4YWA

Structural Insight into Divalent Galactoside Binding to Pseudomonas aeruginosa lectin LecA


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.192 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.186 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural Insight into Multivalent Galactoside Binding to Pseudomonas aeruginosa Lectin LecA.

Visini, R.Jin, X.Bergmann, M.Michaud, G.Pertici, F.Fu, O.Pukin, A.Branson, T.R.Thies-Weesie, D.M.Kemmink, J.Gillon, E.Imberty, A.Stocker, A.Darbre, T.Pieters, R.J.Reymond, J.L.

(2015) Acs Chem.Biol. 10: 2455-2462

  • DOI: 10.1021/acschembio.5b00302
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Multivalent galactosides inhibiting Pseudomonas aeruginosa biofilms may help control this problematic pathogen. To understand the binding mode of tetravalent glycopeptide dendrimer GalAG2 [(Gal-β-OC6H4CO-Lys-Pro-Leu)4(Lys-Phe-Lys-Ile)2Lys-His-Ile-NH2 ...

    Multivalent galactosides inhibiting Pseudomonas aeruginosa biofilms may help control this problematic pathogen. To understand the binding mode of tetravalent glycopeptide dendrimer GalAG2 [(Gal-β-OC6H4CO-Lys-Pro-Leu)4(Lys-Phe-Lys-Ile)2Lys-His-Ile-NH2] to its target lectin LecA, crystal structures of LecA complexes with divalent analog GalAG1 [(Gal-β-OC6H4CO-Lys-Pro-Leu)2Lys-Phe-Lys-Ile-NH2] and related glucose-triazole linked bis-galactosides 3u3 [Gal-β-O(CH2)n-(C2HN3)-4-Glc-β-(C2HN3)-[β-Glc-4-(N3HC2)]2-(CH2)n-O-β-Gal (n = 1)] and 5u3 (n = 3) were obtained, revealing a chelate bound 3u3, cross-linked 5u3, and monovalently bound GalAG1. Nevertheless, a chelate bound model better explaining their strong LecA binding and the absence of lectin aggregation was obtained by modeling for all three ligands. A model of the chelate bound GalAG2·LecA complex was also obtained rationalizing its unusually tight LecA binding (KD = 2.5 nM) and aggregation by lectin cross-linking. The very weak biofilm inhibition with divalent LecA inhibitors suggests that lectin aggregation is necessary for biofilm inhibition by GalAG2, pointing to multivalent glycoclusters as a unique opportunity to control P. aeruginosa biofilms.


    Organizational Affiliation

    Department of Chemistry and Biochemistry, University of Berne , Freiestrasse 3, 3012 Berne, Switzerland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
PA-I galactophilic lectin
A, B, C, D
121Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)Mutation(s): 0 
Gene Names: lecA (pa1L)
Find proteins for Q05097 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1))
Go to UniProtKB:  Q05097
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
4J9
Query on 4J9

Download SDF File 
Download CCD File 
A, C
(2R,3R,4S,5R,6R,2'R,3'R,4'S,5'R,6'R)-2,2'-([(2R,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]bis{1H-1,2,3-triazole-1,4-diyl[(2S,3R,4S,5S,6S)-3,4-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2,5-diyl]-1H-1,2,3-triazole-1,4-diylmethanediyloxy})bis[6-(hydroxymethyl)tetrahydro-2H-pyran-3,4,5-triol]
C40 H60 N12 O24
VSDJVODUXIZSKO-LYPAKNIXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.192 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.186 
  • Space Group: P 1
Unit Cell:
Length (Å)Angle (°)
a = 40.770α = 117.23
b = 72.320β = 105.00
c = 78.710γ = 89.94
Software Package:
Software NamePurpose
SCALAdata scaling
PHENIXrefinement
MOSFLMdata reduction
PDB_EXTRACTdata extraction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2015-09-09
    Type: Initial release
  • Version 1.1: 2015-12-02
    Type: Database references