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

Aizi Nor Mazila Ramli, Mohd Akmal Azhar, Mohd Shahir Shamsir, Amir Rabu, Abdul Munir Abd. Murad, Nor Muhammad Mahadi, Rosli Md. Illias

Research output: Contribution to journalArticle

9 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)3369-3383
Number of pages15
JournalJournal of Molecular Modeling
Volume19
Issue number8
DOIs
Publication statusPublished - Aug 2013

Fingerprint

Amylases
Antarctic regions
Ions
templates
Bacillus
Bacilli
calcium
Calcium
ions
stearothermophilus
Temperature scales
polymerase chain reaction
walking
temperature scales
Polymerase chain reaction
homology
Binding sites
Transcription
determinants
amino acids

Keywords

  • Cold-adaptation
  • Cold-adapted α-amylase
  • Flexibility
  • Glaciozyma antarctica PI12

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Catalysis
  • Organic Chemistry
  • Inorganic Chemistry

Cite this

Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis. / Ramli, Aizi Nor Mazila; Azhar, Mohd Akmal; Shamsir, Mohd Shahir; Rabu, Amir; Abd. Murad, Abdul Munir; Mahadi, Nor Muhammad; Md. Illias, Rosli.

In: Journal of Molecular Modeling, Vol. 19, No. 8, 08.2013, p. 3369-3383.

Research output: Contribution to journalArticle

Ramli, Aizi Nor Mazila ; Azhar, Mohd Akmal ; Shamsir, Mohd Shahir ; Rabu, Amir ; Abd. Murad, Abdul Munir ; Mahadi, Nor Muhammad ; Md. Illias, Rosli. / Sequence and structural investigation of a novel psychrophilic α-amylase from Glaciozyma antarctica PI12 for cold-adaptation analysis. In: Journal of Molecular Modeling. 2013 ; Vol. 19, No. 8. pp. 3369-3383.
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