The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation
- Published
- Accepted
- Subject Areas
- Biochemistry, Biophysics, Computational Biology, Molecular Biology
- Keywords
- E. coli, Multisubunit enzyme complex, Molecular modeling, Domain interactions, DNA restriction enzymes
- Copyright
- © 2017 Bialevich et al.
- Licence
- This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ Preprints) and either DOI or URL of the article must be cited.
- Cite this article
- 2017. The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation. PeerJ Preprints 5:e2680v1 https://doi.org/10.7287/peerj.preprints.2680v1
Abstract
Type I restriction-modification enzymes are multisubunit, multifunctional molecular machines that recognize specific DNA target sequences, and their multisubunit organization underlies their multifunctionality. EcoR124I is the archetype of Type I restriction-modification family IC and is composed of three subunit types, HsdS, HsdM, and HsdR. DNA cleavage and ATP-dependent DNA translocation activities are housed in the distinct domains of the endonuclease/motor subunit HsdR. Because the multiple functions are integrated in this large subunit of 1038 residues, a large number of interdomain contacts might be expected. The crystal structure of EcoR124I HsdR reveals a surprisingly sparse number of contacts between helicase domain 2 and the C-terminal helical domain that is thought to be involved in assembly with HsdM. Only two potential hydrogen-bonding contacts are found in a very small contact region. In the present work, the relevance of these two potential hydrogen-bonding interactions for the multiple activities of EcoR124I is evaluated by analysing mutant enzymes using in vivo and in vitro experiments. Molecular dynamics simulations are employed to provide structural interpretation of the functional data. The results indicate that the helical C-terminal domain is involved in the DNA translocation, cleavage, and ATPase activities of HsdR, and a role in controlling those activities is suggested.
Author Comment
This is a submission to PeerJ for review.
Supplemental Information
Structural models of WT and mutants in PDB format
The file contains the pdb files of all created models of EcoR124I HsdR, WT as well as of each mutant. All initial models used for molecular dynamics and the final equilibrated structure after molecular dynamics are included for each structure.