Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Dihedral - D2  (3D View)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 50.03 kDa 
• Atom Count: 4453 
• Residue Count: 456 
• Unique protein chains: 1

5A6Z

Structure of the LecB lectin from Pseudomonas aeruginosa strain PA14 in complex with lewis a

• DOI: 10.2210/pdb5A6Z/pdb

• Classification: SUGAR BINDING PROTEIN
• Organism(s): Pseudomonas aeruginosa UCBPP-PA14
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2015-07-02 Released: 2016-05-25 
• Deposition Author(s): Sommer, R., Wagner, S., Varrot, A., Khaledi, A., Haussler, S., Imberty, A., Titz, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.155 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 

Literature

The virulence factor LecB varies in clinical isolates: consequences for ligand binding and drug discovery.

Sommer, R., Wagner, S., Varrot, A., Nycholat, C.M., Khaledi, A., Haussler, S., Paulson, J.C., Imberty, A., Titz, A.

(2016) Chem Sci 7: 4990-5001

• PubMed: 30155149 
• DOI: 10.1039/c6sc00696e
• Primary Citation of Related Structures:  
  5A6Z, 5A6Y, 5A6X, 5A6Q


• PubMed Abstract: 
  

P. aeruginosa causes a substantial number of nosocomial infections and is the leading cause of death of cystic fibrosis patients. This Gram-negative bacterium is highly resistant against antibiotics and further protects itself by forming a biofilm. Moreover, a high genomic variability among clinical isolates complicates therapy. Its lectin LecB is a virulence factor and necessary for adhesion and biofilm formation. We analyzed the sequence of LecB variants in a library of clinical isolates and demonstrate that it can serve as a marker for strain family classification. LecB from the highly virulent model strain PA14 presents 13% sequence divergence with LecB from the well characterized PAO1 strain. These differences might result in differing ligand binding specificities and ultimately in reduced efficacy of drugs directed towards LecB. Despite several amino acid variations at the carbohydrate binding site, glycan array analysis showed a comparable binding pattern for both variants. A common high affinity ligand could be identified and after its chemoenzymatic synthesis verified in a competitive binding assay: an N -glycan presenting two blood group O epitopes (H-type 2 antigen). Molecular modeling of the complex suggests a bivalent interaction of the ligand with the LecB tetramer by bridging two separate binding sites. This binding rationalizes the strong avidity (35 nM) of LecB _PA14 to this human fucosylated N-glycan. Biochemical evaluation of a panel of glycan ligands revealed that LecB _PA14 demonstrated higher glycan affinity compared to LecB _PAO1 including the extraordinarily potent affinity of 70 nM towards the monovalent human antigen Lewis ^a . The structural basis of this unusual high affinity ligand binding for lectins was rationalized by solving the protein crystal structures of LecB _PA14 with several glycans.

---

Organizational Affiliation: 

Deutsches Zentrum für Infektionsforschung (DZIF) , Standort Hannover , Braunschweig , Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LECB	A, B, C, D	114	Pseudomonas aeruginosa UCBPP-PA14	Mutation(s): 0  Gene Names: lecB, PA14_20610
Find proteins for A0A0H2ZE85 (Pseudomonas aeruginosa (strain UCBPP-PA14)) Explore A0A0H2ZE85  Go to UniProtKB:  A0A0H2ZE85

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-alpha-D-galactopyranose	E, H	4		N/A

Entity ID: 3
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose	F	3		N/A

Entity ID: 4
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
beta-D-galactopyranose-(1-3)-[alpha-L-fucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-beta-D-galactopyranose	G	4		N/A

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PEG	D	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	A, B, C	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CA	A, B, C, D	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.155 
• R-Value Work: 0.131 
• R-Value Observed: 0.132 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.976	α = 90
b = 63.772	β = 91.25
c = 64.513	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2015-07-02 
• Released Date: 2016-05-25 
Deposition Author(s): Sommer, R., Wagner, S., Varrot, A., Khaledi, A., Haussler, S., Imberty, A., Titz, A.

Revision History 

• Version 1.0: 2016-05-25
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2020-01-22
  Changes: Data collection, Derived calculations, Other, Structure summary
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary