6FLU

Photorhabdus asymbiotica lectin (PHL) in complex with synthetic C-fucoside

Summary for 6FLU

• Entry DOI: 10.2210/pdb6flu/pdb
• Descriptor: Photorhabdus asymbitoca lectin PHL, (2~{S},3~{S},4~{R},5~{S},6~{S})-2-[[(2~{R},3~{S},4~{R},6~{S})-2-(hydroxymethyl)-6-methoxy-3-oxidanyl-oxan-4-yl]methyl]-6-methyl-oxane-3,4,5-triol, SODIUM ION, ... (5 entities in total)
• Functional Keywords: lectin, seven-bladed beta-propeller, sugar binding protein, c-fucoside, methyl 2, 3-dideoxy-3-c-[(a-l-fucopyranosyl)methyl]-a-d- arabino-hexopyranoside
• Biological source: Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77) (Xenorhabdus luminescens (strain 2))
• Total number of polymer chains: 2
• Total formula weight: 84576.10

Authors

Houser, J.,Jancarikova, G.,Wimmerova, M. (deposition date: 2018-01-28, release date: 2019-02-06, Last modification date: 2024-10-16)

Primary citation

Paulikova, G.,Houser, J.,Kasakova, M.,Oroszova, B.,Bertolotti, B.,Parkan, K.,Moravcova, J.,Wimmerova, M.
Fucosylated inhibitors of recently identified bangle lectin from Photorhabdus asymbiotica.
Sci Rep, 9:14904-14904, 2019

PubMed Abstract: A recently described bangle lectin (PHL) from the bacterium Photorhabdus asymbiotica was identified as a mainly fucose-binding protein that could play an important role in the host-pathogen interaction and in the modulation of host immune response. Structural studies showed that PHL is a homo-dimer that contains up to seven L-fucose-specific binding sites per monomer. For these reasons, potential ligands of the PHL lectin: α-L-fucopyranosyl-containing mono-, di-, tetra-, hexa- and dodecavalent ligands were tested. Two types of polyvalent structures were investigated - calix[4]arenes and dendrimers. The shared feature of all these structures was a C-glycosidic bond instead of the more common but physiologically unstable O-glycosidic bond. The inhibition potential of the tested structures was assessed using different techniques - hemagglutination, surface plasmon resonance, isothermal titration calorimetry, and cell cross-linking. All the ligands proved to be better than free L-fucose. The most active hexavalent dendrimer exhibited affinity three orders of magnitude higher than that of standard L-fucose. To determine the binding mode of some ligands, crystal complex PHL/fucosides 2 - 4 were prepared and studied using X-ray crystallography. The electron density in complexes proved the presence of the compounds in 6 out of 7 fucose-binding sites.

PubMed: 31624296
DOI: 10.1038/s41598-019-51357-9

Experimental method

X-RAY DIFFRACTION (1.78 Å)