7EBI

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

Replaces:  6LZR

Summary for 7EBI

• Entry DOI: 10.2210/pdb7ebi/pdb
• Related: 6LZQ 6LZS 6LZT 6LZU 6LZV 6LZW
• Descriptor: Peptide ABC transporter, periplasmic peptide-binding protein, 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose, 1,2-ETHANEDIOL, ... (7 entities in total)
• Functional Keywords: complex, chitin, periplasmic solute-binding protein, vibrios, sugar binding protein
• Biological source: Vibrio harveyi (strain 1DA3)
• Total number of polymer chains: 1
• Total formula weight: 62767.63

Authors

Kitaoku, Y.,Ubonbal, P.,Tran, L.T.,Robinson, R.C.,Suginta, W. (deposition date: 2021-03-09, release date: 2021-09-08, Last modification date: 2023-11-29)

Primary citation

Kitaoku, Y.,Fukamizo, T.,Kumsaoad, S.,Ubonbal, P.,Robinson, R.C.,Suginta, W.
A structural model for (GlcNAc) 2 translocation via a periplasmic chitooligosaccharide-binding protein from marine Vibrio bacteria.
J.Biol.Chem., 297:101071-101071, 2021

PubMed Abstract: VhCBP is a periplasmic chitooligosaccharide-binding protein mainly responsible for translocation of the chitooligosaccharide (GlcNAc) across the double membranes of marine bacteria. However, structural and thermodynamic understanding of the sugar-binding/-release processes of VhCBP is relatively less. VhCBP displayed the greatest affinity toward (GlcNAc), with lower affinity for longer-chain chitooligosaccharides [(GlcNAc)]. (GlcNAc) 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, Asp, and Trp) to Ala resulted in drastic decreases in the binding affinity toward the preferred substrate (GlcNAc), indicating their significant contributions to sugar binding. The structure of the W513A-(GlcNAc) complex in a 'half-open' conformation unveiled the intermediary step of the (GlcNAc) translocation from the soluble CBP in the periplasm to the inner membrane-transporting components. Isothermal calorimetry data suggested that VhCBP adopts the high-affinity conformation to bind (GlcNAc), while 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.

PubMed: 34400168
DOI: 10.1016/j.jbc.2021.101071

Experimental method

X-RAY DIFFRACTION (1.5 Å)