title: Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis.
abstract: A novel α-amylase was isolated successfully from Glaciozyma antarctica PI12 using DNA walking and reverse transcription-polymerase chain reaction (RT-PCR) methods. The structure of this psychrophilic α-amylase (AmyPI12) from G. antarctica PI12 has yet to be studied in detail. A 3D model of AmyPI12 was built using a homology modelling approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9.9. Analysis of the AmyPI12 model revealed the presence of binding sites for a conserved calcium ion (CaI), non-conserved calcium ions (CaII and CaIII) and a sodium ion (Na). Compared with its template-the thermostable α-amylase from Bacillus stearothermophilus (BSTA)-the binding of CaII, CaIII and Na ions in AmyPI12 was observed to be looser, which suggests that the low stability of AmyPI12 allows the protein to work at different temperature scales. The AmyPI12 amino acid sequence and model were compared with thermophilic α-amylases from Bacillus species that provided the highest structural similarities with AmyPI12. These comparative studies will enable identification of possible determinants of cold adaptation.
authors.affiliation: Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia.
authors.forename: Aizi Nor Mazila
authors.initials: AN
authors.lastname: Ramli
authors.forename: Mohd Akmal
authors.initials: MA
authors.lastname: Azhar
authors.forename: Mohd Shahir
authors.initials: MS
authors.lastname: Shamsir
authors.forename: Amir
authors.initials: A
authors.lastname: Rabu
authors.forename: Abdul Munir Abdul
authors.initials: AM
authors.lastname: Murad
authors.forename: Nor Muhammad
authors.initials: NM
authors.lastname: Mahadi
authors.forename: Rosli Md
authors.initials: RM
authors.lastname: Illias
mesh_terms: D000222:Adaptation, Physiological; D000595:Amino Acid Sequence; D000864:Antarctic Regions; D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D001487:Basidiomycota / Q000737:chemistry* / Q000201:enzymology / Q000235:genetics; D002118:Calcium / Q000737:chemistry; D002412:Cations; D003080:Cold Temperature; D005656:Fungal Proteins / Q000737:chemistry* / Q000145:classification / Q000235:genetics; D001411:Geobacillus stearothermophilus / Q000737:chemistry* / Q000201:enzymology / Q000235:genetics; D006358:Hot Temperature; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D011485:Protein Binding; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D012964:Sodium / Q000737:chemistry; D040681:Structural Homology, Protein; D000516:alpha-Amylases / Q000737:chemistry* / Q000145:classification / Q000235:genetics
chemical_list: D001426:Bacterial Proteins; D002412:Cations; D005656:Fungal Proteins; D012964:Sodium; D000516:alpha-Amylases; D002118:Calcium