title: Similarity of different beta-strands flanked in loops by glycines and prolines from distinct (alpha/beta)8-barrel enzymes: chance or a homology?
abstract: Many (alpha/beta)8-barrel enzymes contain their conserved sequence regions at or around the beta-strand segments that are often preceded and succeeded by glycines and prolines, respectively. alpha-Amylase is one of these enzymes. Its sequences exhibit a very low degree of similarity, but strong conservation is seen around its beta-strands. These conserved regions were used in the search for similarities with beta-strands of other (alpha/beta)8-barrel enzymes. The analysis revealed an interesting similarity between the segment around the beta 2-strand of alpha-amylase and the one around the beta 4-strand of glycolate oxidase that are flanked in loops by glycines and prolines. The similarity can be further extended on other members of the alpha-amylase and glycolate oxidase subfamilies, i.e., cyclodextrin glycosyltransferase and oligo-1,6-glucosidase, and flavocytochrome b2, respectively. Moreover, the alpha-subunit of tryptophan synthase, the (alpha/beta)8-barrel enzyme belonging to the other subfamily of (alpha/beta)8-barrels, has both investigated strands, beta 2 and beta 4, similar to beta 2 of alpha-amylase and beta 4 of glycolate oxidase. The possibilities of whether this similarity exists only by chance or is a consequence of some processes during the evolution of (alpha/beta)8-barrel proteins are briefly discussed.
authors.affiliation: Institute of Ecobiology, Slovak Academy of Sciences, Bratislava.
authors.forename: S
authors.initials: S
authors.lastname: Janecek
mesh_terms: D000595:Amino Acid Sequence; D005075:Biological Evolution; D017124:Conserved Sequence; D004798:Enzymes / Q000737:chemistry* / Q000235:genetics*; D005964:Glucosyltransferases / Q000737:chemistry / Q000235:genetics; D005998:Glycine / Q000737:chemistry / Q000235:genetics; D007770:L-Lactate Dehydrogenase / Q000737:chemistry / Q000235:genetics; D042844:L-Lactate Dehydrogenase (Cytochrome); D008969:Molecular Sequence Data; D009834:Oligo-1,6-Glucosidase / Q000737:chemistry / Q000235:genetics; D011336:Probability; D011392:Proline / Q000737:chemistry / Q000235:genetics; D017433:Protein Structure, Secondary; D017386:Sequence Homology, Amino Acid; D014367:Tryptophan Synthase / Q000737:chemistry / Q000235:genetics
chemical_list: D004798:Enzymes; D011392:Proline; D007770:L-Lactate Dehydrogenase; D042844:L-Lactate Dehydrogenase (Cytochrome); D005964:Glucosyltransferases; C019963:cyclomaltodextrin glucanotransferase; D009834:Oligo-1,6-Glucosidase; D014367:Tryptophan Synthase; D005998:Glycine