-amylase at 1.8 A resolution and comparisons with related enzymes.
Structure of Human Salivary [alpha]-Amylase at 1.6 A Resolution: Implications for its Role in the Oral Cavity.
Production and certification of an enzyme reference material for pancreatic alpha-amylase (CRM 476).
Crystal structure of pig pancreatic alpha-amylase isoenzyme II, in complex with the carbohydrate inhibitor acarbose.
X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS), AND REVISIONS
Carbohydrate and protein-based inhibitors of porcine pancreatic alpha-amylase: structure analysis and comparison of their binding characteristics.
Crystallization and preliminary X-ray diffraction studies of alpha-amylase from the antarctic psychrophile Alteromonas haloplanctis A23.
Substrate mimicry in the active center of a mammalian alpha-amylase: structural analysis of an enzyme-inhibitor complex.
X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF COMPLEX WITH INHIBITOR
Unequivocal identification of Asp-214 as the catalytic nucleophile of Saccharomyces cerevisiae alpha-glucosidase using 5-fluoro glycosyl fluorides.
Structure of the Aspergillus oryzae alpha-amylase complexed with the inhibitor acarbose at 2.0 A resolution.
Effect of pressure on the mechanism of hydrolysis of maltotetraose, maltopentaose, and maltohexose catalyzed by porcine pancreatic alpha-amylase.
Structure and possible catalytic residues of Taka-amylase A.
The alpha-amylase from the yellow meal worm: complete primary structure, crystallization and preliminary X-ray analysis.
Improved activity and modulated action pattern obtained by random mutagenesis at the fourth beta-alpha loop involved in substrate binding to the catalytic (beta/alpha)8-barrel domain of barley alpha-amylase 1.
Structure of a pancreatic alpha-amylase bound to a substrate analogue at 2.03 A resolution.
Structure, function and protein engineering of starch-degrading enzymes.
Crystal structure of a catalytic-site mutant alpha-amylase from Bacillus subtilis complexed with maltopentaose.
X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS) OF 42-466
Molecular structure of a barley alpha-amylase-inhibitor complex: implications for starch binding and catalysis.
Crystal structure of yellow meal worm alpha-amylase at 1.64 A resolution.
Crystal structures of the psychrophilic alpha-amylase from Alteromonas haloplanctis in its native form and complexed with an inhibitor.
X-RAY CRYSTALLOGRAPHY (2.0 ANGSTROMS) OF 25-477
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
A novel strategy for inhibition of alpha-amylases: yellow meal worm alpha-amylase in complex with the Ragi bifunctional inhibitor at 2.5 A resolution.
On porcine pancreatic alpha-amylase action: kinetic evidence for the binding of two maltooligosaccharide molecules (maltose, maltotriose and o-nitrophenylmaltoside) by inhibition studies. Correlation with the five-subsite energy profile.
Barley alpha-amylase bound to its endogenous protein inhibitor BASI: crystal structure of the complex at 1.9 A resolution.
X-RAY CRYSTALLOGRAPHY (1.9 ANGSTROMS) OF COMPLEX WITH BASI
A plant-seed inhibitor of two classes of alpha-amylases: X-ray analysis of Tenebrio molitor larvae alpha-amylase in complex with the bean Phaseolus vulgaris inhibitor.
Amylose chain behavior in an interacting context. III. Complete occupancy of the AMY2 barley alpha-amylase cleft and comparison with biochemical data.
Post-translational processing of two alpha-amylase inhibitors and an arcelin from the common bean, Phaseolus vulgaris.
Characterization of a thermostable alpha-amylase from a thermophilic Streptomyces megasporus strain SD12.
Crystal structure of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVAII) hydrolyzing cyclodextrins and pullulan at 2.6 A resolution.
Roles of catalytic residues in alpha-amylases as evidenced by the structures of the product-complexed mutants of a maltotetraose-forming amylase.
Cloning, mutagenesis, and structural analysis of human pancreatic alpha-amylase expressed in Pichia pastoris.
Specific inhibition of insect alpha-amylases: yellow meal worm alpha-amylase in complex with the amaranth alpha-amylase inhibitor at 2.0 A resolution.
Crystal structures of human pancreatic alpha-amylase in complex with carbohydrate and proteinaceous inhibitors.
