Molecular structure of a barley α-amylase-inhibitor complex: implications for starch binding and catalysis

Kadziola, Anders; Søgaard, Morten; Svensson, Birte; Haser, R.

doi:10.1006/jmbi.1998.1683

Cited by 176 publications

(239 citation statements)

References 63 publications

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“…It should be pointed out that the tryptophan equivalent with Trp195 of T. hydrothermalis ␣-amylase is present in 16 out of 17 plant ␣-amylases available in the SWISS-PROT (Barioch and Apweiler 1998) and GenBank (Benson et al 1998) databases, and the glycine corresponding to Gly202 of the archaeal ␣-amylase is found at the end of this region of all plant ␣-amylases. While no special role for tryptophan equivalent to Trp195 has been assigned in the structure of the barley ␣-amylase-acarbose complex, the glycine corresponding to Gly202 provides in the plant enzyme a specific ligand for calcium ion (Kadziola et al 1998). It is worth mentioning that no other ␣-amylase from more than 100 available in the sequence databases contains either the tryptophan or the glycine in this region except for the ␣-amylase from Dictyoglomus thermophilum AmyB (Horinouchi et al 1988) containing the glycine at the end of the ␤4-strand region (Š .…”

Section: Resultsmentioning

confidence: 99%

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Janeček

Lévêque²,

Belarbi³

et al. 1999

J Mol Evol

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Abstract. The amino acid sequences of 22 ␣-amylases from family 13 of glycosyl hydrolases were analyzed with the aim of revealing the evolutionary relationships between the archaeal ␣-amylases and their eubacterial and eukaryotic counterparts. Two evolutionary distance trees were constructed: (i) the first one based on the alignment of extracted best-conserved sequence regions (58 residues) comprising ␤2, ␤3, ␤4, ␤5, ␤7, and ␤8 strand segments of the catalytic (␣/␤) 8 -barrel and a short conserved stretch in domain B protruding out of the barrel in the ␤3 → ␣3 loop, and (ii) the second one based on the alignment of the substantial continuous part of the (␣/␤) 8 -barrel involving the entire domain B (consensus length: 386 residues). With regard to archaeal ␣-amylases, both trees compared brought, in fact, the same results; i.e., all family 13 ␣-amylases from domain Archaea were clustered with barley pI isozymes, which represent all plant ␣-amylases. The enzymes from Bacillus licheniformis and Escherichia coli, representing liquefying and cytoplasmic ␣-amylases, respectively, seem to be the further closest relatives to archaeal ␣-amylases. This evolutionary relatedness clearly reflects the discussed similarities in the amino acid sequences of these ␣-amylases, especially in the bestconserved sequence regions. Since the results for ␣-amylases belonging to all three domains (Eucarya, Eubacteria, Archaea) offered by both evolutionary trees are very similar, it is proposed that the investigated conserved sequence regions may indeed constitute the ''sequence fingerprints'' of a given ␣-amylase.

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Section: Resultsmentioning

confidence: 99%

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Janeček

Lévêque²,

Belarbi³

et al. 1999

J Mol Evol

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“…Several α-amylases are described to possess this type of binding sites (Gibson & Svensson 1987;Larson et al 1994;Kadziola et al 1998;Dauter et al 1999;Brzozowski et al 2000;Ramasubbu et al 2003;Robert et al 2003Robert et al , 2005Lyhne-Iversen et al 2006;Vujicic-Žagar & Dijkstra, 2006;Ragunath et al 2008). In barley α-amylase isozyme 1 (AMY1), the crystal structure of the inactive catalytic nucleophile D180A mutant in complex with maltoheptaose ( Fig.…”

Section: Impact Of Secondary Binding Sites On Functionmentioning

confidence: 99%

An enzyme family reunion — similarities, differences and eccentricities in actions on α-glucans

et al. 2008

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α-Glucans in general, including starch, glycogen and their derived oligosaccharides are processed by a host of more or less closely related enzymes that represent wide diversity in structure, mechanism, specificity and biological role. Sophisticated three-dimensional structures continue to emerge hand-in-hand with the gaining of novel insight in modes of action. We are witnessing the "test of time" blending with remaining questions and new relationships for these enzymes. Information from both within and outside of ALAMY 3 Symposium will provide examples on what the family contains and outline some future directions. In 2007 a quantum leap crowned the structural biology by the glucansucrase crystal structure. This initiates the disclosure of the mystery on the organisation of the multidomain structure and the "robotics mechanism" of this group of enzymes. The central issue on architecture and domain interplay in multidomain enzymes is also relevant in connection with the recent focus on carbohydrate-binding domains as well as on surface binding sites and their long underrated potential. Other questions include, how different or similar are glycoside hydrolase families 13 and 31 and is the lid finally lifted off the disguise of the starch lyase, also belonging to family 31? Is family 57 holding back secret specificities? Will the different families be sporting new "eccentric" functions, are there new families out there, and why are crystal structures of "simple" enzymes still missing? Indeed new understanding and discovery of biological roles continuously emphasize value of the collections of enzyme models, sequences, and evolutionary trees which will also be enabling advancement in design for useful and novel applications.

