5NM7

Crystal structure of Burkholderia AP3 phage endolysin

Summary for 5NM7

• Entry DOI: 10.2210/pdb5nm7/pdb
• Descriptor: Peptidoglycan-binding domain 1, GLYCINE, TRIETHYLENE GLYCOL, ... (4 entities in total)
• Functional Keywords: peptidoglycan binding domain, lysozyme family, hydrolase
• Biological source: Burkholderia
• Total number of polymer chains: 2
• Total formula weight: 58501.50

Authors

Zrubek, K.,Wisniewska, M.,Rembacz, K.,Maciejewska, B.,Drulis-Kawa, Z.,Dubin, G. (deposition date: 2017-04-05, release date: 2018-02-14, Last modification date: 2024-05-08)

Primary citation

Maciejewska, B.,Zrubek, K.,Espaillat, A.,Wisniewska, M.,Rembacz, K.P.,Cava, F.,Dubin, G.,Drulis-Kawa, Z.
Modular endolysin of Burkholderia AP3 phage has the largest lysozyme-like catalytic subunit discovered to date and no catalytic aspartate residue.
Sci Rep, 7:14501-14501, 2017

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.

PubMed: 29109551
DOI: 10.1038/s41598-017-14797-9

Experimental method

X-RAY DIFFRACTION (1.72 Å)