9K4B
Cryo-EM structure of depolymerase S2-4 from Klebsiella phage K64-1
Summary for 9K4B
| Entry DOI | 10.2210/pdb9k4b/pdb |
| Related | 9K4A |
| EMDB information | 62052 |
| Descriptor | Depolymerase, capsule K1-specific (1 entity in total) |
| Functional Keywords | depolymerase, degradation of host capsule, antimicrobial protein |
| Biological source | Klebsiella phage K64-1 |
| Total number of polymer chains | 3 |
| Total formula weight | 302988.44 |
| Authors | |
| Primary citation | Zhao, R.,Du, T.,Ji, Y.,Ren, Z.,Jiang, S.,Ru, H.,Gu, J. Characterization of the phage Phi K64 depolymerase S2-4 and its therapeutic effect against K1 serotype Klebsiella pneumoniae. Microbiol Res, 307:128475-128475, 2026 Cited by PubMed Abstract: 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 ΦK64 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 µg 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. PubMed: 41702136DOI: 10.1016/j.micres.2026.128475 PDB entries with the same primary citation |
| Experimental method | ELECTRON MICROSCOPY (2.18 Å) |
Structure validation
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