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Bialevich V, Sinha D, Shamayeva K, Guzanova A, Řeha D, Csefalvay E, Carey J, Weiserova M, Ettrich RH. The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation. PeerJ 2017; 5:e2887. [PMID: 28133570 PMCID: PMC5248579 DOI: 10.7717/peerj.2887] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 12/08/2016] [Indexed: 01/20/2023] Open
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 1,038 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.
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Affiliation(s)
- Vitali Bialevich
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Dhiraj Sinha
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Katsiaryna Shamayeva
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
| | - Alena Guzanova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - David Řeha
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
| | - Eva Csefalvay
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
| | - Jannette Carey
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Chemistry Department, Princeton University, Princeton, NJ, United States
| | - Marie Weiserova
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Rüdiger H. Ettrich
- Center for Nanobiology and Structural Biology, Institute of Microbiology of the Academy of Sciences of the Czech Republic, Nove Hrady, Czech Republic
- Faculty of Sciences, University of South Bohemia in Ceske Budejovice, Nove Hrady, Czech Republic
- College of Medical Sciences, Nova Southeastern University, Fort Lauderdale, FL, United States
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2
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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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3
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Simons M, Diffin FM, Szczelkun MD. ClpXP protease targets long-lived DNA translocation states of a helicase-like motor to cause restriction alleviation. Nucleic Acids Res 2014; 42:12082-91. [PMID: 25260590 PMCID: PMC4231737 DOI: 10.1093/nar/gku851] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
We investigated how Escherichia coli ClpXP targets the helicase-nuclease (HsdR) subunit of the bacterial Type I restriction–modification enzyme EcoKI during restriction alleviation (RA). RA is a temporary reduction in endonuclease activity that occurs when Type I enzymes bind unmodified recognition sites on the host genome. These conditions arise upon acquisition of a new system by a naïve host, upon generation of new sites by genome rearrangement/mutation or during homologous recombination between hemimethylated DNA. Using recombinant DNA and proteins in vitro, we demonstrate that ClpXP targets EcoKI HsdR during dsDNA translocation on circular DNA but not on linear DNA. Protein roadblocks did not activate HsdR proteolysis. We suggest that DNA translocation lifetime, which is elevated on circular DNA relative to linear DNA, is important to RA. To identify the ClpX degradation tag (degron) in HsdR, we used bioinformatics and biochemical assays to design N- and C-terminal mutations that were analysed in vitro and in vivo. None of the mutants produced a phenotype consistent with loss of the degron, suggesting an as-yet-unidentified recognition pathway. We note that an EcoKI nuclease mutant still produces cell death in a clpx− strain, consistent with DNA damage induced by unregulated motor activity.
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Affiliation(s)
- Michelle Simons
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Fiona M Diffin
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark D Szczelkun
- DNA-Protein Interactions Unit, School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
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Simons M, Szczelkun MD. Recycling of protein subunits during DNA translocation and cleavage by Type I restriction-modification enzymes. Nucleic Acids Res 2011; 39:7656-66. [PMID: 21712244 PMCID: PMC3177213 DOI: 10.1093/nar/gkr479] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The Type I restriction-modification enzymes comprise three protein subunits; HsdS and HsdM that form a methyltransferase (MTase) and HsdR that associates with the MTase and catalyses Adenosine-5′-triphosphate (ATP)-dependent DNA translocation and cleavage. Here, we examine whether the MTase and HsdR components can ‘turnover’ in vitro, i.e. whether they can catalyse translocation and cleavage events on one DNA molecule, dissociate and then re-bind a second DNA molecule. Translocation termination by both EcoKI and EcoR124I leads to HsdR dissociation from linear DNA but not from circular DNA. Following DNA cleavage, the HsdR subunits appear unable to dissociate even though the DNA is linear, suggesting a tight interaction with the cleaved product. The MTases of EcoKI and EcoAI can dissociate from DNA following either translocation or cleavage and can initiate reactions on new DNA molecules as long as free HsdR molecules are available. In contrast, the MTase of EcoR124I does not turnover and additional cleavage of circular DNA is not observed by inclusion of RecBCD, a helicase–nuclease that degrades the linear DNA product resulting from Type I cleavage. Roles for Type I restriction endonuclease subunit dynamics in restriction alleviation in the cell are discussed.
