Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 58.50 kDa 
• Atom Count: 4207 
• Residue Count: 519 
• Unique protein chains: 1

5NM7

Crystal structure of Burkholderia AP3 phage endolysin

• DOI: 10.2210/pdb5NM7/pdb

• Classification: HYDROLASE
• Organism(s): Burkholderia
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-04-05 Released: 2018-02-14 
• Deposition Author(s): Zrubek, K., Wisniewska, M., Rembacz, K., Maciejewska, B., Drulis-Kawa, Z., Dubin, G.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.235 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 

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

• PubMed: 29109551 
• DOI: 10.1038/s41598-017-14797-9
• Structures With Same Primary Citation


• 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 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. [e-mail].

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Peptidoglycan-binding domain 1	A, G	266	Burkholderia	Mutation(s): 0  Gene Names: MYA_3986
Find proteins for A0A1S5NV50 (Burkholderia phage vB_BceM_AP3) Go to UniProtKB:  A0A1S5NV50

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PGE	G	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GLY	A, G	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.72 Å
• R-Value Free: 0.235 
• R-Value Work: 0.208 
• R-Value Observed: 0.210 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 154.615	α = 90
b = 154.615	β = 90
c = 125.823	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-04-05 
• Released Date: 2018-02-14 
Deposition Author(s): Zrubek, K., Wisniewska, M., Rembacz, K., Maciejewska, B., Drulis-Kawa, Z., Dubin, G.

Revision History 

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