5MXF

Photorhabdus asymbiotica lectin (PHL) in complex with alpha-methyl fucoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Characterization of novel bangle lectin from Photorhabdus asymbiotica with dual sugar-binding specificity and its effect on host immunity.

Jancarikova, G.Houser, J.Dobes, P.Demo, G.Hyrsl, P.Wimmerova, M.

(2017) PLoS Pathog. 13: e1006564-e1006564

  • DOI: 10.1371/journal.ppat.1006564
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes ...

    Photorhabdus asymbiotica is one of the three recognized species of the Photorhabdus genus, which consists of gram-negative bioluminescent bacteria belonging to the family Morganellaceae. These bacteria live in a symbiotic relationship with nematodes from the genus Heterorhabditis, together forming a complex that is highly pathogenic for insects. Unlike other Photorhabdus species, which are strictly entomopathogenic, P. asymbiotica is unique in its ability to act as an emerging human pathogen. Analysis of the P. asymbiotica genome identified a novel fucose-binding lectin designated PHL with a strong sequence similarity to the recently described P. luminescens lectin PLL. Recombinant PHL exhibited high affinity for fucosylated carbohydrates and the unusual disaccharide 3,6-O-Me2-Glcβ1-4(2,3-O-Me2)Rhaα-O-(p-C6H4)-OCH2CH2NH2 from Mycobacterium leprae. Based on its crystal structure, PHL forms a seven-bladed β-propeller assembling into a homo-dimer with an inter-subunit disulfide bridge. Investigating complexes with different ligands revealed the existence of two sets of binding sites per monomer-the first type prefers l-fucose and its derivatives, whereas the second type can bind d-galactose. Based on the sequence analysis, PHL could contain up to twelve binding sites per monomer. PHL was shown to interact with all types of red blood cells and insect haemocytes. Interestingly, PHL inhibited the production of reactive oxygen species induced by zymosan A in human blood and antimicrobial activity both in human blood, serum and insect haemolymph. Concurrently, PHL increased the constitutive level of oxidants in the blood and induced melanisation in haemolymph. Our results suggest that PHL might play a crucial role in the interaction of P. asymbiotica with both human and insect hosts.


    Organizational Affiliation

    Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Photorhabdus asymbiotica lectin PHL
A
369Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77)Mutation(s): 0 
Find proteins for C7BLE4 (Photorhabdus asymbiotica subsp. asymbiotica (strain ATCC 43949 / 3105-77))
Go to UniProtKB:  C7BLE4
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NA
Query on NA

Download SDF File 
Download CCD File 
A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download SDF File 
Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MFU
Query on MFU

Download SDF File 
Download CCD File 
A
ALPHA-L-METHYL-FUCOSE
C7 H14 O5
OHWCAVRRXKJCRB-CXNFULCWSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.196 
  • R-Value Work: 0.167 
  • Space Group: P 31 2 1
Unit Cell:
Length (Å)Angle (°)
a = 81.249α = 90.00
b = 81.249β = 90.00
c = 113.231γ = 120.00
Software Package:
Software NamePurpose
SCALAdata scaling
REFMACrefinement
MOLREPphasing
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2017-08-09
    Type: Initial release
  • Version 1.1: 2017-08-23
    Type: Database references
  • Version 1.2: 2018-01-24
    Type: Source and taxonomy