9K4A image
Deposition Date 2024-10-21
Release Date 2026-03-25
Last Version Date 2026-03-25
Entry Detail
PDB ID:
9K4A
Title:
Cryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1
Biological Source:
Source Organism(s):
Expression System(s):
Method Details:
Experimental Method:
Resolution:
2.24 Å
Aggregation State:
PARTICLE
Reconstruction Method:
SINGLE PARTICLE
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Depolymerase, capsule K1-spec
Chain IDs:A, B, C
Chain Length:922
Number of Molecules:3
Biological Source:Klebsiella phage K64-1
Ligand Molecules
Primary Citation
Characterization of the phage Phi K64 depolymerase S2-4 and its therapeutic effect against K1 serotype Klebsiella pneumoniae.
Microbiol Res 307 128475 128475 (2026)
PMID: 41702136 DOI: 10.1016/j.micres.2026.128475

Abstact

The infection rate and drug resistance of Klebsiella pneumoniae containing capsular polysaccharides (CPSs) have been increasing annually, resulting in severe human and animal infections. Depolymerases derived from bacteriophages can degrade CPSs and thus hold potential for treating bacterial infections. However, little is known about the mechanism by which K. pneumoniae phage depolymerases hydrolyze CPSs. In this study, the S2-4 encoded by the phage PhiK64 was identified as a potent depolymerase against K1 serotype Klebsiella CPSs. Cryo-electron microscopy structural analysis revealed that S2-4 forms a homotrimer with a spindle-like structure comprising a particle-binding domain, a core receptor-binding domain, an insertion domain, and a C-terminal domain. The results of structural assays suggest that S2-4 possesses multiple catalytic centers, which may contribute to its potent depolymerase activity. S2-4 inhibited K. pneumoniae biofilm formation, disrupted preformed biofilms, and enhanced macrophage adhesion and phagocytosis in depolymerase-treated bacteria. In a murine model, a single dose of 5 microg of S2-4 provided full protection against bacterial infection, underscoring the potent depolymerase activity of S2-4. These results indicate that S2-4 is a potent depolymerase against K1 serotype Klebsiella CPSs and has the potential to be a promising candidate for the clinical control of K. pneumoniae infections.

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Primary Citation of related structures
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