1
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Horton NC, Lyumkis D. Structures, mechanisms, and kinetic advantages of the SgrAI filament forming mechanism. Crit Rev Biochem Mol Biol 2024:1-39. [PMID: 39699272 DOI: 10.1080/10409238.2024.2440315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/27/2024] [Revised: 12/04/2024] [Accepted: 12/06/2024] [Indexed: 12/20/2024]
Abstract
This review documents investigations leading to the unprecedented discovery of filamentation as a mode of enzyme regulation in the type II restriction endonuclease SgrAI. Filamentation is defined here as linear or helical polymerization of a single enzyme as occurs for SgrAI, and has now been shown to occur in many other enzyme systems, including conserved metabolic enzymes. In the case of SgrAI, filamentation activates the DNA cleavage rate by up to 1000-fold and also alters the enzyme's DNA sequence specificity. The investigations began with the observation that SgrAI cleaves two types of recognition sequences, primary and secondary, but cleaves the secondary sequences only when present on the same DNA as at least one primary. DNA cleavage rate measurements showed how the primary sequence is both a substrate and an allosteric effector of SgrAI. Biophysical measurements indicated that the activated form of SgrAI, stimulated by binding to the primary sequence, consisted of varied numbers of the SgrAI bound to DNA. Structural studies revealed the activated state of SgrAI as a left-handed helical filament which stabilizes an altered enzyme conformation, which binds a second divalent cation in the active site. Efforts to determine the mechanism of DNA sequence specificity alteration are ongoing and current models are discussed. Finally, global kinetic modeling of the filament mediated DNA cleavage reaction and simulations of in vivo activity suggest that the filament mechanism evolved to rapidly cleave invading DNA while protecting the Streptomyces host genome.
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Affiliation(s)
- Nancy C Horton
- Department of Molecular and Cellular Biology, University of Arizona, Tucson, Arizona, USA
| | - Dmitry Lyumkis
- The Salk Institute for Biological Studies, La Jolla, California, USA
- Department of Integrative Structural and Computational Biology, Scripps Research, La Jolla, California, USA
- Graduate School of Biological Sciences, Section of Molecular Biology, University of California San Diego, La Jolla, California, USA
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2
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Tamulaitiene G, Manakova E, Jovaisaite V, Tamulaitis G, Grazulis S, Bochtler M, Siksnys V. Unique mechanism of target recognition by PfoI restriction endonuclease of the CCGG-family. Nucleic Acids Res 2019; 47:997-1010. [PMID: 30445642 PMCID: PMC6344858 DOI: 10.1093/nar/gky1137] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/14/2018] [Accepted: 10/26/2018] [Indexed: 01/23/2023] Open
Abstract
Restriction endonucleases (REs) of the CCGG-family recognize a set of 4–8 bp target sequences that share a common CCGG or CCNGG core and possess PD…D/ExK nuclease fold. REs that interact with 5 bp sequence 5′-CCNGG flip the central N nucleotides and ‘compress’ the bound DNA to stack the inner base pairs to mimic the CCGG sequence. PfoI belongs to the CCGG-family and cleaves the 7 bp sequence 5′-T|CCNGGA ("|" designates cleavage position). We present here crystal structures of PfoI in free and DNA-bound forms that show unique active site arrangement and mechanism of sequence recognition. Structures and mutagenesis indicate that PfoI features a permuted E…ExD…K active site that differs from the consensus motif characteristic to other family members. Although PfoI also flips the central N nucleotides of the target sequence it does not ‘compress’ the bound DNA. Instead, PfoI induces a drastic change in DNA backbone conformation that shortens the distance between scissile phosphates to match that in the unperturbed CCGG sequence. Our data demonstrate the diversity and versatility of structural mechanisms employed by restriction enzymes for recognition of related DNA sequences.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Virginija Jovaisaite
