5ysd | pdb_00005ysd

Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose

spinqualitylabelsall models 5ysd, resolution 2.10Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 5ysd is a 2 chain structure. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Ligands: BGC, GLC, MG, MPD Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Publication Abstract from PubMed beta-1,2-Glucans are bacterial carbohydrates that exist in cyclic or linear forms and play an important role in infections and symbioses involving Gram-negative bacteria. Although several beta-1,2-glucan-associated enzymes have been characterized, little is known about how beta-1,2-glucan and its shorter oligosaccharides (Sopns) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of Sopn-binding protein (SO-BP, Lin1841) associated with the ABC transporter from the Gram-positive bacterium Listeria innocua Calorimetric analysis revealed that SO-BP specifically binds to Sopns with degree of polymerization of 3 or more, with Kd values in the micromolar range. The crystal structures of SO-BP in an unliganded open form and in closed complexes with tri-, tetra-, and pentaoligosaccharides (Sop3-5) were determined to a maximum resolution of 1.6 A. The binding site displayed shape complementarity to Sopn,which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop3-5by SO-BP, consistent with its binding thermodynamics. Computational free-energy calculations and a mutational analysis confirmed that interactions with the third glucose moiety of Sopns are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sopns were explained by conformational entropy changes. Phylogenetic and sequence analyses indicated that SO-BP ABC transporter homologs, glycoside hydrolases, and other related proteins are co-localized in the genomes of several bacteria. This study may improve our understanding of bacterial beta-1,2-glucan metabolism and promote discovery of unidentified beta-1,2-glucan-associated proteins. Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein in Listeria innocua.,Abe K, Sunagawa N, Terada T, Takahashi Y, Arakawa T, Igarashi K, Samejima M, Nakai H, Taguchi H, Nakajima M, Fushinobu S J Biol Chem. 2018 Apr 20. pii: RA117.001536. doi: 10.1074/jbc.RA117.001536. PMID:29678880 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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