6K5J

Structure of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7

Summary for 6K5J

• Entry DOI: 10.2210/pdb6k5j/pdb
• Descriptor: GH3 beta-N-acetylglucosaminidase, 2-acetamido-2-deoxy-beta-D-glucopyranose, GLYCEROL, ... (4 entities in total)
• Functional Keywords: glucosidase, hydrolase
• Biological source: Paenibacillaceae
• Total number of polymer chains: 1
• Total formula weight: 57363.76

Authors

Itoh, T.,Araki, T.,Nishiyama, T.,Hibi, T.,Kimoto, H. (deposition date: 2019-05-29, release date: 2019-09-25, Last modification date: 2024-10-23)

Primary citation

Itoh, T.,Araki, T.,Nishiyama, T.,Hibi, T.,Kimoto, H.
Structural and functional characterization of a glycoside hydrolase family 3 beta-N-acetylglucosaminidase from Paenibacillus sp. str. FPU-7.
J.Biochem., 166:503-515, 2019

PubMed Abstract: Chitin, a β-1,4-linked homopolysaccharide of N-acetyl-d-glucosamine (GlcNAc), is one of the most abundant biopolymers on Earth. Paenibacillus sp. str. FPU-7 produces several different chitinases and converts chitin into N,N'-diacetylchitobiose ((GlcNAc)2) in the culture medium. However, the mechanism by which the Paenibacillus species imports (GlcNAc)2 into the cytoplasm and divides it into the monomer GlcNAc remains unclear. The gene encoding Paenibacillus β-N-acetyl-d-glucosaminidase (PsNagA) was identified in the Paenibacillus sp. str. FPU-7 genome using an expression cloning system. The deduced amino acid sequence of PsNagA suggests that the enzyme is a part of the glycoside hydrolase family 3 (GH3). Recombinant PsNagA was successfully overexpressed in Escherichia coli and purified to homogeneity. As assessed by gel permeation chromatography, the enzyme exists as a 57-kDa monomer. PsNagA specifically hydrolyses chitin oligosaccharides, (GlcNAc)2-4, 4-nitrophenyl N-acetyl β-d-glucosamine (pNP-GlcNAc) and pNP-(GlcNAc)2-6, but has no detectable activity against 4-nitrophenyl β-d-glucose, 4-nitrophenyl β-d-galactosamine and colloidal chitin. In this study, we present a 1.9 Å crystal structure of PsNagA bound to GlcNAc. The crystal structure reveals structural features related to substrate recognition and the catalytic mechanism of PsNagA. This is the first study on the structural and functional characterization of a GH3 β-N-acetyl-d-glucosaminidase from Paenibacillus sp.

PubMed: 31501879
DOI: 10.1093/jb/mvz072

Experimental method

X-RAY DIFFRACTION (1.903 Å)