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Grazulis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Matthias Bochtler
- Laboratory of Structural Biology, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland.,Dept. of Bioinformatics, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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3
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Shen BW, Doyle L, Bradley P, Heiter DF, Lunnen KD, Wilson GG, Stoddard BL. Structure, subunit organization and behavior of the asymmetric Type IIT restriction endonuclease BbvCI. Nucleic Acids Res 2019; 47:450-467. [PMID: 30395313 PMCID: PMC6326814 DOI: 10.1093/nar/gky1059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 08/28/2018] [Revised: 10/15/2018] [Accepted: 10/17/2018] [Indexed: 11/17/2022] Open
Abstract
BbvCI, a Type IIT restriction endonuclease, recognizes and cleaves the seven base pair sequence 5'-CCTCAGC-3', generating 3-base, 5'-overhangs. BbvCI is composed of two protein subunits, each containing one catalytic site. Either site can be inactivated by mutation resulting in enzyme variants that nick DNA in a strand-specific manner. Here we demonstrate that the holoenzyme is labile, with the R1 subunit dissociating at low pH. Crystallization of the R2 subunit under such conditions revealed an elongated dimer with the two catalytic sites located on opposite sides. Subsequent crystallization at physiological pH revealed a tetramer comprising two copies of each subunit, with a pair of deep clefts each containing two catalytic sites appropriately positioned and oriented for DNA cleavage. This domain organization was further validated with single-chain protein constructs in which the two enzyme subunits were tethered via peptide linkers of variable length. We were unable to crystallize a DNA-bound complex; however, structural similarity to previously crystallized restriction endonucleases facilitated creation of an energy-minimized model bound to DNA, and identification of candidate residues responsible for target recognition. Mutation of residues predicted to recognize the central C:G base pair resulted in an altered enzyme that recognizes and cleaves CCTNAGC (N = any base).
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Affiliation(s)
- Betty W Shen
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Lindsey Doyle
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Phil Bradley
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
| | - Daniel F Heiter
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | - Keith D Lunnen
- New England Biolabs, Inc., 240 County Road, Ipswich, MA 01938, USA
| | | | - Barry L Stoddard
- Division of Basic Sciences, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave. N., Seattle, WA 98109, USA
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4
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Tamulaitiene G, Jovaisaite V, Tamulaitis G, Songailiene I, Manakova E, Zaremba M, Grazulis S, Xu SY, Siksnys V. Restriction endonuclease AgeI is a monomer which dimerizes to cleave DNA. Nucleic Acids Res 2017; 45:3547-3558. [PMID: 28039325 PMCID: PMC5389614 DOI: 10.1093/nar/gkw1310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 09/22/2016] [Revised: 12/13/2016] [Accepted: 12/19/2016] [Indexed: 01/19/2023] Open
Abstract
Although all Type II restriction endonucleases catalyze phosphodiester bond hydrolysis within or close to their DNA target sites, they form different oligomeric assemblies ranging from monomers, dimers, tetramers to higher order oligomers to generate a double strand break in DNA. Type IIP restriction endonuclease AgeI recognizes a palindromic sequence 5΄-A/CCGGT-3΄ and cuts it ('/' denotes the cleavage site) producing staggered DNA ends. Here, we present crystal structures of AgeI in apo and DNA-bound forms. The structure of AgeI is similar to the restriction enzymes that share in their target sites a conserved CCGG tetranucleotide and a cleavage pattern. Structure analysis and biochemical data indicate, that AgeI is a monomer in the apo-form both in the crystal and in solution, however, it binds and cleaves the palindromic target site as a dimer. DNA cleavage mechanism of AgeI is novel among Type IIP restriction endonucleases.
