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 

wwPDB Validation 3D Report Full Report


This is version 1.3 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: 10.1186/1472-6807-7-36
  • Primary Citation of Related Structures:  
    2JDP, 2JDN, 2JDM, 2JDY, 2JDU

  • 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 ...

    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.


    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
    • A New Ralstonia Solanacearum High-Affinity Mannose- Binding Lectin Rs-Iil Structurally Resembling the Pseudomonas Aeruginosa Fucose-Specific Lectin Pa- Iil
      Sudakevitz, D., Kostlanova, N., Blatmanjan, G., Mitchell, E., Lerrer, B., Wimmerova, M., Katcoff, D., Imberty, A., Gilboagarber, N.
      (2004) Mol Microbiol 52: 691

    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)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FUCOSE-BINDING LECTIN PA-IILABCD115Pseudomonas aeruginosaMutation(s): 1 
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
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MMA
Query on MMA

Download CCD File 
B, C, D
methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
 Ligand Interaction
FUC
Query on FUC

Download CCD File 
A
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
SO4
Query on SO4

Download CCD File 
A, C
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CA
Query on CA

Download CCD File 
A, B, C, D
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MMAKd :  2780   nM  PDBBind
MMAKd:  2780   nM  Binding MOAD
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 

  • 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