9IB8 image
Deposition Date 2025-02-11
Release Date 2025-10-29
Last Version Date 2025-10-29
Entry Detail
PDB ID:
9IB8
Title:
Tumor necrosis factor-like lectin PLTL from Photorhabdus laumondii in complex with Lewis Y tetrasaccharide
Biological Source:
Host Organism:
Method Details:
Experimental Method:
Resolution:
1.60 Å
R-Value Free:
0.20
R-Value Work:
0.17
Space Group:
P 41 21 2
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Photorhabdus luminescens subsp. laumondii TTO1 complete genome segment 15/17
Gene (Uniprot):plu4240
Chain IDs:A (auth: C), B (auth: A), C (auth: B)
Chain Length:139
Number of Molecules:3
Biological Source:Photorhabdus laumondii subsp. laumondii TTO1
Primary Citation
Structural and functional characterization of the newly identified Photorhabdus laumondii tumor necrosis factor-like lectin.
Febs J. ? ? ? (2025)
PMID: 41105922 DOI: 10.1111/febs.70293

Abstact

Photorhabdus bacteria live in mutualistic relationships with Heterorhabditis nematodes, and together, they act as effective insect pathogens. These bacteria produce a diverse array of lectins, sugar-binding proteins that are believed to play crucial roles in the complex tripartite interaction among Photorhabdus, nematodes, and their insect hosts. One such lectin, Photorhabdus laumondii tumor necrosis factor (TNF)-like lectin (PLTL), identified in Photorhabdus laumondii subsp. laumondii TTO1, exhibits notable sequence similarity to the N-terminal domain of the BC2L-C lectin (BC2L-CN), a TNF-like lectin recognized for its specificity toward fucosylated glycans associated with human embryonic stem cells and certain cancers. Through glycan array analysis and surface plasmon resonance, we identified PLTL's binding preference for branched histo-blood group oligosaccharides. The crystallographic structure of PLTL in complex with the BLeb pentasaccharide reveals a network of direct and water-mediated hydrogen bonds simultaneously stabilizing the Fucα1-2 and Galα1-3 moieties, which define its narrow glycan specificity. A combination of mass spectrometry, protein crystallography, and analytical ultracentrifugation showed a unique hexameric PLTL architecture stabilized by intermolecular disulfide bridges. Our data suggest that PLTL may contribute to the mutualistic relationship between Photorhabdus and its nematode symbiont, Heterorhabditis bacteriophora, rather than playing a role in the interaction with the insect host. This study provides a structural and functional characterization of PLTL, a newly identified member of the TNF-like lectin family. Comparative analysis with BC2L-CN highlights both conserved and distinct structural features, suggesting potential applications in glycan recognition-based diagnostics or biotechnological tools beyond its biological role. Our findings underscore its complex glycan specificity and offer insights into its potential role in Photorhabdus-nematode symbiosis.

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