Int J Biochem Mol Biol 2013;4(4):166-178
Original Article
Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its
dual action of hydrolysis and transglycosylation
Jogi Madhuprakash, Avinash Singh, Sanjit Kumar, Mau Sinha, Punit Kaur, Sujata Sharma, Appa R Podile, Tej P Singh
Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India; Department of Biophysics, All India Institute
of Medical Sciences, New Delhi, India. Equal contributors.
Received September 11, 2013; Accepted November 15, 2013; Epub December 15, 2013; Published December 30, 2013
Abstract: Chitinases are known to hydrolyze chitin polymers into smaller chitooligosaccharides. Chitinase from bacterium Serratia
proteamaculans (SpChiD) is found to exhibit both hydrolysis and transglycosylation activities. SpChiD belongs to family 18 of glycosyl
hydrolases (GH-18). The recombinant SpChiD was crystallized and its three-dimensional structure was determined at 1.49 Å resolution. The
structure was refined to an R-factor of 16.2%. SpChiD consists of 406 amino acid residues. The polypeptide chain of SpChiD adopts a (β/α)8
triosephosphate isomerase (TIM) barrel structure. SpChiD contains three acidic residues, Asp149, Asp151 and Glu153 as part of its catalytic
scheme. While both Asp149 and Glu153 adopt single conformations, Asp151 is observed in two conformations. The substrate binding cleft is
partially obstructed by a protruding loop, Asn30 - Asp42 causing a considerable reduction in the number of available subsites in the substrate
binding site. The positioning of loop, Asn30 - Asp42 appears to be responsible for the transglycosylation activity. The structure determination
indicated the presence of sulfone Met89 (SMet89). The sulfone methionine residue is located on the surface of the protein at a site where extra
domain is attached in other chitinases. This is the first structure of a single domain chitinase with hydrolytic and transglycosylation activities.
(IJBMB1309004).
Keywords: Chitinase D, chitooligosaccharides, Serratia proteamaculans, hydrolysis, transglycosylation, constrained substrate binding cleft
Address correspondence to: Dr. Tej P Singh, Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110
029, India. Tel: +91-11-2658-8931; Fax: +91-11-2658-8663; E-mail: tpsingh.aiims@gmail.com
Original Article
Structure of chitinase D from Serratia proteamaculans reveals the structural basis of its
dual action of hydrolysis and transglycosylation
Jogi Madhuprakash, Avinash Singh, Sanjit Kumar, Mau Sinha, Punit Kaur, Sujata Sharma, Appa R Podile, Tej P Singh
Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India; Department of Biophysics, All India Institute
of Medical Sciences, New Delhi, India. Equal contributors.
Received September 11, 2013; Accepted November 15, 2013; Epub December 15, 2013; Published December 30, 2013
Abstract: Chitinases are known to hydrolyze chitin polymers into smaller chitooligosaccharides. Chitinase from bacterium Serratia
proteamaculans (SpChiD) is found to exhibit both hydrolysis and transglycosylation activities. SpChiD belongs to family 18 of glycosyl
hydrolases (GH-18). The recombinant SpChiD was crystallized and its three-dimensional structure was determined at 1.49 Å resolution. The
structure was refined to an R-factor of 16.2%. SpChiD consists of 406 amino acid residues. The polypeptide chain of SpChiD adopts a (β/α)8
triosephosphate isomerase (TIM) barrel structure. SpChiD contains three acidic residues, Asp149, Asp151 and Glu153 as part of its catalytic
scheme. While both Asp149 and Glu153 adopt single conformations, Asp151 is observed in two conformations. The substrate binding cleft is
partially obstructed by a protruding loop, Asn30 - Asp42 causing a considerable reduction in the number of available subsites in the substrate
binding site. The positioning of loop, Asn30 - Asp42 appears to be responsible for the transglycosylation activity. The structure determination
indicated the presence of sulfone Met89 (SMet89). The sulfone methionine residue is located on the surface of the protein at a site where extra
domain is attached in other chitinases. This is the first structure of a single domain chitinase with hydrolytic and transglycosylation activities.
(IJBMB1309004).
Keywords: Chitinase D, chitooligosaccharides, Serratia proteamaculans, hydrolysis, transglycosylation, constrained substrate binding cleft
Address correspondence to: Dr. Tej P Singh, Department of Biophysics, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110
029, India. Tel: +91-11-2658-8931; Fax: +91-11-2658-8663; E-mail: tpsingh.aiims@gmail.com
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