Crystal structure of a pesticin (translocation and receptor binding domain) from Y. pestis and T4-lysozyme chimera

Experimental Data Snapshot

  • Resolution: 2.59 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 

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

  • 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 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.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
339Yersinia pestisTequatrovirus T4
This entity is chimeric
Mutation(s): 2 
Find proteins for P00720 (Enterobacteria phage T4)
Explore P00720 
Go to UniProtKB:  P00720
Find proteins for Q57159 (Yersinia pestis)
Explore Q57159 
Go to UniProtKB:  Q57159
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupsP00720Q57159
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.59 Å
  • R-Value Free: 0.237 
  • R-Value Work: 0.192 
  • R-Value Observed: 0.194 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 194.874α = 90
b = 51.507β = 91.01
c = 107.921γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2012-05-09
    Type: Initial release
  • Version 1.1: 2012-05-30
    Changes: Other
  • Version 1.2: 2012-07-18
    Changes: Other
  • Version 1.3: 2012-10-31
    Changes: Structure summary
  • Version 1.4: 2013-09-25
    Changes: Derived calculations
  • Version 1.5: 2017-03-15
    Changes: Source and taxonomy
  • Version 1.6: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other