Malaysian Applied Biology Journal

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46_01_17

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Malays. Appl. Biol. (2017) 46(1): 117–123


IN SILICO ANALYSIS AND 3D STRUCTURE PREDICTION

OF A CHITINASE FROM PSYCHROPHILIC YEAST

Glaciozyma antarctica PI12

YUSOF, N.Y.1,2, FIRDAUS-RAIH, M.1, MAHADI, N.M.3, ILLIAS, R.M.4, ABU BAKAR, F.D.1

and MURAD, A.M.A.1*

1School of Biosciences and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600 Bangi, Selangor, Malaysia
2Institute for Research in Molecular Medicine, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
3Malaysia Genome Institute, Jalan Bangi Lama, 43000 Kajang, Selangor, Malaysia 4Department of Bioprocess Engineering, Faculty of Chemical Engineering,
Universiti Teknologi Malaysia, 81300 Skudai, Johor, Malaysia

*Email: This e-mail address is being protected from spambots. You need JavaScript enabled to view it

Accepted 2 February 2017, Published online 31 March 2017

 

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.

Key words: Chitinase, Glaciozyma antarctica, protein structure, molecular modelling

 

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