3OD9

Crystal structure of PliI-Ah, periplasmic lysozyme inhibitor of I-type lysozyme from Aeromonas hydrophyla


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.411 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 

wwPDB Validation 3D Report Full Report


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Literature

Molecular Basis of Bacterial Defense against Host Lysozymes: X-ray Structures of Periplasmic Lysozyme Inhibitors PliI and PliC.

Leysen, S.Van Herreweghe, J.M.Callewaert, L.Heirbaut, M.Buntinx, P.Michiels, C.W.Strelkov, S.V.

(2011) J.Mol.Biol. 405: 1233-1245

  • DOI: 10.1016/j.jmb.2010.12.007
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Lysozymes play a key role in the innate immune system of vertebrates and invertebrates by hydrolyzing peptidoglycan, a vital component of the bacterial cell wall. Gram-negative bacteria produce various types of lysozyme inhibitors that allow them to ...

    Lysozymes play a key role in the innate immune system of vertebrates and invertebrates by hydrolyzing peptidoglycan, a vital component of the bacterial cell wall. Gram-negative bacteria produce various types of lysozyme inhibitors that allow them to survive the bactericidal action of lysozyme when their outer membrane is permeabilized. So far, three lysozyme inhibitor families have been described: the Ivy (inhibitor of vertebrate lysozyme) family, the MliC/PliC (membrane-associated/periplasmic lysozyme inhibitor of C-type lysozyme) family, and the PliI (periplasmic lysozyme inhibitor of I-type lysozyme) family. Here, we report high-resolution crystal structures of Salmonella typhimurium PliC (PliC-St) and Aeromonas hydrophila PliI (PliI-Ah). The structure of PliI-Ah is the first in the recently discovered PliI family of lysozyme inhibitors, while the structure of PliC-St is the first structure of a periplasmic lysozyme inhibitor from the PliC/MliC family. Using small-angle X-ray scattering, we demonstrate that both PliC-St and PliI-Ah form stable dimers in solution. The functional dimer architecture of PliC-St is very different from that of the recently described MliC from Pseudomonas aeruginosa (MliC-Pa), despite the close resemblance of their monomers. Furthermore, PliI-Ah has distinctly different monomer and dimer folds compared to PliC, MliC, and Ivy proteins. Site-directed mutagenesis suggests that the inhibitory action of PliI-Ah proceeds via an insertion of a loop containing the conserved SGxY motif into the active center of I-type lysozymes. This motif is related to the functional SGxxY motif found in the MliC/PliC family.


    Organizational Affiliation

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




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Putative exported protein
A, B, C
135Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240)Mutation(s): 0 
Find proteins for A0KHJ5 (Aeromonas hydrophila subsp. hydrophila (strain ATCC 7966 / DSM 30187 / JCM 1027 / KCTC 2358 / NCIMB 9240))
Go to UniProtKB:  A0KHJ5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A, B
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

Download SDF File 
Download CCD File 
A, B, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.411 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.161 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 103.021α = 90.00
b = 60.327β = 115.65
c = 82.187γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
SCALAdata scaling
MOLREPphasing
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-12-22
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance