Download MendeleySubstrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii
Nakamura, T., Yonezawa, Y., Tsuchiya, Y., Niiyama, M., Ida, K., Oshima, M., Morita, J., Uegaki, K.(2016) J Struct Biol 195: 286-293
- PubMed: 27456364
- DOI: https://doi.org/10.1016/j.jsb.2016.07.015
- Primary Citation of Related Structures:
5B2E, 5B2F - PubMed Abstract:
Enzymes of carbohydrate esterase (CE) family 14 catalyze hydrolysis of N-acetyl groups at the non-reducing end of the N-acetylglucosamine (GlcNAc) residue of chitooligosaccharides or related compounds. N,N'-diacetylchitobiose deacetylase (Dac) belongs to the CE-14 family and plays a role in the chitinolytic pathway in archaea by deacetylating N,N'-diacetylchitobiose (GlcNAc2), which is the end product of chitinase. In this study, we revealed the structural basis of reaction specificity in CE-14 deacetylases by solving a crystal structure of Dac from Pyrococcus horikoshii (Ph-Dac) in complex with a novel reaction intermediate analog. We developed 2-deoxy-2-methylphosphoramido-d-glucose (MPG) as the analog of the tetrahedral oxyanion intermediate of the monosaccharide substrate GlcNAc. The crystal structure of Ph-Dac in complex with MPG demonstrated that Arg92, Asp115, and His152 side chains interact with hydroxyl groups of the glucose moiety of the non-reducing-end GlcNAc residue. The amino acid residues responsible for recognition of the MPG glucose moiety are spatially conserved in other CE-14 deacetylases. Molecular dynamics simulation of the structure of the Ph-Dac-GlcNAc2 complex indicated that the reducing GlcNAc residue is placed in a large intermolecular cleft and is not involved with specific interactions with the enzyme. This observation was consistent with results indicating that Ph-Dac displayed similar kinetic parameters for both GlcNAc and GlcNAc2. This study provides the structural basis of reaction-site specificity of Dac and related CE-14 enzymes.
Organizational Affiliation:
National Institute of Advanced Industrial Science and Technology, Osaka 563-8577, Japan. Electronic address: nakamura-t@aist.go.jp.
