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A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I
D. Sinha, V. Bialevich, K. Shamayeva, A. Guzanova, A. Sisakova, E. Csefalvay, D. Reha, L. Krejci, J. Carey, M. Weiserova, R. Ettrich,
Language English Country Germany
Document type Journal Article
- MeSH
- Adenosine Triphosphate chemistry MeSH
- Enzyme Activation MeSH
- Principal Component Analysis MeSH
- DNA Helicases chemistry genetics metabolism MeSH
- Hydrolysis MeSH
- Protein Interaction Domains and Motifs * MeSH
- Protein Conformation MeSH
- Multienzyme Complexes chemistry MeSH
- Mutation MeSH
- Protein Subunits chemistry genetics metabolism MeSH
- Deoxyribonucleases, Type I Site-Specific chemistry genetics metabolism MeSH
- Amino Acid Sequence MeSH
- Molecular Dynamics Simulation MeSH
- Publication type
- Journal Article MeSH
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.
References provided by Crossref.org
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- $a Sinha, Dhiraj $u Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic.
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- $a A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I / $c D. Sinha, V. Bialevich, K. Shamayeva, A. Guzanova, A. Sisakova, E. Csefalvay, D. Reha, L. Krejci, J. Carey, M. Weiserova, R. Ettrich,
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- $a 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.
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- $a Guzanova, Alena $u Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4, Czech Republic.
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- $a Reha, David $u Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic. Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic.
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- $a Krejci, Lumir $u Department of Biology, Faculty of Medicine, Masaryk University, Brno, Kamenice 5/A7, 625 00, Brno, Czech Republic. National Centre for Biomolecular Research, Masaryk University, Kamenice 5/A4, 625 00, Brno, Czech Republic. International Clinical Research Center, Center for Biomolecular and Cellular Engineering, St. Anne's University Hospital Brno, Brno, Czech Republic.
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- $a Carey, Jannette $u Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic. Chemistry Department, Princeton University, Princeton, NJ, 08544-1009, USA.
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- $a Weiserova, Marie $u Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20, Praha 4, Czech Republic.
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- $a Ettrich, Rüdiger $u Center for Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33, Nove Hrady, Czech Republic. ettrich@nh.cas.cz. College of Biomedical Sciences, Larkin University, 18301 North Miami Avenue, Miami, FL, 33169, USA. ettrich@nh.cas.cz.
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