Homology modeling, molecular docking and molecular dynamics studies of the catalytic domain of chitin deacetylase from Cryptococcus laurentii strain RY1.
This study provides structural insights into chitin deacetylase, over-expressing under nitrogen limiting condition in Cryptococcus laurentii strain RY1. The enzyme converts chitin, the second most abundant natural biopolymer, to chitosan, which offers tremendous applications in diverse fields. To elucidate the structure-function relationship of this biologically and industrially important enzyme, a homology model of the catalytic domain was constructed. The stability of the structure was assessed by molecular dynamics simulation studies. Tryptophan 151 of the domain was identified to form hydrogen bond and stacking interaction with chitin upon docking. In Silico substitution of Tryptophan (W) to Alanine (A), Phenylalanine (F) and Aspartate (D) corroborated the importance of the Tryptophan residue in interaction with the substrate. This is the first report of unravelling the structural characteristics of chitin deacetylase from Cryptococcus and understanding the approach of the enzyme towards its substrate. Our results would be helpful to perform experimental validations and apply quantum mechanics/molecular mechanics techniques to determine the detailed catalytic mechanism and enhance the industrial potency of the enzyme.
Department of Life Science & Biotechnology, Jadavpur University, India.
Soumyadev
S
Sarkar
Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, India.
Suchetana
S
Gupta
Department of Life Science & Biotechnology, Jadavpur University, India.
Writachit
W
Chakraborty
Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, India.
Sanjib
S
Senapati
Department of Life Science & Biotechnology, Jadavpur University, India. Electronic address: ratangachhui@yahoo.com.
Ratan
R
Gachhui
D000581:Amidohydrolases / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D000595:Amino Acid Sequence; D020134:Catalytic Domain; D002686:Chitin / Q000378:metabolism; D003454:Cryptococcus / Q000201:enzymology*; D062105:Molecular Docking Simulation; D056004:Molecular Dynamics Simulation; D016296:Mutagenesis; D017386:Sequence Homology, Amino Acid
D002686:Chitin; D000581:Amidohydrolases; C019866:chitin deacetylase
Chitin deacetylase; Cryptococcus laurentii strain RY1; Molecular dynamics