4G9S

Crystal structure of Escherichia coli PliG in complex with Atlantic salmon g-type lysozyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history


Literature

Structural basis of bacterial defense against g-type lysozyme-based innate immunity.

Leysen, S.Vanderkelen, L.Weeks, S.D.Michiels, C.W.Strelkov, S.V.

(2013) Cell Mol Life Sci 70: 1113-1122

  • DOI: 10.1007/s00018-012-1184-1
  • Structures With Same Primary Citation

  • PubMed Abstract: 
  • Gram-negative bacteria can produce specific proteinaceous inhibitors to defend themselves against the lytic action of host lysozymes. So far, four different lysozyme inhibitor families have been identified. Here, we report the crystal structure of th ...

    Gram-negative bacteria can produce specific proteinaceous inhibitors to defend themselves against the lytic action of host lysozymes. So far, four different lysozyme inhibitor families have been identified. Here, we report the crystal structure of the Escherichia coli periplasmic lysozyme inhibitor of g-type lysozyme (PliG-Ec) in complex with Atlantic salmon g-type lysozyme (SalG) at a resolution of 0.95 Å, which is exceptionally high for a complex of two proteins. The structure reveals for the first time the mechanism of g-type lysozyme inhibition by the PliG family. The latter contains two specific conserved regions that are essential for its inhibitory activity. The inhibitory complex formation is based on a double 'key-lock' mechanism. The first key-lock element is formed by the insertion of two conserved PliG regions into the active site of the lysozyme. The second element is defined by a distinct pocket of PliG accommodating a lysozyme loop. Computational analysis indicates that this pocket represents a suitable site for small molecule binding, which opens an avenue for the development of novel antibacterial agents that suppress the inhibitory activity of PliG.


    Organizational Affiliation

    Laboratory for Biocrystallography, Department of Pharmaceutical and Pharmacological Sciences, Katholieke Universiteit Leuven, Herestraat 49 bus 822, 3000, Leuven, Belgium.



Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Goose-type lysozymeA187Salmo salarMutation(s): 1 
Gene Names: lysGLYGLOC100136420
EC: 3.2.1.17
Find proteins for A6PZ97 (Salmo salar)
Explore A6PZ97 
Go to UniProtKB:  A6PZ97
Protein Feature View
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  • Reference Sequence

Find similar proteins by: Sequence  |  Structure

Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Inhibitor of g-type lysozymeB111Escherichia coliMutation(s): 0 
Gene Names: pliGycgK
Find proteins for P76002 (Escherichia coli (strain K12))
Explore P76002 
Go to UniProtKB:  P76002
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
FLC
Query on FLC

Download CCD File 
B
CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

Download CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 0.95 Å
  • R-Value Free: 0.136 
  • R-Value Work: 0.129 
  • R-Value Observed: 0.129 
  • Space Group: P 65
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 132.182α = 90
b = 132.182β = 90
c = 42.902γ = 120
Software Package:
Software NamePurpose
XDSdata scaling
PHASERphasing
PHENIXrefinement
XDSdata reduction
SCALAdata scaling

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-11-07
    Type: Initial release
  • Version 1.1: 2013-03-06
    Changes: Database references