5YSB

Crystal structure of beta-1,2-glucooligosaccharide binding protein in ligand-free form

DOI: 10.2210/pdb5YSB/pdb

Classification: SUGAR BINDING PROTEIN
Organism(s): Listeria innocua Clip11262
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2017-11-13 Released: 2018-05-02
Deposition Author(s): Abe, K., Nakajima, M., Taguchi, H., Arakawa, T., Fushinobu, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.247
R-Value Work: 0.190
R-Value Observed: 0.192

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.

Abe, K., Sunagawa, N., Terada, T., Takahashi, Y., Arakawa, T., Igarashi, K., Samejima, M., Nakai, H., Taguchi, H., Nakajima, M., Fushinobu, S.

(2018) J Biol Chem 293: 8812-8828

PubMed: 29678880 Search on PubMedSearch on PubMed Central
DOI: 10.1074/jbc.RA117.001536
Primary Citation of Related Structures:
5YSB, 5YSD, 5YSF, 5YSE

PubMed Abstract:

β-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 β-1,2-glucan-associated enzymes have been characterized, little is known about how β-1,2-glucan and its shorter oligosaccharides (Sop _n s) are captured and imported into the bacterial cell. Here, we report the biochemical and structural characteristics of the Sop _n -binding protein (SO-BP, Lin1841) associated with the ATP-binding cassette (ABC) transporter from the Gram-positive bacterium Listeria innocua Calorimetric analysis revealed that SO-BP specifically binds to Sop _n s with a degree of polymerization of 3 or more, with K _d 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 (Sop _3-5) were determined to a maximum resolution of 1.6 Å. The binding site displayed shape complementarity to Sop _n , which adopted a zigzag conformation. We noted that water-mediated hydrogen bonds and stacking interactions play a pivotal role in the recognition of Sop _3-5 by SO-BP, consistent with its binding thermodynamics. Computational free-energy calculations and a mutational analysis confirmed that interactions with the third glucose moiety of Sop _n s are significantly responsible for ligand binding. A reduction in unfavorable changes in binding entropy that were in proportion to the lengths of the Sop _n s was 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 β-1,2-glucan metabolism and promote the discovery of unidentified β-1,2-glucan-associated proteins.

Organizational Affiliation:

From the Department of Biotechnology, asfushi@mail.ecc.u-tokyo.ac.jp.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lin1841 protein	A, B	397	Listeria innocua Clip11262	Mutation(s): 0 Gene Names: lin1841
Find proteins for Q92AS8 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)) Explore Q92AS8 Go to UniProtKB: Q92AS8
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PEG Query on PEG Download CCD File	A, B	DI(HYDROXYETHYL)ETHER C₄ H₁₀ O₃ MTHSVFCYNBDYFN-UHFFFAOYSA-N		Ligand Interaction
ZN Query on ZN Download CCD File	A, B	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction