8X8M

Cryo-EM structure of a bacteriophage tail- spike protein against Klebsiella pneumoniae K64,ORF41(K64-ORF41)

これはPDB形式変換不可エントリーです。

8X8M の概要

• エントリーDOI: 10.2210/pdb8x8m/pdb
• EMDBエントリー: 38149
• 分子名称: Probable tail spike protein (1 entity in total)
• 機能のキーワード: k64-orf41, depolymerase, cryo-em, klebsiella pneumoniae k64, capsule polysaccharide, lyase
• 由来する生物種: Klebsiella phage SH-Kp 152410
• タンパク質・核酸の鎖数: 3
• 化学式量合計: 336754.50

構造登録者

Xie, Y.,Huang, T.,Zhang, Z.,Tao, X. (登録日: 2023-11-27, 公開日: 2024-09-04, 最終更新日: 2025-06-25)

主引用文献

Huang, T.,Zhang, Z.,Tao, X.,Shi, X.,Lin, P.,Liao, D.,Ma, C.,Cai, X.,Lin, W.,Jiang, X.,Luo, P.,Wu, S.,Xie, Y.
Structural and functional basis of bacteriophage K64-ORF41 depolymerase for capsular polysaccharide degradation of Klebsiella pneumoniae K64.
Int.J.Biol.Macromol., 265:130917-130917, 2024

PubMed Abstract: Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using phage-derived depolymerases to degrade the capsular polysaccharide and expose and sensitize the bacteria to the host immune system. Here we determined the cryo-electron microscopy (cryo-EM) structures of a bacteriophage tail-spike protein against K. pneumoniae K64, ORF41 (K64-ORF41) and ORF41 in EDTA condition (K64-ORF41), at 2.37 Å and 2.50 Å resolution, respectively, for the first time. K64-ORF41 exists as a trimer and each protomer contains a β-helix domain including a right-handed parallel β-sheet helix fold capped at both ends, an insertion domain, and one β-sheet jellyroll domain. Moreover, our structural comparison with other depolymerases of K. pneumoniae suggests that the catalytic residues (Tyr528, His574 and Arg628) are highly conserved although the substrate of capsule polysaccharide is variable. Besides that, we figured out the important residues involved in the substrate binding pocket including Arg405, Tyr526, Trp550 and Phe669. This study establishes the structural and functional basis for the promising phage-derived broad-spectrum activity depolymerase therapeutics and effective CPS-degrading agents for the treatment of carbapenem-resistant K. pneumoniae K64 infections.

PubMed: 38513899
DOI: 10.1016/j.ijbiomac.2024.130917

実験手法

ELECTRON MICROSCOPY (2.37 Å)