Structural prediction of a novel chitinase from the psychrophilic Glaciozyma antarctica PI12 and an analysis of its structural properties and function.
The structure of psychrophilic chitinase (CHI II) from Glaciozyma antarctica PI12 has yet to be studied in detail. Due to its low sequence identity (<30 %), the structural prediction of CHI II is a challenge. A 3D model of CHI II was built by first using a threading approach to search for a suitable template and to generate an optimum target-template alignment, followed by model building using MODELLER9v7. Analysis of the catalytic insertion domain structure in CHI II revealed an increase in the number of aromatic residues and longer loops compared to mesophilic and thermophilic chitinases. A molecular dynamics simulation was used to examine the stability of the CHI II structure at 273, 288 and 300 K. Structural analysis of the substrate-binding cleft revealed a few exposed aromatic residues. Substitutions of certain amino acids in the surface and loop regions of CHI II conferred an increased flexibility to the enzyme, allowing for an adaptation to cold temperatures. A substrate binding comparison of CHI II with the mesophilic chitinase from Coccidioides immitis, 1D2K, suggested that the psychrophilic adaptation and catalytic activity at low temperatures were achieved through a reduction in the number of salt bridges, fewer hydrogen bonds and an increase in the exposure of the hydrophobic side chains to the solvent.
Department of Bioprocess Engineering, Universiti Teknologi Malaysia, Skudai, Johor, Malaysia.
Aizi Nor Mazila
AN
Ramli
Nor Muhammad
NM
Mahadi
Mohd Shahir
MS
Shamsir
Amir
A
Rabu
Kwee Hong
KH
Joyce-Tan
Abdul Munir Abdul
AM
Murad
Rosli Md
RM
Illias
D000222:Adaptation, Physiological; D000595:Amino Acid Sequence; D001487:Basidiomycota / Q000201:enzymology*; D020134:Catalytic Domain; D002688:Chitinases / Q000737:chemistry*; D003080:Cold Temperature; D006860:Hydrogen Bonding; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D008969:Molecular Sequence Data
D002688:Chitinases