Database of articles cited by EMDB/PDB/SASBDB data

Keywords
Structure methods	All X-ray diffraction NMR electron microscopy small angle scattering neutron diffraction fiber diffraction powder diffraction infrared spectroscopy EPR fluorescence transfer theoretical model Hybrid
Author
Journal
IF	>30 >20 >10 >5 all

Title	Structural biology and functional features of phage-derived depolymerase Depo32 on with K2 serotype capsular polysaccharides.
Journal, issue, pages	Microbiol Spectr, Vol. 11, Issue 5, Page e0530422, Year 2023
Publish date	Sep 26, 2023
Authors	Ruopeng Cai / Zhuolu Ren / Rihong Zhao / Yan Lu / Xinwu Wang / Zhimin Guo / Jinming Song / Wentao Xiang / Rui Du / Xiaokang Zhang / Wenyu Han / Heng Ru / Jingmin Gu /
PubMed Abstract	Hypervirulent with capsular polysaccharides (CPSs) causes severe nosocomial- and community-acquired infections. Phage-derived depolymerases can degrade CPSs from to attenuate bacterial virulence, ...Hypervirulent with capsular polysaccharides (CPSs) causes severe nosocomial- and community-acquired infections. Phage-derived depolymerases can degrade CPSs from to attenuate bacterial virulence, but their antimicrobial mechanisms and clinical potential are not well understood. In the present study, phage GH-K3-derived depolymerase Depo32 (encoded by gene ) was identified to exhibit high efficiency in specifically degrading the CPSs of K2 serotype . The cryo-electron microscopy structure of trimeric Depo32 at a resolution up to 2.32 Å revealed potential catalytic centers in the cleft of each of the two adjacent subunits. subjected to Depo32 became more sensitive to phagocytosis by RAW264.7 cells and activated the cells by the mitogen-activated protein kinase signaling pathway. In addition, intranasal inoculation with Depo32 (a single dose of 200 µg, 20 µg daily for 3 days, or in combination with gentamicin) rescued all C57BL/6J mice infected with a lethal dose of K7 without interference from its neutralizing antibody. In summary, this work elaborates on the mechanism by which Depo32 targets the degradation of K2 serotype CPSs and its potential as an antivirulence agent. IMPORTANCE Depolymerases specific to more than 20 serotypes of spp. have been identified, but most studies only evaluated the single-dose treatment of depolymerases with relatively simple clinical evaluation indices and did not reveal the anti-infection mechanism of these depolymerases in depth. On the basis of determining the biological characteristics, the structure of Depo32 was analyzed by cryo-electron microscopy, and the potential active center was further identified. In addition, the effects of Depo32 on macrophage phagocytosis, signaling pathway activation, and serum killing were revealed, and the efficacy of the depolymerase (single treatment, multiple treatments, or in combination with gentamicin) against acute pneumonia caused by was evaluated. Moreover, the roles of the active sites of Depo32 were also elucidated in the and studies. Therefore, through structural biology, cell biology, and experiments, this study demonstrated the mechanism by which Depo32 targets K2 serotype . infection.
External links	Microbiol Spectr / PubMed:37750730 / PubMed Central
Methods	EM (single particle)
Resolution	2.32 - 2.46 Å
Structure data	32215 7vyv EMDB-32215, PDB-7vyv: Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targets the K2 serotype K. pneumoniae Method: EM (single particle) / Resolution: 2.32 Å 32219 7vz3 EMDB-32219, PDB-7vz3: Cryo-EM structure of Depo32, a Klebsiella phage depolymerase targets the K2 serotype K. pneumoniae Method: EM (single particle) / Resolution: 2.46 Å
Source	Klebsiella phage 020009 (virus) klebsiella phage gh-k3 (virus)
Keywords	LYASE / Depolymerase / Klebsiella pneumoniae / K2 capsular type / Capsular polysaccharides / HYDROLASE