Hydrophobic cluster analysis of the primary sequences of α-amylases

Raimbaud, Eric; Buléon, Alain; Pérez, Serge; Henrissat, Bernard

doi:10.1016/0141-8130(89)90072-x

Cited by 38 publications

(22 citation statements)

References 33 publications

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“…Amongst the 84 residues forming the hydrophobic clusters of the porcine a-amylase (Raimbaud et al, 1989), 25 subsitutions were noted in the corresponding positions of A. haloplanctis a-amylase. 80% of these substitutions are accompanied by a sharp decrease of the hydrophobicity index using either the statistical PRTFT scale or the experimental scale of Aboderin (see Cornette et al, 1987 for normalized values).…”

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

202

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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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

202

129

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“…All known archaeal ␣-amylases with determined sequence were used. As far as the ␣-amylases from Eubacteria and Eucarya are concerned, respectively, they were chosen as representatives of previously identified evolutionary related groups (Raimbaud et al 1989;Janeček 1994Janeček , 1995Janeček , 1997Jespersen et al 1993;Janeček et al 1997). Thus the studied ␣-amylases represent a wide spectrum of taxonomically different species.…”

Section: Methodsmentioning

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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“…15 In the case of a-amylases whose 3D structures are similar despite the extensive divergence of their amino acid sequences, HCA readily allowed the alignment of the secondary structure elements of the (Pa)s barrel. 16 Recently, a structure conservation has been suggested between the yeast CCP and the LIII lignin peroxidase of Phlebia radiata on the basis of a hydrophobic profile comparison." In the present article, we present the results of the hydrophobic cluster analysis of peroxidase sequences.…”

Section: Introductionmentioning

confidence: 99%

Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis

et al. 1990

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A number of peroxidase amino acid sequences show limited homology to short regions comprising the known active site cleft of yeast cytochrome c peroxidase. Otherwise no clear homology is visible in linear alignments between this enzyme and other peroxidases. We have subjected eight peroxidase sequences to hydrophobic cluster analysis. Our results suggest that these peroxidases are evolutionary related and that they share many folding characteristics.

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Hydrophobic cluster analysis of the primary sequences of α-amylases

Cited by 38 publications

References 33 publications

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

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

Close Evolutionary Relatedness of α-Amylases from Archaea and Plants

Structural homology among the peroxidase enzyme family revealed by hydrophobic cluster analysis

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