4RKI

Crystal structure of sliding beta clamp from Helicobacter pylori

Summary for 4RKI

• Entry DOI: 10.2210/pdb4rki/pdb
• Descriptor: DNA polymerase III subunit beta (2 entities in total)
• Functional Keywords: processivity promoting factor, transferase
• Biological source: Helicobacter pylori 26695
• Cellular location: Cytoplasm : O25242
• Total number of polymer chains: 1
• Total formula weight: 43309.58

Authors

Satyawali, P.,Tarique, K.F.,Abdul Rehman, S.A.,Gourinath, S. (deposition date: 2014-10-13, release date: 2016-01-13, Last modification date: 2023-09-20)

Primary citation

Pandey, P.,Tarique, K.F.,Mazumder, M.,Rehman, S.A.,Kumari, N.,Gourinath, S.
Structural insight into beta-Clamp and its interaction with DNA Ligase in Helicobacter pylori.
Sci Rep, 6:31181-31181, 2016

PubMed 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.

PubMed: 27499105
DOI: 10.1038/srep31181

Experimental method

X-RAY DIFFRACTION (2.05 Å)