5C9O

Crystal structure of recombinant PLL lectin from Photorhabdus luminescens at 1.5 A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.131 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

A Novel Fucose-binding Lectin from Photorhabdus luminescens (PLL) with an Unusual Heptabladed beta-Propeller Tetrameric Structure.

Kumar, A.Sykorova, P.Demo, G.Dobes, P.Hyrsl, P.Wimmerova, M.

(2016) J.Biol.Chem. 291: 25032-25049

  • DOI: 10.1074/jbc.M115.693473
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Photorhabdus luminescens is known for its symbiosis with the entomopathogenic nematode Heterorhabditis bacteriophora and its pathogenicity toward insect larvae. A hypothetical protein from P. luminescens was identified, purified from the native sourc ...

    Photorhabdus luminescens is known for its symbiosis with the entomopathogenic nematode Heterorhabditis bacteriophora and its pathogenicity toward insect larvae. A hypothetical protein from P. luminescens was identified, purified from the native source, and characterized as an l-fucose-binding lectin, named P. luminescens lectin (PLL). Glycan array and biochemical characterization data revealed PLL to be specific toward l-fucose and the disaccharide glycan 3,6-O-Me2-Glcβ1-4(2,3-O-Me2)Rhaα-O-(p-C6H4)-OCH2CH2NH2 PLL was discovered to be a homotetramer with an intersubunit disulfide bridge. The crystal structures of native and recombinant PLL revealed a seven-bladed β-propeller fold creating seven putative fucose-binding sites per monomer. The crystal structure of the recombinant PLL·l-fucose complex confirmed that at least three sites were fucose-binding. Moreover, the crystal structures indicated that some of the other sites are masked either by the tetrameric nature of the lectin or by incorporation of the C terminus of the lectin into one of these sites. PLL exhibited an ability to bind to insect hemocytes and the cuticular surface of a nematode, H. bacteriophora.


    Organizational Affiliation

    From the Central European Institute of Technology (CEITEC).




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PLL lectin
A
381Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01)Mutation(s): 0 
Find proteins for Q7N8J0 (Photorhabdus luminescens subsp. laumondii (strain DSM 15139 / CIP 105565 / TT01))
Go to UniProtKB:  Q7N8J0
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GOL
Query on GOL

Download SDF File 
Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.152 
  • R-Value Work: 0.131 
  • Space Group: I 2 2 2
Unit Cell:
Length (Å)Angle (°)
a = 71.787α = 90.00
b = 87.825β = 90.00
c = 158.336γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
MOLREPphasing
SCALAdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Czech Science FoundationCzech Republic13-25401S
European Regional Development FundCzech RepublicCZ.1.05/1.1.00/02.0068
SYLICACzech RepublicCZ.1.05/1.1.00/02.0068

Revision History 

  • Version 1.0: 2016-10-19
    Type: Initial release
  • Version 1.1: 2016-11-02
    Type: Database references
  • Version 1.2: 2016-12-07
    Type: Database references
  • Version 1.3: 2018-03-07
    Type: Data collection