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“…In the barley α amylases three structural calcium ions are present. 20,21) They superimpose perfectly in AMY1 and AMY2 and also share all protein ligands. Calcium, however, has distinctly different effects on stability and enzymatic activity of AMY1 and AMY2 and the isozymes, therefore, represent a unique source to understand structural features that modulate the impact of calcium on the behaviour of α amylases.…”

mentioning

confidence: 85%

“…28) This surface site was subsequently observed in the crystal structure of the AMY 2 acarbose complex to accommodate two rings defined from bound acarbose, a pseudotetrasaccharide inhibitor. 20) A few years ago a new surface site for GH13 was discovered, in this case in AMY1.…”

Section: )mentioning

confidence: 99%

Interactions between Barley .ALPHA.-Amylases, Substrates, Inhibitors and Regulatory Proteins

et al. 2006

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α Amylases belong to the glycoside hydrolase family 13 (GH13) that together with glycoside hydrolase families 70 and 77 constitute clan H of glycoside hydrolases (GH H).1) GH H contains approximately 30 different enzyme specificities acting in hydrolase and transglucosidase reactions on α 1,4 and or α 1,6 glucan and α glucoside substrates.2)The three dimensional structures of α amylases mostly contain three domains; domain A, a (β α)8 barrel; domain B a small protruding loop situated between β strand and α helix 3 in the (β α)8 barrel; and domain C, a C terminal anti parallel β sheet composed of 5 10 strands. The substrate binding site is made from residues of domains A and B and the three acid residues involved in catalysis are situated at the C terminal ends of β strands 4, 5 and 7.2) These three catalytic residues are the only invariant residues in GH H.3) A few new complexes between amylolytic enzymes and substrates or substrate analogues have been recently published. 4,5) These structures provide novel insight in particular with respect to Abstract: Barley α-amylase binds sugars at two sites on the enzyme surface in addition to the active site. Crystallography and site-directed mutagenesis highlight the importance of aromatic residues at these surface sites as demonstrated by Kd values determined for β-cyclodextrin by surface plasmon resonance and for starch granules by adsorption analysis. Activity towards amylopectin and amylose follows two different kinetic models, degradation of amylopectin being composed of a fast and a slow component, perhaps reflecting attack on A and B chains, respectively, whereas amylose hydrolysis follows a simple Michaelian kinetics. β-cyclodextrin binding at surface sites inhibits only the fast reaction in amylopectin degradation. Site-directed mutagenesis and activity analysis, furthermore show that one of the surface binding sites as well as individual subsites in the active site cleft have distinct roles in the multiple attack on amylose. Although the two isozymes AMY1 and AMY2 share ligands for three structural calcium ions, they differ importantly in the effect of calcium on activity and stability, AMY1 having the higher affinity and the lower stability. The role of the individual calcium ions is studied by mutagenesis, crystallography and microcalorimetry. Further improvement of recombinant AMY2 production allows future direct mutational analysis in this isozyme. Specific proteinaceous inhibitors act on α-amylases of different origin. In the complex of barley α-amylase subtilisin inhibitor (BASI) with AMY2, a fully hydrated calcium ion at the protein interface mediates contact between inhibitor residues and the enzyme catalytic groups in a manner that depends on calcium and which can be suppressed by site-directed mutagenesis of Glu168 in BASI. Finally certain inhibitors and enzymes are targets of the disulphide reductase thioredoxin h that attacks a specific disulphide bond in BASI and, remarkably, reduces two different disulphide bonds in the barley monomeric and dimeri...

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Molecular structure of a barley α-amylase-inhibitor complex: implications for starch binding and catalysis

Cited by 176 publications

References 63 publications

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

An enzyme family reunion — similarities, differences and eccentricities in actions on α-glucans

Interactions between Barley .ALPHA.-Amylases, Substrates, Inhibitors and Regulatory Proteins

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