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 

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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
  • Primary Citation of Related Structures:  
    4G9S

  • 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 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 ...

    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
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Goose-type lysozymeA187Salmo salarMutation(s): 1 
Gene Names: lysG, LYG, LOC100136420
EC: 3.2.1.17
UniProt
Find proteins for A6PZ97 (Salmo salar)
Explore A6PZ97 
Go to UniProtKB:  A6PZ97
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupA6PZ97
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Inhibitor of g-type lysozymeB111Escherichia coliMutation(s): 0 
Gene Names: pliG, ycgK
UniProt
Find proteins for P76002 (Escherichia coli (strain K12))
Explore P76002 
Go to UniProtKB:  P76002
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP76002
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 Ideal Coordinates CCD File 
D [auth B]CITRATE ANION
C6 H5 O7
KRKNYBCHXYNGOX-UHFFFAOYSA-K		 Ligand Interaction
CL
Query on CL
Download Ideal Coordinates CCD File 
C [auth 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

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Entry History 

Deposition Data

Revision History  (Full details and data files)

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