In silico analysis and 3D structure prediction of a chitinase from psychrophilic yeast Glaciozyma Antarctica PI12

N. Y. Yusof, Mohd Firdaus Mohd Raih, N. M. Mahadi, R. M. Illias, Farah Diba Abu Bakar, Abdul Munir Abd. Murad

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Chitinases are a group of glycosyl hydrolases that are essential to recycle chitin presence in nature. The aim of this work is to characterise the sequence of a chitinase isolated from a psychrophilic yeast, Glaciozyma antarctica PI12 and to predict and analyse the 3-dimensional protein structure. The cDNA for the G. antarctica chitinase gene, GaCHT43, with a length of 1,176 bp was reverse transcribed from mRNA, cloned and sequenced. The gene encodes a mature protein of 391 amino acids with an expected molecular weight of 43 kDa. Sequence analysis showed that GaCh43 has high similarity to the endochitinase family 18 proteins of other fungi. A three-dimensional (3D) model of GaCht43 was built by homology modelling with Aspergillus fumigatus chitinase (1W9P) as the template. Validation analysis via PROCHECK, VERIFY3D and ERRAT showed that the GaCht43 model surpassed the quality requirements and was accepted for further analysis. GaCht43 contained chitinase conserved regions, SxGG and DxxDxDxE that are required in the catalytic mechanism. Analysis of the GaCht43 structure showed the presence of extra loop regions compared to mesophilic chitinases, which might contribute to the flexibility of the protein.

Original languageEnglish
Pages (from-to)117-123
Number of pages7
JournalMalaysian Applied Biology
Volume46
Issue number1
Publication statusPublished - 1 Mar 2017

Fingerprint

Chitinases
chitinase
Computer Simulation
Antarctica
Yeasts
yeasts
prediction
Proteins
proteins
glycosidases
Aspergillus fumigatus
protein structure
Chitin
chitin
Hydrolases
genes
Genes
sequence analysis
Sequence Analysis
molecular weight

Keywords

  • Chitinase
  • Glaciozyma antarctica
  • Molecular modelling
  • Protein structure

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

In silico analysis and 3D structure prediction of a chitinase from psychrophilic yeast Glaciozyma Antarctica PI12. / Yusof, N. Y.; Mohd Raih, Mohd Firdaus; Mahadi, N. M.; Illias, R. M.; Abu Bakar, Farah Diba; Abd. Murad, Abdul Munir.

In: Malaysian Applied Biology, Vol. 46, No. 1, 01.03.2017, p. 117-123.

Research output: Contribution to journalArticle

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