Endolysin from bacteriophage Enc34, catalytic domain

Experimental Data Snapshot

  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 

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This is version 2.2 of the entry. See complete history


Diversity of the lysozyme fold: structure of the catalytic domain from an unusual endolysin encoded by phage Enc34.

Cernooka, E.Rumnieks, J.Zrelovs, N.Tars, K.Kazaks, A.

(2022) Sci Rep 12: 5005-5005

  • DOI: https://doi.org/10.1038/s41598-022-08765-1
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Endolysins are bacteriophage-encoded peptidoglycan-degrading enzymes with potential applications for treatment of multidrug-resistant bacterial infections. Hafnia phage Enc34 encodes an unusual endolysin with an N-terminal enzymatically active domain and a C-terminal transmembrane domain. The catalytic domain of the endolysin belongs to the conserved protein family PHA02564 which has no recognizable sequence similarity to other known endolysin types. Turbidity reduction assays indicate that the Enc34 enzyme is active against peptidoglycan from a variety of Gram-negative bacteria including the opportunistic pathogen Pseudomonas aeruginosa PAO1. The crystal structure of the catalytic domain of the Enc34 endolysin shows a distinctive all-helical architecture that distantly resembles the α-lobe of the lysozyme fold. Conserved catalytically important residues suggest a shared evolutionary history between the Enc34 endolysin and GH73 and GH23 family glycoside hydrolases and propose a molecular signature for substrate cleavage for a large group of peptidoglycan-degrading enzymes.

  • Organizational Affiliation

    Latvian Biomedical Research and Study Centre, Ratsupites 1 k-1, Riga, 1067, Latvia.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
170Hafnia phage Enc34Mutation(s): 0 
Find proteins for H6WYJ5 (Hafnia phage Enc34)
Explore H6WYJ5 
Go to UniProtKB:  H6WYJ5
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupH6WYJ5
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.60 Å
  • R-Value Free: 0.209 
  • R-Value Work: 0.177 
  • R-Value Observed: 0.179 
  • Space Group: P 21 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 65.304α = 90
b = 128.993β = 90
c = 36.279γ = 90
Software Package:
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
Cootmodel building
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
Other privateLatviaSIA Mikrotikls scholarship for exact and medical sciences
Other governmentLatviaESF project

Revision History  (Full details and data files)

  • Version 1.0: 2021-11-17
    Type: Initial release
  • Version 2.0: 2022-02-09
    Type: Coordinate replacement
    Reason: Model completeness
    Changes: Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary
  • Version 2.1: 2022-06-01
    Changes: Database references
  • Version 2.2: 2024-05-01
    Changes: Data collection, Refinement description