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Csefalvay E, Lapkouski M, Guzanova A, Csefalvay L, Baikova T, Shevelev I, Bialevich V, Shamayeva K, Janscak P, Kuta Smatanova I, Panjikar S, Carey J, Weiserova M, Ettrich R. Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme. PLoS One 2015; 10:e0128700. [PMID: 26039067 PMCID: PMC4454674 DOI: 10.1371/journal.pone.0128700] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Accepted: 04/29/2015] [Indexed: 11/20/2022] Open
Abstract
Type I restriction-modification enzymes are multifunctional heteromeric complexes with DNA cleavage and ATP-dependent DNA translocation activities located on motor subunit HsdR. Functional coupling of DNA cleavage and translocation is a hallmark of the Type I restriction systems that is consistent with their proposed role in horizontal gene transfer. DNA cleavage occurs at nonspecific sites distant from the cognate recognition sequence, apparently triggered by stalled translocation. The X-ray crystal structure of the complete HsdR subunit from E. coli plasmid R124 suggested that the triggering mechanism involves interdomain contacts mediated by ATP. In the present work, in vivo and in vitro activity assays and crystal structures of three mutants of EcoR124I HsdR designed to probe this mechanism are reported. The results indicate that interdomain engagement via ATP is indeed responsible for signal transmission between the endonuclease and helicase domains of the motor subunit. A previously identified sequence motif that is shared by the RecB nucleases and some Type I endonucleases is implicated in signaling.
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Affiliation(s)
- Eva Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Mikalai Lapkouski
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Alena Guzanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Ladislav Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
| | - Tatsiana Baikova
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, 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
| | - Igor Shevelev
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Vitali Bialevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, 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
| | - Katsiaryna Shamayeva
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, 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
| | - Pavel Janscak
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
- Institute of Molecular Cancer Research, University of Zürich, Wintherthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Ivana Kuta Smatanova
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, 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
| | - Santosh Panjikar
- Australian Synchrotron, 800 Blackburn Road, Clayton VIC 3168, Australia
- Department of Biochemistry and Molecular Biology, Monash University, Clayton Campus, Melbourne, VIC 3800 Australia
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, Academy of Sciences of the Czech Republic, Zamek 136, CZ-373 33 Nove Hrady, Czech Republic
- Chemistry Department, Princeton University, Princeton, New Jersey 08544–1009, United States of America
| | - Marie Weiserova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Vídeňská 1083, 142 20 Praha 4, Czech Republic
| | - Rüdiger Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology and Global Change Research Center, 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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Loenen WAM, Dryden DTF, Raleigh EA, Wilson GG. Type I restriction enzymes and their relatives. Nucleic Acids Res 2014; 42:20-44. [PMID: 24068554 PMCID: PMC3874165 DOI: 10.1093/nar/gkt847] [Citation(s) in RCA: 175] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2013] [Revised: 08/26/2013] [Accepted: 08/29/2013] [Indexed: 12/24/2022] Open
Abstract
Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we discuss aspects of the biochemistry, biology and regulation of Type I REases, and of the mechanisms that bacteriophages and plasmids have evolved to evade them. Type I REases have a remarkable ability to change sequence specificity by domain shuffling and rearrangements. We summarize the classic experiments and observations that led to this discovery, and we discuss how this ability depends on the modular organizations of the enzymes and of their S subunits. Finally, we describe examples of Type II restriction-modification systems that have features in common with Type I enzymes, with emphasis on the varied Type IIG enzymes.
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Affiliation(s)
- Wil A. M. Loenen
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - David T. F. Dryden
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Elisabeth A. Raleigh
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
| | - Geoffrey G. Wilson
- Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands, EastChem School of Chemistry, University of Edinburgh, West Mains Road, Edinburgh EH9, 3JJ, Scotland, UK and New England Biolabs Inc., 240 County Road Ipswich, MA 01938-2723, USA
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Uyen NT, Nishi K, Park SY, Choi JW, Lee HJ, Kim JS. Crystallization and preliminary X-ray diffraction analysis of the HsdR subunit of a putative type I restriction enzyme from Vibrio vulnificus YJ016. Acta Crystallogr Sect F Struct Biol Cryst Commun 2008; 64:926-928. [PMID: 18931437 PMCID: PMC2564879 DOI: 10.1107/s1744309108027516] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2008] [Accepted: 08/27/2008] [Indexed: 05/26/2023]
Abstract
Type I restriction enzymes are multimeric proteins that consist of three subunits. The HsdS and HsdM subunits form a complex protein that shows methyltransferase activity, while the HsdR subunit functions as an endonuclease as well as as a translocase. Of these three subunits, no structural information on the HsdR subunit is yet available. The putative HsdR gene from Vibrio vulnificus YJ016 (HsdR_Vv) was cloned and expressed and the expressed protein HsdR_Vv was purified. HsdR_Vv was crystallized from 8%(w/v) polyethylene glycol 3350, 0.15 M ammonium chloride, 0.1 M HEPES pH 7.5 and 2 mM beta-mercaptoethanol. Diffraction data were collected to 2.60 A resolution using synchrotron radiation. The crystal belongs to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 71.01, b = 89.04, c = 113.66 A. With one HsdR_Vv molecule in the asymmetric unit, the Matthews coefficient was 2.14 A(3) Da(-1) and the solvent content was 42%.
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Affiliation(s)
- Nguyen To Uyen
- Interdisciplinary Graduate Program in Molecular Medicine, Gwangju 501-746, Republic of Korea
- Institute of Molecular Science, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Kosuke Nishi
- Institute of Molecular Science, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Suk-Youl Park
- Institute of Molecular Science, Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Ji-Woo Choi
- Institute of Molecular Science, Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Hyun-Ju Lee
- Institute of Molecular Science, Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
| | - Jeong-Sun Kim
- Interdisciplinary Graduate Program in Molecular Medicine, Gwangju 501-746, Republic of Korea
- Institute of Molecular Science, Chonnam National University, Gwangju 500-757, Republic of Korea
- Department of Chemistry and Institute of Basic Sciences, Chonnam National University, Gwangju 500-757, Republic of Korea
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