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Affiliation(s)
- Michelle Simons
- School of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
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5
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Smith RM, Josephsen J, Szczelkun MD. The single polypeptide restriction-modification enzyme LlaGI is a self-contained molecular motor that translocates DNA loops. Nucleic Acids Res 2010; 37:7219-30. [PMID: 19783815 PMCID: PMC2790907 DOI: 10.1093/nar/gkp794] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
To cleave DNA, the single polypeptide restriction–modification enzyme LlaGI must communicate between a pair of indirectly repeated recognition sites. We demonstrate that this communication occurs by a 1-dimensional route, namely unidirectional dsDNA loop translocation rightward of the specific recognition sequence 5′-CTnGAyG-3′ as written (where n is either A, G, C or T and y is either C or T). Motion across thousands of base pairs is catalysed by the helicase domain and requires the hydrolysis of 1.5-2 ATP per base pair. DNA loop extrusion is accompanied by changes in DNA twist consistent with the motor following the helical pitch of the polynucleotide track. LlaGI is therefore an example of a polypeptide that is a completely self-contained, multi-functional molecular machine.
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Affiliation(s)
- Rachel M Smith
- DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, Bristol, BS8 1TD, UK
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Ishikawa K, Handa N, Kobayashi I. Cleavage of a model DNA replication fork by a Type I restriction endonuclease. Nucleic Acids Res 2009; 37:3531-44. [PMID: 19357093 PMCID: PMC2699502 DOI: 10.1093/nar/gkp214] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Cleavage of a DNA replication fork leads to fork restoration by recombination repair. In prokaryote cells carrying restriction-modification systems, fork passage reduces genome methylation by the modification enzyme and exposes the chromosome to attack by the restriction enzyme. Various observations have suggested a relationship between the fork and Type I restriction enzymes, which cleave DNA at a distance from a recognition sequence. Here, we demonstrate that a Type I restriction enzyme preparation cleaves a model replication fork at its branch. The enzyme probably tracks along the DNA from an unmethylated recognition site on the daughter DNA and cuts the fork upon encountering the branch point. Our finding suggests that these restriction-modification systems contribute to genome maintenance through cell death and indicates that DNA replication fork cleavage represents a critical point in genome maintenance to choose between the restoration pathway and the destruction pathway.
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Affiliation(s)
- Ken Ishikawa
- Graduate Program in Biophysics and Biochemistry, Graduate School of Science, University of Tokyo, Tokyo 108-8639, Japan
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7
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Sisáková E, Weiserová M, Dekker C, Seidel R, Szczelkun MD. The interrelationship of helicase and nuclease domains during DNA translocation by the molecular motor EcoR124I. J Mol Biol 2008; 384:1273-86. [PMID: 18952104 PMCID: PMC2602864 DOI: 10.1016/j.jmb.2008.10.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2008] [Revised: 10/02/2008] [Accepted: 10/02/2008] [Indexed: 11/25/2022]
Abstract
The type I restriction–modification enzyme EcoR124I comprises three subunits with the stoichiometry HsdR2/HsdM2/HsdS1. The HsdR subunits are archetypical examples of the fusion between nuclease and helicase domains into a single polypeptide, a linkage that is found in a great many other DNA processing enzymes. To explore the interrelationship between these physically linked domains, we examined the DNA translocation properties of EcoR124I complexes in which the HsdR subunits had been mutated in the RecB-like nuclease motif II or III. We found that nuclease mutations can have multiple effects on DNA translocation despite being distinct from the helicase domain. In addition to reductions in DNA cleavage activity, we also observed decreased translocation and ATPase rates, different enzyme populations with different characteristic translocation rates, a tendency to stall during initiation and altered HsdR turnover dynamics. The significance of these observations to our understanding of domain interactions in molecular machines is discussed.
