5Z06

Crystal structure of beta-1,2-glucanase from Parabacteroides distasonis

Summary for 5Z06

• Entry DOI: 10.2210/pdb5z06/pdb
• Descriptor: BDI_3064 protein, CALCIUM ION, GLYCEROL, ... (4 entities in total)
• Functional Keywords: sophorose, parabacteroides, gh144, glycoside hydrolase, beta-1, 2-glucanase, 2-glucan, 2-glucooligosaccharide, hydrolase
• Biological source: Parabacteroides distasonis ATCC 8503
• Total number of polymer chains: 2
• Total formula weight: 164890.55

Authors

Shimizu, H.,Nakajima, M.,Miyanaga, A.,Takahashi, Y.,Tanaka, N.,Kobayashi, K.,Sugimoto, N.,Nakai, H.,Taguchi, H. (deposition date: 2017-12-18, release date: 2018-05-30, Last modification date: 2023-11-22)

Primary citation

Shimizu, H.,Nakajima, M.,Miyanaga, A.,Takahashi, Y.,Tanaka, N.,Kobayashi, K.,Sugimoto, N.,Nakai, H.,Taguchi, H.
Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on beta-1,2-Glucooligosaccharides from Parabacteroides distasonis
Biochemistry, 57:3849-3860, 2018

PubMed Abstract: β-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-β-1,2-glucanase from Chitinophaga pinensis ( CpSGL) as an enzyme comprising a new family. Here, we report the characteristics and crystal structure of a CpSGL homologue from Parabacteroides distasonis, an intestinal bacterium (BDI_3064 protein), which exhibits distinctive properties of known β-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear β-1,2-glucan and β-1,2-glucooligosaccharides with degrees of polymerization (DPs) of ≥4 to produce sophorose specifically but did not hydrolyze cyclic β-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced sophorose from β-1,2-glucooligosaccharide analogues that have a modified reducing end, indicating that BDI_3064 acts on its substrates from the nonreducing end. The crystal structure showed that BDI_3064 possesses additional N-terminal domains 1 and 2, unlike CpSGL. Superimposition of BDI_3064 and CpSGL complexed with ligands showed that R93 in domain 1 overlapped subsite -3 in CpSGL. Docking analysis involving a β-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked β-1,2-glucooligosaccharide. This indicates that BDI_3064 employs a distinct mechanism of recognition at the nonreducing end of substrates to act as an exo-type enzyme. Thus, we propose 2-β-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064.

PubMed: 29763309
DOI: 10.1021/acs.biochem.8b00385

Experimental method

X-RAY DIFFRACTION (2.1 Å)