Biological Assembly 1  

 3D View: Structure | 1D-3D View | Electron Density | Validation Report | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PQS (software)

Macromolecule Content

• Total Structure Weight: 49.07 kDa 
• Atom Count: 4070 
• Modelled Residue Count: 456 
• Deposited Residue Count: 460 
• Unique protein chains: 1

2JDU

Mutant (G24N) of Pseudomonas aeruginosa lectin II (PA-IIL) complexed with methyl-a-L-fucopyranoside

• PDB DOI: 10.2210/pdb2JDU/pdb

• Classification: LECTIN
• Organism(s): Pseudomonas aeruginosa
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2007-01-12 Released: 2007-06-12 
• Deposition Author(s): Adam, J., Pokorna, M., Sabin, C., Mitchell, E.P., Imberty, A., Wimmerova, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.193 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 

Literature

Engineering of Pa-Iil Lectin from Pseudomonas Aeruginosa - Unravelling the Role of the Specificity Loop for Sugar Preference.

Adam, J., Pokorna, M., Sabin, C., Mitchell, E.P., Imberty, A., Wimmerova, M.

(2007) BMC Struct Biol 7: 36

• PubMed: 17540045 
• DOI: 10.1186/1472-6807-7-36
• Primary Citation of Related Structures:  
  2JDM, 2JDN, 2JDP, 2JDU, 2JDY


• PubMed Abstract: 
  

Lectins are proteins of non-immune origin capable of binding saccharide structures with high specificity and affinity. Considering the high encoding capacity of oligosaccharides, this makes lectins important for adhesion and recognition. The present study is devoted to the PA-IIL lectin from Pseudomonas aeruginosa, an opportunistic human pathogen capable of causing lethal complications in cystic fibrosis patients. The lectin may play an important role in the process of virulence, recognizing specific saccharide structures and subsequently allowing the bacteria to adhere to the host cells. It displays high values of affinity towards monosaccharides, especially fucose--a feature caused by unusual binding mode, where two calcium ions participate in the interaction with saccharide. Investigating and understanding the nature of lectin-saccharide interactions holds a great potential of use in the field of drug design, namely the targeting and delivery of active compounds to the proper site of action.

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Related Citations: 

• Structural Basis for Oligosaccharide-Mediated Adhesion of Pseudomonas Aeruginosa in the Lungs of Cystic Fibrosis Patients
  Mitchell, E., Houles, C., Sudakevitz, D., Wimmerova, M., Gautier, C., Perez, S., Wu, A., Gilboa-Garber, N., Imberty, A.
  (2002) Nat Struct Biol 9: 918

• Binding of Different Monosaccharides by Lectin Pa-Iil from Pseudomonas Aeruginosa: Thermodynamics Data Correlated with X-Ray Structures.
  Sabin, C., Mitchell, E., Pokorna, M., Gautier, C., Utille, J., Wimmerova M, M., Imberty, A.
  (2006) FEBS Lett 580: 982

• Unusual Entropy-Driven Affinity of Chromobacterium Violaceum Lectin Cv-Iil Toward Fucose and Mannose.
  Pokorna, M., Cioci, G., Perret, S., Rebuffet, E., Kostlanova, N., Adam, J., Gilboa-Garber, N., Mitchell, E., Imberty, A., Wimmerova, M.
  (2006) Biochemistry 45: 7501

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Organizational Affiliation: 

National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FUCOSE-BINDING LECTIN PA-IIL	A, B, C, D	115	Pseudomonas aeruginosa	Mutation(s): 1
UniProt
Find proteins for Q9HYN5 (Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)) Explore Q9HYN5  Go to UniProtKB:  Q9HYN5

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MFU	M [auth C], R [auth D]	methyl alpha-L-fucopyranoside C7 H14 O5 OHWCAVRRXKJCRB-CXNFULCWSA-N
SO4	F [auth A], G [auth A], I [auth B], J [auth B], N [auth C], O [auth C], S [auth D]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], H [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CA	K [auth C], L [auth C], P [auth D], Q [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
MFU	Binding MOAD:  2JDU	Kd: 190 (nM) from 1 assay(s)
	PDBBind:  2JDU	Kd: 190 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.193 
• R-Value Work: 0.149 
• R-Value Observed: 0.151 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.627	α = 90
b = 74.886	β = 114.71
c = 53.466	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2007-01-12 
• Released Date: 2007-06-12 
Deposition Author(s): Adam, J., Pokorna, M., Sabin, C., Mitchell, E.P., Imberty, A., Wimmerova, M.

Revision History  

• Version 1.0: 2007-06-12
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Other, Structure summary