Open AccessStructural insight into β-Clamp and its interaction with DNA Ligase in Helicobacter pylori
Author(s) -
Preeti Pandey,
K.F. Tarique,
Mohit Mazumder,
S.A. Abdul Rehman,
Nilima Kumari,
S. Gourinath
Publication year - 2016
Publication title -
scientific reports
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 1.24
H-Index - 213
ISSN - 2045-2322
DOI - 10.1038/srep31181
Subject(s) - dna ligase , dna clamp , dna polymerase , biology , dna replication , clamp , dna , dna repair , dna polymerase delta , protein subunit , dna polymerase ii , microbiology and biotechnology , biochemistry , polymerase chain reaction , gene , mechanical engineering , reverse transcriptase , clamping , engineering
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.