7EHU

Chitin oligosaccharide binding protein

Summary for 7EHU

• Entry DOI: 10.2210/pdb7ehu/pdb
• Related: 7EHO 7EHQ
• Related PRD ID: PRD_900017
• Descriptor: Chitin oligosaccharide binding protein NagB2, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, DI(HYDROXYETHYL)ETHER, ... (4 entities in total)
• Functional Keywords: chitin oligosaccharide binding protein, sugar binding protein
• Biological source: Paenibacillus sp. FPU-7
• Total number of polymer chains: 1
• Total formula weight: 48059.06

Authors

Itoh, T.,Hibi, T.,Kimoto, H. (deposition date: 2021-03-30, release date: 2021-07-07, Last modification date: 2023-11-29)

Primary citation

Itoh, T.,Yaguchi, M.,Nakaichi, A.,Yoda, M.,Hibi, T.,Kimoto, H.
Structural characterization of two solute-binding proteins for N,N' -diacetylchitobiose/ N,N',N'' -triacetylchitotoriose of the gram-positive bacterium, Paenibacillus sp. str. FPU-7.
J Struct Biol X, 5:100049-100049, 2021

PubMed Abstract: The chitinolytic bacterium sp. str. FPU-7 efficiently degrades chitin into oligosaccharides such as -acetyl-D-glucosamine (GlcNAc) and disaccharides (GlcNAc) through multiple secretory chitinases. Transport of these oligosaccharides by . str. FPU-7 has not yet been clarified. In this study, we identified , predicted to encode a sugar solute-binding protein (SBP), which is a component of the ABC transport system. However, the genes next to were predicted to encode two-component regulatory system proteins rather than transmembrane domains (TMDs). We also identified , which is highly homologous to . Adjacent to , two genes were predicted to encode TMDs. Binding experiments of the recombinant NagB1 and NagB2 to several oligosaccharides using differential scanning fluorimetry and surface plasmon resonance confirmed that both proteins are SBPs of (GlcNAc) and (GlcNAc). We determined their crystal structures complexed with and without chitin oligosaccharides at a resolution of 1.2 to 2.0 Å. The structures shared typical SBP structural folds and were classified as subcluster D-I. Large domain motions were observed in the structures, suggesting that they were induced by ligand binding via the "Venus flytrap" mechanism. These structures also revealed chitin oligosaccharide recognition mechanisms. In conclusion, our study provides insight into the recognition and transport of chitin oligosaccharides in bacteria.

PubMed: 34195603
DOI: 10.1016/j.yjsbx.2021.100049

Experimental method

X-RAY DIFFRACTION (1.2 Å)