24UU

Crystal structure of Endonuclease IV from Chlamydophila pneumoniae

Summary for 24UU

• Entry DOI: 10.2210/pdb24uu/pdb
• Descriptor: Probable endonuclease 4, ZINC ION, MAGNESIUM ION, ... (10 entities in total)
• Functional Keywords: endonuclease iv, hydrolase
• Biological source: Chlamydia pneumoniae
• Total number of polymer chains: 2
• Total formula weight: 64559.89

Authors

Jin, J.L.,Zhang, Y.T.,Gao, W. (deposition date: 2026-03-22, release date: 2026-06-03)

Primary citation

Jin, J.,Zhang, Y.,Guo, S.,Yang, L.,Liu, H.,Liu, L.,Gao, W.
Crystal Structure and Activity Analysis of Chlamydophila pneumoniae AP Endonuclease IV.
Biomolecules, 16:-, 2026

PubMed Abstract: DNA damage requires repair via the endonuclease IV-mediated base excision repair (BER) pathway, which corrects apurinic/apyrimidinic (AP) sites. AP endonuclease IV (CpEndoIV), the sole AP endonuclease in this pathogen, is crucial for genomic integrity. As humans lack a homologous protein, it represents a potential therapeutic target. In this study, we report the first crystal structure of CpEndoIV at 1.97 Å resolution. The structure reveals two Zn, one Mg, and a malonate molecule bound in the active site, marking the first observation of Mg coordination in the EndoIV family. Compared to the three-Zn model with a narrow, deep pocket for precise AP-site cleavage, the Zn/Mg-bound state has a wider, shallower pocket that might promote diverse catalytic activities. Combined with enzymatic assays, we suggest that the mixed Zn/Mg model is better adapted for CpEndoIV to operate under host oxidative stress. Malonate binds to the metal ions, occupying the positions normally coordinated by water molecules. This binding mode may mimic the coordination of the substrate to the metal ions, and the protein conformation resembles that of the enzyme upon substrate binding at the active site. This study provides a structural basis for the functional characterization of CpEndoIV and offers a reference for the development of targeted inhibitors against diseases caused by .

PubMed: 42072715
DOI: 10.3390/biom16040594

Experimental method

X-RAY DIFFRACTION (1.97 Å)