7ebi | pdb_00007ebi

Chitin-specific solute binding protein from Vibrio harveyi co-crystalized with chitotetraose.

spinqualitylabelsall models 7ebi, resolution 1.50Å Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Structural highlights 7ebi is a 1 chain structure with sequence from Vibrio harveyi 1DA3. This structure supersedes the now removed PDB entry 6lzr. Full crystallographic information is available from OCA. For a guided tour on the structure components use FirstGlance. Method: X-ray diffraction, Resolution 1.5Å Ligands: CA, CL, EDO, MG, NAG Resources: FirstGlance, OCA, PDBe, RCSB, PDBsum, ProSAT Function D0XC84_VIBH1 Publication Abstract from PubMed VhCBP is a periplasmic chitooligo saccharide-specific binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc)2 across the double membranes of marine bacteria Vibrio harveyi. However, structural and thermodynamic understanding of the sugar binding/release processes of VhCBP are relatively unknown. VhCBP displayed the greatest affinity towards (GlcNAc)2, with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)3-4]. (GlcNAc)4 partially occupied the closed sugar-binding groove, with two reducing-end GlcNAc units extending beyond the sugar-binding groove and barely characterized by weak electron density. Mutation of three conserved residues (Trp(363), Asp(365) and Trp(513)) to Ala resulted in drastic decreases in the binding affinity towards the preferred substrate (GlcNAc)2, indicating their significant contributions to sugar binding. The structure of the W513A-(GlcNAc)2 complex in a 'half-open' conformation unveiled the intermediary step of the (GlcNAc)2 translocation from the soluble CBP in periplasm to the inner membrane-transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high affinity conformation to bind (GlcNAc)2, whilst its low affinity conformation facilitated sugar release. Thus, chitooligosaccharide translocation, conferred by periplasmic VhCBP, is a crucial step in the chitin catabolic pathway, allowing Vibrio bacteria to thrive in oceans where chitin is their major source of nutrients. A structural model for (GlcNAc)2 translocation via a periplasmic chitooligosaccharide binding protein from marine Vibrio bacteria.,Kitaoku Y, Fukamizo T, Kumsaoad S, Ubonbal P, Robinson RC, Suginta W J Biol Chem. 2021 Aug 13:101071. doi: 10.1016/j.jbc.2021.101071. PMID:34400168 From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.

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