A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I

Dhiraj Sinha, Vitali Bialevich, Katsiaryna Shamayeva, Alena Guzanova, Alexandra Sisakova, Eva Csefalvay, David Reha, Lumir Krejci, Jannette Carey, Marie Weiserova, Rüdiger Ettrich

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Abstract

Type I restriction-modification enzymes differ significantly from the type II enzymes commonly used as molecular biology reagents. On hemi-methylated DNAs type I enzymes like the EcoR124I restriction-modification complex act as conventional adenine methylases at their specific target sequences, but unmethylated targets induce them to translocate thousands of base pairs through the stationary enzyme before cleaving distant sites nonspecifically. EcoR124I is a superfamily 2 DEAD-box helicase like eukaryotic double-strand DNA translocase Rad54, with two RecA-like helicase domains and seven characteristic sequence motifs that are implicated in translocation. In Rad54 a so-called extended region adjacent to motif III is involved in ATPase activity. Although the EcoR124I extended region bears sequence and structural similarities with Rad54, it does not influence ATPase or restriction activity as shown in this work, but mutagenesis of the conserved glycine residue of its motif III does alter ATPase and DNA cleavage activity. Through the lens of molecular dynamics, a full model of HsdR of EcoR124I based on available crystal structures allowed interpretation of functional effects of mutants in motif III and its extended region. The results indicate that the conserved glycine residue of motif III has a role in positioning the two helicase domains.

Original languageEnglish (US)
Article number176
JournalJournal of Molecular Modeling
Volume24
Issue number7
DOIs
StatePublished - Jul 1 2018

All Science Journal Classification (ASJC) codes

  • Catalysis
  • Computer Science Applications
  • Physical and Theoretical Chemistry
  • Organic Chemistry
  • Computational Theory and Mathematics
  • Inorganic Chemistry

Keywords

  • DNA restriction enzymes
  • Domain interactions
  • Molecular mechanics
  • Molecular modeling
  • Multisubunit enzyme complex
  • Principal components analysis

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    Sinha, D., Bialevich, V., Shamayeva, K., Guzanova, A., Sisakova, A., Csefalvay, E., Reha, D., Krejci, L., Carey, J., Weiserova, M., & Ettrich, R. (2018). A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I. Journal of Molecular Modeling, 24(7), [176]. https://doi.org/10.1007/s00894-018-3722-8