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Structural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori
Preeti Pandey1,2, Khaja Faisal Tarique1, Mohit Mazumder1
1School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.
Abstract:
Helicobacter pylori, a gram-negative and microaerophilic bacterium, is the major cause of chronic gastritis, gastric ulcers and gastric cancer. Owing to its central role, DNA replication machinery has emerged as a prime target for the development of antimicrobial drugs. Here, we report 2Å structure of β-clamp from H. pylori (Hpβ-clamp), which is one of the critical components of DNA polymerase III. Despite of similarity in the overall fold of eubacterial β-clamp structures, some distinct features in DNA interacting loops exists that have not been reported previously. The in silico prediction identified the potential binders of β-clamp such as alpha subunit of DNA pol III and DNA ligase with identification of β-clamp binding regions in them and validated by SPR studies. Hpβ-clamp interacts with DNA ligase in micromolar binding affinity. Moreover, we have successfully determined the co-crystal structure of β-clamp with peptide from DNA ligase (not reported earlier in prokaryotes) revealing the region from ligase that interacts with β-clamp.
Insights
Researchers determined the structure of Helicobacter pylori beta-clamp, a key DNA replication component. This finding reveals unique DNA-interacting regions and interactions with DNA ligase, offering new antimicrobial drug targets.
Area of Science:
- Microbiology
- Structural Biology
- Biochemistry
Background:
- Helicobacter pylori is a major cause of gastric diseases.
- Its DNA replication machinery is a target for antimicrobial drug development.
Purpose of the Study:
- To determine the structure of H. pylori beta-clamp (Hpβ-clamp).
- To identify potential Hpβ-clamp binding partners and their interaction regions.
Main Methods:
- X-ray crystallography to determine Hpβ-clamp structure at 2Å resolution.
- In silico prediction and Surface Plasmon Resonance (SPR) studies to identify and validate binding interactions.
- Co-crystallization of Hpβ-clamp with a DNA ligase peptide.
Main Results:
- The 2Å structure of Hpβ-clamp revealed distinct DNA-interacting loops compared to other eubacterial β-clamps.
- In silico analysis identified interactions with DNA polymerase III alpha subunit and DNA ligase.
- SPR studies confirmed micromolar binding affinity between Hpβ-clamp and DNA ligase.
- The co-crystal structure elucidated the specific interaction interface between Hpβ-clamp and DNA ligase peptide.
Conclusions:
- Hpβ-clamp possesses unique structural features potentially exploitable for drug design.
- The interaction with DNA ligase presents a novel target for developing H. pylori-specific antimicrobials.
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