6L00

Crystal structure of the cell-wall binding domain (CBD) of endolysin LysIME-EF1

Summary for 6L00

• Entry DOI: 10.2210/pdb6l00/pdb
• Descriptor: Lysin (2 entities in total)
• Functional Keywords: lyase
• Biological source: Enterococcus phage IMEEF1
• Total number of polymer chains: 1
• Total formula weight: 8166.40

Authors

Ouyang, S.Y.,Zhen, X.K. (deposition date: 2019-09-25, release date: 2020-02-19, Last modification date: 2023-11-22)

Primary citation

Zhou, B.,Zhen, X.,Zhou, H.,Zhao, F.,Fan, C.,Perculija, V.,Tong, Y.,Mi, Z.,Ouyang, S.
Structural and functional insights into a novel two-component endolysin encoded by a single gene in Enterococcus faecalis phage.
Plos Pathog., 16:e1008394-e1008394, 2020

PubMed Abstract: Using bacteriophage-derived endolysins as an alternative strategy for fighting drug-resistant bacteria has recently been garnering renewed interest. However, their application is still hindered by their narrow spectra of activity. In our previous work, we demonstrated that the endolysin LysIME-EF1 possesses efficient bactericidal activity against multiple strains of Enterococcus faecalis (E. faecalis). Herein, we observed an 8 kDa fragment and hypothesized that it contributes to LysIME-EF1 lytic activity. To examine our hypothesis, we determined the structure of LysIME-EF1 at 1.75 Å resolution. LysIME-EF1 exhibits a unique architecture in which one full-length LysIME-EF1 forms a tetramer with three additional C-terminal cell-wall binding domains (CBDs) that correspond to the abovementioned 8 kDa fragment. Furthermore, we identified an internal ribosomal binding site (RBS) and alternative start codon within LysIME-EF1 gene, which are demonstrated to be responsible for the translation of the truncated CBD. To elucidate the molecular mechanism for the lytic activity of LysIME-EF1, we combined mutagenesis, lytic activity assays and in vivo animal infection experiments. The results confirmed that the additional LysIME-EF1 CBDs are important for LysIME-EF1 architecture and its lytic activity. To our knowledge, this is the first determined structure of multimeric endolysin encoded by a single gene in E. faecalis phages. As such, it may provide valuable insights into designing potent endolysins against the opportunistic pathogen E. faecalis.

PubMed: 32176738
DOI: 10.1371/journal.ppat.1008394

Experimental method

X-RAY DIFFRACTION (1.75 Å)