4AQN

Crystal structure of pesticin from Y. pestis


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

Structure and Mechanistic Studies of Pesticin, a Bacterial Homolog of Phage Lysozymes.

Patzer, S.I.Albrecht, R.Braun, V.Zeth, K.

(2012) J Biol Chem 287: 23381

  • DOI: 10.1074/jbc.M112.362913
  • Primary Citation of Related Structures:  
    4AQN, 4ARM, 4ARP, 4ARQ, 4ARJ, 4ARL

  • PubMed Abstract: 
  • Yersinia pestis produces and secretes a toxin named pesticin that kills related bacteria of the same niche. Uptake of the bacteriocin is required for activity in the periplasm leading to hydrolysis of peptidoglycan. To understand the uptake mechanism ...

    Yersinia pestis produces and secretes a toxin named pesticin that kills related bacteria of the same niche. Uptake of the bacteriocin is required for activity in the periplasm leading to hydrolysis of peptidoglycan. To understand the uptake mechanism and to investigate the function of pesticin, we combined crystal structures of the wild type enzyme, active site mutants, and a chimera protein with in vivo and in vitro activity assays. Wild type pesticin comprises an elongated N-terminal translocation domain, the intermediate receptor binding domain, and a C-terminal activity domain with structural analogy to lysozyme homologs. The full-length protein is toxic to bacteria when taken up to the target site via the outer or the inner membrane. Uptake studies of deletion mutants in the translocation domain demonstrate their critical size for import. To further test the plasticity of pesticin during uptake into bacterial cells, the activity domain was replaced by T4 lysozyme. Surprisingly, this replacement resulted in an active chimera protein that is not inhibited by the immunity protein Pim. Activity of pesticin and the chimera protein was blocked through introduction of disulfide bonds, which suggests unfolding as the prerequisite to gain access to the periplasm. Pesticin, a muramidase, was characterized by active site mutations demonstrating a similar but not identical residue pattern in comparison with T4 lysozyme.


    Organizational Affiliation

    Department of Protein Evolution, Max Planck Institute for Developmental Biology, Spemannstrasse 35, 72076 Tübingen, Germany.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
PESTICINAB357Yersinia pestisMutation(s): 0 
Gene Names: pstYPPCP1.05cG4D65_19180GD372_22925
Find proteins for Q57159 (Yersinia pestis)
Explore Q57159 
Go to UniProtKB:  Q57159
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MG
Query on MG

Download Ideal Coordinates CCD File 
B
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.98 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.190 
  • R-Value Observed: 0.192 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 36.55α = 90
b = 86.78β = 96.14
c = 122.27γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
XDSdata reduction
XSCALEdata scaling
SHARPphasing
DMphasing
BUCCANEERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

  • Deposited Date: 2012-04-19 
  • Released Date: 2012-05-02 
  • Deposition Author(s): Zeth, K., Albrecht, R.

Revision History 

  • Version 1.0: 2012-05-02
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Other
  • Version 1.2: 2012-07-18
    Changes: Other