5B2F

N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii complexed with its inhibitor MPG (phosphate-containing condition)

Summary for 5B2F

• Entry DOI: 10.2210/pdb5b2f/pdb
• Related: 5B2E
• Descriptor: Putative uncharacterized protein PH0499, ZINC ION, 2-deoxy-2-{[(S)-hydroxy(methyl)phosphoryl]amino}-beta-D-glucopyranose, ... (4 entities in total)
• Functional Keywords: deacetylase carbohydrate esterase 14 inhibitor complex, hydrolase-hydrolase inhibitor complex, hydrolase/hydrolase inhibitor
• Biological source: Pyrococcus horikoshii OT3
• Total number of polymer chains: 3
• Total formula weight: 95870.31

Authors

Nakamura, T.,Niiyama, M.,Ida, K.,Uegaki, K. (deposition date: 2016-01-15, release date: 2016-08-10, Last modification date: 2024-03-20)

Primary citation

Nakamura, T.,Yonezawa, Y.,Tsuchiya, Y.,Niiyama, M.,Ida, K.,Oshima, M.,Morita, J.,Uegaki, K.
Substrate recognition of N,N'-diacetylchitobiose deacetylase from Pyrococcus horikoshii
J.Struct.Biol., 195:286-293, 2016

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.

PubMed: 27456364
DOI: 10.1016/j.jsb.2016.07.015

Experimental method

X-RAY DIFFRACTION (1.9 Å)