5NM7

Crystal structure of Burkholderia AP3 phage endolysin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history. 

Literature

Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue.

Maciejewska, B., Zrubek, K., Espaillat, A., Wisniewska, M., Rembacz, K.P., Cava, F., Dubin, G., Drulis-Kawa, Z.

(2017) Sci Rep 7: 14501-14501

  • DOI: 10.1038/s41598-017-14797-9

  • PubMed Abstract: 

    • Endolysins are peptidoglycan-degrading enzymes utilized by bacteriophages to release the progeny from bacterial cells. The lytic properties of phage endolysins make them potential antibacterial agents for medical and industrial applications. Here, we ...

    Endolysins are peptidoglycan-degrading enzymes utilized by bacteriophages to release the progeny from bacterial cells. The lytic properties of phage endolysins make them potential antibacterial agents for medical and industrial applications. Here, we present a comprehensive characterization of phage AP3 modular endolysin (AP3gp15) containing cell wall binding domain and an enzymatic domain (DUF3380 by BLASTP), both widespread and conservative. Our structural analysis demonstrates the low similarity of an enzymatic domain to known lysozymes and an unusual catalytic centre characterized by only a single glutamic acid residue and no aspartic acid. Thus, our findings suggest distinguishing a novel class of muralytic enzymes having the activity and catalytic centre organization of DUF3380. The lack of amino acid sequence homology between AP3gp15 and other known muralytic enzymes may reflect the evolutionary convergence of analogous glycosidases. Moreover, the broad antibacterial spectrum, lack of cytotoxic effect on human cells and the stability characteristics of AP3 endolysin advocate for its future application development.

    Organizational Affiliation: 

    Institute of Genetics and Microbiology, University of Wroclaw, Przybyszewskiego 63/77, 51-148, Wroclaw, Poland.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Peptidoglycan-binding domain 1
G, A
266Burkholderia phage vB_BceM_AP3Mutation(s): 0 
Find proteins for A0A1S5NV50 (Burkholderia phage vB_BceM_AP3)
Go to UniProtKB:  A0A1S5NV50
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GLY
Query on GLY
Download SDF File 
Download CCD File 
A, G
GLYCINE
C2 H5 N O2
DHMQDGOQFOQNFH-UHFFFAOYSA-N
 Ligand Interaction
PGE
Query on PGE
Download SDF File 
Download CCD File 
G
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.72 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.208 
  • Space Group: H 3 2
Unit Cell:
Length (Å)Angle (°)
a = 154.615α = 90.00
b = 154.615β = 90.00
c = 125.823γ = 120.00
Software Package:
Software NamePurpose
MOLREPphasing
REFMACrefinement
Aimlessdata scaling
iMOSFLMdata reduction

Structure Validation

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View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-02-14
    Type: Initial release