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Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis

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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.

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Acknowledgments

Special thanks to thank my colleagues Nazihah Abdul Hamid from the Universiti Teknologi Malaysia and Fathin Nur Syafiqah Jafri from the Universiti Putra Malaysia for their help and valuable discussions. This work was supported by a research grant from the Molecular Biology and Genomic Initiative Program of the Malaysia Genome Institute (Project No. 10-05-16-MB002 and 07-05-MGI-GMB014). We would also like to express our appreciation to the Malaysia Antarctic Research Programme for their support. Aizi Nor Mazila Ramli is a researcher of Universiti Teknologi Malaysia under the Post-Doctoral Fellowship Scheme.

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Authors and Affiliations

  1. Department of Bioprocess Engineering, Faculty of Chemical Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia

    Aizi Nor Mazila Ramli, Mohd Akmal Azhar & Rosli Md. Illias

  2. Faculty of Bioscience and Medical Engineering, Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia

    Mohd Shahir Shamsir

  3. School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia

    Amir Rabu & Abdul Munir Abdul Murad

  4. Malaysia Genome Institute (MGI), Jalan Bangi Lama, 43600, Bangi, Selangor, Malaysia

    Nor Muhammad Mahadi

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  1. Aizi Nor Mazila Ramli
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Ramli, A.N.M., Azhar, M.A., Shamsir, M.S. et al. Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis. J Mol Model 19, 3369–3383 (2013). https://doi.org/10.1007/s00894-013-1861-5

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