Purification and characterization of alpha-amylase from rat pancreatic acinar carcinoma. Comparison with pancreatic alpha-amylase.
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.
Subsite mapping of the human pancreatic alpha-amylase active site through structural, kinetic, and mutagenesis techniques.
Protein engineering of bacterial alpha-amylases.
Structural equilibrium fluctuations in mesophilic and thermophilic alpha-amylase.
Analysis of catalytic residues of Thermoactinomyces vulgaris R-47 alpha-amylase II (TVA II) by site-directed mutagenesis.
Structural similarities and evolutionary relationships in chloride-dependent alpha-amylases.
A functional raw starch-binding domain of barley alpha-amylase expressed in Escherichia coli.
Analysis of structural and physico-chemical parameters involved in the specificity of binding between alpha-amylases and their inhibitors.
Specificity modulation of barley alpha-amylase through biased random mutagenesis involving a conserved tripeptide in beta --> alpha loop 7 of the catalytic (beta/alpha)(8)-barrel domain.
Enzyme-catalyzed condensation reaction in a mammalian alpha-amylase. High-resolution structural analysis of an enzyme-inhibitor complex.
Three dimensional structure of porcine pancreatic alpha-amylase at 2.9 A resolution. Role of calcium in structure and activity.
Relationship of sequence and structure to specificity in the alpha-amylase family of enzymes.
An investigation of the action of porcine pancreatic alpha-amylase on native and gelatinised starches.
Role of Phe286 in the recognition mechanism of cyclomaltooligosaccharides (cyclodextrins) by Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structures of the mutant TVAIIs, F286A and F286Y, and kinetic analyses of the Phe286-replaced mutant TVAIIs.
Amylolytic enzymes: molecular aspects of their properties.
Studies on the hydrolyzing mechanism for cyclodextrins of Thermoactinomyces vulgaris R-47 alpha-amylase 2 (TVAII). X-ray structure of the mutant E354A complexed with beta-cyclodextrin, and kinetic analyses on cyclodextrins.
The determinants of alpha-amylase pH-activity profiles.
Deletion analysis of the C-terminal region of the alpha-amylase of Bacillus sp. strain TS-23.
Crystallographic evidence of a transglycosylation reaction: ternary complexes of a psychrophilic alpha-amylase.
Mechanistic analyses of catalysis in human pancreatic alpha-amylase: detailed kinetic and structural studies of mutants of three conserved carboxylic acids.
Barley alpha-amylase Met53 situated at the high-affinity subsite -2 belongs to a substrate binding motif in the beta-->alpha loop 2 of the catalytic (beta/alpha)8-barrel and is critical for activity and substrate specificity.
Functional mimicry between anti-Tendamistat antibodies and alpha-amylase.
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.
Kinetics and energetics of the binding between barley alpha-amylase/subtilisin inhibitor and barley alpha-amylase 2 analyzed by surface plasmon resonance and isothermal titration calorimetry.
Relation between domain evolution, specificity, and taxonomy of the alpha-amylase family members containing a C-terminal starch-binding domain.
Detection of a covalent intermediate in the mechanism of action of porcine pancreatic alpha-amylase by using 13C nuclear magnetic resonance.
ASN 88;GLN 135;ASP 144;HIS 178(Calcium binding);ARG 172;ASN 262;LYS 300(Chloride binding)
ASN 101;THR 137;ASP 146;HIS 180(Calcium binding);GLY 169;ASP 171(2nd calcium)
ASN 100;ARG 158;ASP 167;HIS 201(Calcium binding);ARG 195;ASN 298;ARG 337(Chloride binding)
ASN 98;ARG 146;ASP 155;HIS 189(Calcium binding);ARG 183;ASN 285;ARG 321(Chloride binding)
ASN 91;PHE 143;ASP 148;ASP 142(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)
ASN 91;ASP 142;PHE 143;ASP 148(Calcium binding);GLU 108;THR 111;ASP 113;ASP 117(2nd calcium);ASP 127;ASP 138;ALA 141;ALA 146(3rd calcium)
ASP 121;GLU 162;ASP 175;GLU 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)
ASN 121;GLU 162;ASP 175;HIS 210(Calcium binding);ASP 206;GLU 230(Inhibitory calcium binding)