5z06 | pdb_00005z06

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

spinqualitylabelsall models 5z06, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5z06 is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: CA, GOL Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed beta-1,2-Glucan is a polysaccharide produced mainly by some Gram-negative bacteria as a symbiosis and infectious factor. We recently identified endo-beta-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 beta-1,2-glucan-degrading enzymes. BDI_3064 hydrolyzed linear beta-1,2-glucan and beta-1,2-glucooligosaccharides with degrees of polymerization (DPs) of >/=4 to produce sophorose specifically but did not hydrolyze cyclic beta-1,2-glucan. This result indicates that BDI_3064 is a new exo-type enzyme. BDI_3064 also produced sophorose from beta-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 beta-1,2-glucooligosaccharide with DP4 showed that R93 completely blocks the nonreducing end of the docked beta-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-beta-d-glucooligosaccharide sophorohydrolase (nonreducing end) as a systematic name for BDI_3064. Characterization and Structural Analysis of a Novel exo-Type Enzyme Acting on beta-1,2-Glucooligosaccharides from Parabacteroides distasonis.,Shimizu H, Nakajima M, Miyanaga A, Takahashi Y, Tanaka N, Kobayashi K, Sugimoto N, Nakai H, Taguchi H Biochemistry. 2018 May 25. doi: 10.1021/acs.biochem.8b00385. PMID:29763309 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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