3M7J

Crystal structure of the bacteriocin LLPA from pseudomonas sp. in complex with Met-mannose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history


Literature

Structural Determinants for Activity and Specificity of the Bacterial Toxin LlpA

Ghequire, M.G.Garcia-Pino, A.Lebbe, E.K.Spaepen, S.Loris, R.De Mot, R.

(2013) PLoS Pathog 9: e1003199-e1003199

  • DOI: https://doi.org/10.1371/journal.ppat.1003199
  • Primary Citation of Related Structures:  
    3M7H, 3M7J, 4GC1, 4GC2

  • PubMed Abstract: 

    Lectin-like bacteriotoxic proteins, identified in several plant-associated bacteria, are able to selectively kill closely related species, including several phytopathogens, such as Pseudomonas syringae and Xanthomonas species, but so far their mode of action remains unrevealed. The crystal structure of LlpABW, the prototype lectin-like bacteriocin from Pseudomonas putida, reveals an architecture of two monocot mannose-binding lectin (MMBL) domains and a C-terminal β-hairpin extension. The C-terminal MMBL domain (C-domain) adopts a fold very similar to MMBL domains from plant lectins and contains a binding site for mannose and oligomannosides. Mutational analysis indicates that an intact sugar-binding pocket in this domain is crucial for bactericidal activity. The N-terminal MMBL domain (N-domain) adopts the same fold but is structurally more divergent and lacks a functional mannose-binding site. Differential activity of engineered N/C-domain chimers derived from two LlpA homologues with different killing spectra, disclosed that the N-domain determines target specificity. Apparently this bacteriocin is assembled from two structurally similar domains that evolved separately towards dedicated functions in target recognition and bacteriotoxicity.


  • Organizational Affiliation

    Centre of Microbial and Plant Genetics, University of Leuven, Heverlee-Leuven, Belgium.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Putidacin L1
A, B
276Pseudomonas putidaMutation(s): 0 
Gene Names: llpa
UniProt
Find proteins for Q8GEJ9 (Pseudomonas putida)
Explore Q8GEJ9 
Go to UniProtKB:  Q8GEJ9
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ8GEJ9
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
MMA
Query on MMA

Download Ideal Coordinates CCD File 
C [auth A],
D [auth B]
methyl alpha-D-mannopyranoside
C7 H14 O6
HOVAGTYPODGVJG-VEIUFWFVSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.26 Å
  • R-Value Free: 0.213 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 148.973α = 90
b = 153.201β = 90
c = 33.914γ = 90
Software Package:
Software NamePurpose
MAR345data collection
PHASERphasing
PHENIXrefinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2011-03-23
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2013-04-10
    Changes: Database references
  • Version 1.3: 2017-11-08
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Derived calculations, Structure summary
  • Version 1.5: 2023-11-01
    Changes: Data collection, Database references, Refinement description, Structure summary