5GZK

Endo-beta-1,2-glucanase from Chitinophaga pinensis - sophorotriose and glucose complex

Summary for 5GZK

• Entry DOI: 10.2210/pdb5gzk/pdb
• Related: 5GZH
• Descriptor: Uncharacterized protein, beta-D-glucopyranose-(1-2)-beta-D-glucopyranose-(1-2)-beta-D-glucopyranose, PHOSPHATE ION, ... (10 entities in total)
• Functional Keywords: hydrolase, (alpha/alpha)6-barrel
• Biological source: Chitinophaga pinensis (strain ATCC 43595 / DSM 2588 / NCIB 11800 / UQM 2034)
• Total number of polymer chains: 2
• Total formula weight: 106996.68

Authors

Abe, K.,Nakajima, M.,Arakawa, T.,Fushinobu, S.,Taguchi, H. (deposition date: 2016-09-28, release date: 2017-03-15, Last modification date: 2023-11-08)

Primary citation

Abe, K.,Nakajima, M.,Yamashita, T.,Matsunaga, H.,Kamisuki, S.,Nihira, T.,Takahashi, Y.,Sugimoto, N.,Miyanaga, A.,Nakai, H.,Arakawa, T.,Fushinobu, S.,Taguchi, H.
Biochemical and structural analyses of a bacterial endo-beta-1,2-glucanase reveal a new glycoside hydrolase family
J. Biol. Chem., 292:7487-7506, 2017

PubMed Abstract: β-1,2-Glucan is an extracellular cyclic or linear polysaccharide from Gram-negative bacteria, with important roles in infection and symbiosis. Despite β-1,2-glucan's importance in bacterial persistence and pathogenesis, only a few reports exist on enzymes acting on both cyclic and linear β-1,2-glucan. To this end, we purified an -β-1,2-glucanase to homogeneity from cell extracts of the environmental species , and an -β-1,2-glucanase candidate gene () was cloned from the related species The Cpin_6279 protein specifically hydrolyzed linear β-1,2-glucan with polymerization degrees of ≥5 and a cyclic counterpart, indicating that Cpin_6279 is an -β-1,2-glucananase. Stereochemical analysis demonstrated that the Cpin_6279-catalyzed reaction proceeds via an inverting mechanism. Cpin_6279 exhibited no significant sequence similarity with known glycoside hydrolases (GHs), and thus the enzyme defines a novel GH family, GH144. The crystal structures of the ligand-free and complex forms of Cpin_6279 with glucose (Glc) and sophorotriose (Glc-β-1,2-Glc-β-1,2-Glc) determined up to 1.7 Å revealed that it has a large cavity appropriate for polysaccharide degradation and adopts an (α/α)-fold slightly similar to that of GH family 15 and 8 enzymes. Mutational analysis indicated that some of the highly conserved acidic residues in the active site are important for catalysis, and the Cpin_6279 active-site architecture provided insights into the substrate recognition by the enzyme. The biochemical characterization and crystal structure of this novel GH may enable discovery of other β-1,2-glucanases and represent a critical advance toward elucidating structure-function relationships of GH enzymes.

PubMed: 28270506
DOI: 10.1074/jbc.M116.762724

Experimental method

X-RAY DIFFRACTION (1.7 Å)