2JDN

Mutant (S22A) of Pseudomonas aeruginosa lectin II (PA-IIL) complexed with methyl-a-L-mannopyranoside


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


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

  • DOI: https://doi.org/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. In vitro site-directed mutagenesis of the PA-IIL lectin yielded three single point mutants that were investigated both structurally (by X-ray crystallography) and functionally (by isothermal titration calorimetry). The mutated amino acids (22-23-24 triad) belong to the so-called specificity binding loop responsible for the monosaccharide specificity of the lectin. The mutation of the amino acids resulted in changes to the thermodynamic behaviour of the mutants and subsequently in their relative preference towards monosaccharides. Correlation of the measured data with X-ray structures provided the molecular basis for rationalizing the affinity changes. The mutations either prevent certain interactions to be formed or allow formation of new interactions--both of afore mentioned have strong effects on the saccharide preferences. Mutagenesis of amino acids forming the specificity binding loop allowed identification of one amino acid that is crucial for definition of the lectin sugar preference. Altering specificity loop amino acids causes changes in saccharide-binding preferences of lectins derived from PA-IIL, via creation or blocking possible binding interactions. This finding opens a gate towards protein engineering and subsequent protein design to refine the desired binding properties and preferences, an approach that could have strong potential for drug design.


  • Organizational Affiliation

    National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kotlarska 2, Brno, Czech Republic. honzadam@chemi.muni.cz


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FUCOSE-BINDING LECTIN PA-IIL
A, B, C, D
115Pseudomonas aeruginosaMutation(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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9HYN5
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMA
Query on MMA

Download Ideal Coordinates CCD File 
I [auth B],
L [auth C],
P [auth D]
methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
FUC
Query on FUC

Download Ideal Coordinates CCD File 
H [auth A]alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
G [auth A],
O [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
CA
Query on CA

Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
J [auth B]
K [auth B]
M [auth C]
E [auth A],
F [auth A],
J [auth B],
K [auth B],
M [auth C],
N [auth C],
Q [auth D],
R [auth D]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
MMA PDBBind:  2JDN Kd: 2780 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.155 
  • R-Value Work: 0.138 
  • R-Value Observed: 0.139 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.49α = 90
b = 72.947β = 94.32
c = 54.653γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 1.4: 2023-12-13
    Changes: Data collection, Database references, Refinement description, Structure summary