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Affiliation(s)
- Eva Sisáková
- Institute of Microbiology, v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic
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8
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EcoR124I: from plasmid-encoded restriction-modification system to nanodevice. Microbiol Mol Biol Rev 2008; 72:365-77, table of contents. [PMID: 18535150 DOI: 10.1128/mmbr.00043-07] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
SUMMARY Plasmid R124 was first described in 1972 as being a new member of incompatibility group IncFIV, yet early physical investigations of plasmid DNA showed that this type of classification was more complex than first imagined. Throughout the history of the study of this plasmid, there have been many unexpected observations. Therefore, in this review, we describe the history of our understanding of this plasmid and the type I restriction-modification (R-M) system that it encodes, which will allow an opportunity to correct errors, or misunderstandings, that have arisen in the literature. We also describe the characterization of the R-M enzyme EcoR124I and describe the unusual properties of both type I R-M enzymes and EcoR124I in particular. As we approached the 21st century, we began to see the potential of the EcoR124I R-M enzyme as a useful molecular motor, and this leads to a description of recent work that has shown that the R-M enzyme can be used as a nanoactuator. Therefore, this is a history that takes us from a plasmid isolated from (presumably) an infected source to the potential use of the plasmid-encoded R-M enzyme in bionanotechnology.
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Šišáková E, Stanley LK, Weiserová M, Szczelkun MD. A RecB-family nuclease motif in the Type I restriction endonuclease EcoR124I. Nucleic Acids Res 2008; 36:3939-49. [PMID: 18511464 PMCID: PMC2475608 DOI: 10.1093/nar/gkn333] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2008] [Revised: 04/30/2008] [Accepted: 05/08/2008] [Indexed: 12/03/2022] Open
Abstract
The Type I restriction-modification enzyme EcoR124I is an ATP-dependent endonuclease that uses dsDNA translocation to locate and cleave distant non-specific DNA sites. Bioinformatic analysis of the HsdR subunits of EcoR124I and related Type I enzymes showed that in addition to the principal PD-(E/D)xK Motifs, I, II and III, a QxxxY motif is also present that is characteristic of RecB-family nucleases. The QxxxY motif resides immediately C-terminal to Motif III within a region of predicted alpha-helix. Using mutagenesis, we examined the role of the Q and Y residues in DNA binding, translocation and cleavage. Roles for the QxxxY motif in coordinating the catalytic residues or in stabilizing the nuclease domain on the DNA are discussed.
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Affiliation(s)
- Eva Šišáková
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic and DNA-Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Louise K. Stanley
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic and DNA-Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Marie Weiserová
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic and DNA-Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
| | - Mark D. Szczelkun
- Institute of Microbiology v.v.i., Academy of Sciences of the Czech Republic, Prague, Czech Republic and DNA-Protein Interactions Unit, Department of Biochemistry, University of Bristol, Bristol, BS8 1TD, UK
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Seidel R, Bloom JGP, Dekker C, Szczelkun MD. Motor step size and ATP coupling efficiency of the dsDNA translocase EcoR124I. EMBO J 2008; 27:1388-98. [PMID: 18388857 PMCID: PMC2291450 DOI: 10.1038/emboj.2008.69] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Accepted: 03/03/2008] [Indexed: 11/30/2022] Open
Abstract
The Type I restriction-modification enzyme EcoR124I is an archetypical helicase-based dsDNA translocase that moves unidirectionally along the 3′–5′ strand of intact duplex DNA. Using a combination of ensemble and single-molecule measurements, we provide estimates of two physicochemical constants that are fundamental to a full description of motor protein activity—the ATP coupling efficiency (the number of ATP consumed per base pair) and the step size (the number of base pairs transported per motor step). Our data indicate that EcoR124I makes small steps along the DNA of 1 bp in length with 1 ATP consumed per step, but with some uncoupling of the ATPase and translocase cycles occurring so that the average number of ATP consumed per base pair slightly exceeds unity. Our observations form a framework for understanding energy coupling in a great many other motors that translocate along dsDNA rather than ssDNA.
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Affiliation(s)
- Ralf Seidel
- Kavli Institute of Nanoscience, Delft University of Technology, Delft, The Netherlands
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