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A novel GH13 subfamily of α-amylases with a pair of tryptophans in the helix α3 of the catalytic TIM-barrel, the LPDlx signature in the conserved sequence region V and a conserved aromatic motif at the C-terminus

  • Štefan Janeček EMAIL logo , Andrea Kuchtová and Soňa Petrovičová
Published/Copyright: January 8, 2016
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Biologia
From the journal Biologia Volume 70 Issue 10

Abstract

The α-amylase enzyme specificity has been classified in the Carbohydrate-Active enZyme (CAZy) database into the families GH13, GH57, GH119 and eventually also GH126. α-Amylase is a glycoside hydrolase (GH) that catalyses in an endo-fashion the hydrolysis of the α-1,4-glucosidic linkages in starch and related α-glucans employing the retaining reaction mechanism. The family GH13 is the main α-amylase family with more than 28,000 members and 30 different specificities. The entire family GH13 has already been divided into 40 subfamilies; the α-amylase enzyme specificity being found in the subfamilies GH13 1, 5, 6, 7, 15, 19, 24, 27, 28, 32, 36 and 37. The present in silico study delivers a proposal to create a novel GH13 subfamily with the specificity of α-amylase. The proposal is based on a detailed bioinformatics analysis consisting of sequence, structural and evolutionary comparison of experimentally characterized α-amylases from, e.g., Bacillus aquimaris, Anoxybacillus sp. SK3-4 and DT3-1 and Geobacillus thermoleovorans, and hypothetical proteins, accompanied by α-amylases from well-established GH13 subfamilies and by closely related amylolytic enzymes (mainly from the subfamily GH13 31). Three sequence-structural features can be ascribed to the members of the newly proposed GH13 subfamily: (i) the pair of adjacent tryptophan residues positioned between the CSR-V and CSR-II in the helix α3 of the catalytic TIM-barrel; (ii) the sequence LPDlx in their CSR-V; and (iii) a ~30-residue long C-terminal region with a motif of five conserved aromatic residues. From the evolutionary point of view, the novel GH13 α-amylase subfamily is most closely related to fungal and yeast α-amylases classified in the subfamily GH13_1.

Keywords: α-amylase; family GH13; GH13 subfamilies; unique sequence features; conserved sequence regions; a pair of adjacent tryptophans; evolutionary relatedness

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Received: 2015-9-7
Accepted: 2015-10-30
Published Online: 2016-1-8
Published in Print: 2015-10-1

© 2016

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https://doi.org/10.1515/biolog-2015-0165
Keywords for this article
α-amylase; family GH13; GH13 subfamilies; unique sequence features; conserved sequence regions; a pair of adjacent tryptophans; evolutionary relatedness

Articles in the same Issue

  1. An overview of phytochrome: An important light switch and photo-sensory antenna for regulation of vital functioning of plants
  2. A novel GH13 subfamily of α-amylases with a pair of tryptophans in the helix α3 of the catalytic TIM-barrel, the LPDlx signature in the conserved sequence region V and a conserved aromatic motif at the C-terminus
  3. Biogenic synthesis of silver nanoparticles using cell-free extract of Bacillus safensis LAU 13: antimicrobial, free radical scavenging and larvicidal activities
  4. Understanding taxonomic position of local endemic Agropyron deweyi (Poaceae) using morphological characters and sequences of nuclear and chloroplast DNA regions
  5. Genetic status of the putative hybrid swarms of mountain dwarf pine and Scots pine in contact zones of their distribution in Slovakia
  6. Species delimitation and population structure in three Onosma (Boraginaceae) species
  7. Glycinebetaine priming improves salt tolerance of wheat
  8. The effect of nitrogen level on rice growth, carbon-nitrogen metabolism and gene expression
  9. High efficiency Agrobacterium-mediated transformation of Pinellia ternata using petiole explants from submerged cultures
  10. Cryopreservation of Serbian autochthonous Prunus spp. by droplet-vitrification
  11. Response of green hydra (Hydra viridissima) to variability and directional changes in food availability
  12. Data on some members of the family Tylenchidae (Nematoda: Tylenchina) from Iran
  13. New and firstly recorded oribatid mites from Turkey
  14. Reproductive parameters of four species of water mites (Acari: Hydrachnidia)
  15. A new species of the genus Aeolothrips (Thysanoptera: Aeolothripidae) from Iran
  16. Skull variability of mice and voles inhabiting the territory of a great cormorant colony
  17. High glucose-associated osmolality promotes adipocytogenic differentiation of primary rat osteoblasts in a protein kinase A and phosphatidylinositol 3-kinase/Akt-dependent manner
  18. Direct influence of rooibos-derived compound on rabbit ovarian functions and their response to gonadotropins
  19. Corrective notice to the European mudminnow (Umbra krameri Walbaum, 1792) record from the Black Sea
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