6RGG

Photorhabdus laumondii lectin PLL2 in complex with O-methylated PGL-1-derived disaccharide


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Heptabladed beta-propeller lectins PLL2 and PHL from Photorhabdus spp. recognize O-methylated sugars and influence the host immune system.

Fujdiarova, E.Houser, J.Dobes, P.Paulikova, G.Kondakov, N.Kononov, L.Hyrsl, P.Wimmerova, M.

(2021) FEBS J 288: 1343-1365

  • DOI: https://doi.org/10.1111/febs.15457
  • Primary Citation of Related Structures:  
    6RFZ, 6RG1, 6RG2, 6RGG, 6RGJ, 6RGR, 6RGU, 6RGW

  • PubMed Abstract: 

    O-methylation is an unusual sugar modification with a function that is not fully understood. Given its occurrence and recognition by lectins involved in the immune response, methylated sugars were proposed to represent a conserved pathogen-associated molecular pattern. We describe the interaction of O-methylated saccharides with two β-propeller lectins, the newly described PLL2 from the entomopathogenic bacterium Photorhabdus laumondii, and its homologue PHL from the related human pathogen Photorhabdus asymbiotica. The crystal structures of PLL2 and PHL revealed up to 10 out of 14 potential binding sites per protein subunit to be occupied with O-methylated structures. The avidity effect strengthens the interaction by 4 orders of magnitude. PLL2 and PHL also interfere with the early immune response by modulating the production of reactive oxygen species and phenoloxidase activity. Since bacteria from Photorhabdus spp. have a complex life cycle involving pathogenicity towards different hosts, the involvement of PLL2 and PHL might contribute to the pathogen overcoming insect and human immune system defences in the early stages of infection. DATABASES: Structural data are available in PDB database under the accession numbers 6RG2, 6RGG, 6RFZ, 6RG1, 6RGU, 6RGW, 6RGJ, and 6RGR.


  • Organizational Affiliation

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


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
lectin PLL2 from Photorhabdus laumondii
A, B
371Photorhabdus laumondii subsp. laumondii TTO1Mutation(s): 0 
Gene Names: plu0734
UniProt
Find proteins for Q7N8I8 (Photorhabdus laumondii subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Explore Q7N8I8 
Go to UniProtKB:  Q7N8I8
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ7N8I8
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
K3Q
Query on K3Q

Download Ideal Coordinates CCD File 
C [auth A]
D [auth A]
E [auth A]
K [auth B]
L [auth B]
C [auth A],
D [auth A],
E [auth A],
K [auth B],
L [auth B],
O [auth B]
3,6-O-dimethyl-D-glucose
C8 H16 O6
HXTJYTSBXOATMS-UIAUGNHASA-N
7CV
Query on 7CV

Download Ideal Coordinates CCD File 
F [auth A],
M [auth B]
6-deoxy-2,3-di-O-methyl-alpha-L-mannopyranose
C8 H16 O5
SXWBIRCAXZNEGK-TVNFTVLESA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
N [auth B]1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A],
H [auth A],
I [auth A],
J [auth A],
P [auth B]
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.20 Å
  • R-Value Free: 0.224 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.304α = 90
b = 89.347β = 101.35
c = 68.401γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2020-07-01
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations
  • Version 1.2: 2021-02-24
    Changes: Database references, Derived calculations, Structure summary