4URR

Tailspike protein of Sf6 bacteriophage bound to Shigella flexneri O- antigen octasaccharide fragment

Summary for 4URR

• Entry DOI: 10.2210/pdb4urr/pdb
• Descriptor: BIFUNCTIONAL TAIL PROTEIN, alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose-(1-3)-alpha-L-rhamnopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-L-rhamnopyranose-(1-2)-alpha-L-rhamnopyranose, MANGANESE (II) ION, ... (6 entities in total)
• Functional Keywords: hydrolase, carbohydrate interaction, tailspike protein, beta helix
• Biological source: SHIGELLA PHAGE SF6
• Total number of polymer chains: 6
• Total formula weight: 338629.31

Authors

Gohlke, U.,Heinemann, U.,Seckler, R.,Barbirz, S. (deposition date: 2014-07-01, release date: 2015-07-15, Last modification date: 2024-01-10)

Primary citation

Kang, Y.,Gohlke, U.,Engstrom, O.,Hamark, C.,Scheidt, T.,Kunstmann, S.,Heinemann, U.,Widmalm, G.,Santer, M.,Barbirz, S.
Bacteriophage Tailspikes and Bacterial O-Antigens as a Model System to Study Weak-Affinity Protein-Polysaccharide Interactions.
J.Am.Chem.Soc., 138:9109-9118, 2016

PubMed Abstract: Understanding interactions of bacterial surface polysaccharides with receptor protein scaffolds is important for the development of antibiotic therapies. The corresponding protein recognition domains frequently form low-affinity complexes with polysaccharides that are difficult to address with experimental techniques due to the conformational flexibility of the polysaccharide. In this work, we studied the tailspike protein (TSP) of the bacteriophage Sf6. Sf6TSP binds and hydrolyzes the high-rhamnose, serotype Y O-antigen polysaccharide of the Gram-negative bacterium Shigella flexneri (S. flexneri) as a first step of bacteriophage infection. Spectroscopic analyses and enzymatic cleavage assays confirmed that Sf6TSP binds long stretches of this polysaccharide. Crystal structure analysis and saturation transfer difference (STD) NMR spectroscopy using an enhanced method to interpret the data permitted the detailed description of affinity contributions and flexibility in an Sf6TSP-octasaccharide complex. Dodecasaccharide fragments corresponding to three repeating units of the O-antigen in complex with Sf6TSP were studied computationally by molecular dynamics simulations. They showed that distortion away from the low-energy solution conformation found in the octasaccharide complex is necessary for ligand binding. This is in agreement with a weak-affinity functional polysaccharide-protein contact that facilitates correct placement and thus hydrolysis of the polysaccharide close to the catalytic residues. Our simulations stress that the flexibility of glycan epitopes together with a small number of specific protein contacts provide the driving force for Sf6TSP-polysaccharide complex formation in an overall weak-affinity interaction system.

PubMed: 27045683
DOI: 10.1021/jacs.6b00240

Experimental method

X-RAY DIFFRACTION (1.95 Å)