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Affiliation(s)
- Giedre Tamulaitiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Virginija Jovaisaite
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Gintautas Tamulaitis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Inga Songailiene
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Elena Manakova
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Saulius Grazulis
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
| | - Shuang-yong Xu
- New England Biolabs, Inc. 240 County Road, Ipswich, MA 01938, USA
| | - Virginijus Siksnys
- Institute of Biotechnology, Vilnius University, Sauletekio al. 7, LT-10257 Vilnius, Lithuania
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5
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Tamulaitis G, Rutkauskas M, Zaremba M, Grazulis S, Tamulaitiene G, Siksnys V. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI. Nucleic Acids Res 2015; 43:8100-10. [PMID: 26240380 PMCID: PMC4652773 DOI: 10.1093/nar/gkv768] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 06/11/2015] [Accepted: 07/17/2015] [Indexed: 02/03/2023] Open
Abstract
Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5′-W/CCGGW-3′ (W stands for A or T, ‘/’ denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an ‘open’ configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes.
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Affiliation(s)
- Gintautas Tamulaitis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Marius Rutkauskas
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Mindaugas Zaremba
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Saulius Grazulis
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Giedre Tamulaitiene
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
| | - Virginijus Siksnys
- Department of Protein-DNA Interactions, Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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6
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Single molecular investigation of DNA looping and aggregation by restriction endonuclease BspMI. Sci Rep 2014; 4:5897. [PMID: 25077775 PMCID: PMC4116625 DOI: 10.1038/srep05897] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 04/28/2014] [Accepted: 07/15/2014] [Indexed: 11/09/2022] Open
Abstract
DNA looping and aggregation induced by restriction endonuclease BspMI are studied by atomic force microscopy (AFM) and magnetic tweezers (MT). With Ca(2+) substituted for the normal enzyme cofactor Mg(2+) and enzyme concentration below the critical concentration of 6 units/mL, AFM images of DNA-BspMI complex show that the number of binding and looping events increases with enzyme concentration. At the critical concentration 6 of units/mL, all the BspMI binding sites are saturated. It is worth noting that nonspecific BspMI binding to DNA at saturation concentration represents more than 8% of the total BspMI-DNA complexes directly observed in AFM images. Furthermore, we used MT to prove that additional loops can form when enzyme concentration is higher than its saturation valueand the complex is incubated for a long time (>2 hrs). We ascribe this phenomenon to the aggregation of enzymes. The force spectroscopy of the BspMI-DNA complex shows that the pulling force required to open the loop of the complex at less than saturation concentration has a peak at about 3 pN, which is lower than the force required to open additional loops due to enzyme aggregation at higher than saturation concentration (>6 pN).
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7
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Pingoud A, Wilson GG, Wende W. Type II restriction endonucleases--a historical perspective and more. Nucleic Acids Res 2014; 42:7489-527. [PMID: 24878924 PMCID: PMC4081073 DOI: 10.1093/nar/gku447] [Citation(s) in RCA: 175] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/07/2014] [Revised: 05/02/2014] [Accepted: 05/07/2014] [Indexed: 12/17/2022] Open
Abstract
This article continues the series of Surveys and Summaries on restriction endonucleases (REases) begun this year in Nucleic Acids Research. Here we discuss 'Type II' REases, the kind used for DNA analysis and cloning. We focus on their biochemistry: what they are, what they do, and how they do it. Type II REases are produced by prokaryotes to combat bacteriophages. With extreme accuracy, each recognizes a particular sequence in double-stranded DNA and cleaves at a fixed position within or nearby. The discoveries of these enzymes in the 1970s, and of the uses to which they could be put, have since impacted every corner of the life sciences. They became the enabling tools of molecular biology, genetics and biotechnology, and made analysis at the most fundamental levels routine. Hundreds of different REases have been discovered and are available commercially. Their genes have been cloned, sequenced and overexpressed. Most have been characterized to some extent, but few have been studied in depth. Here, we describe the original discoveries in this field, and the properties of the first Type II REases investigated. We discuss the mechanisms of sequence recognition and catalysis, and the varied oligomeric modes in which Type II REases act. We describe the surprising heterogeneity revealed by comparisons of their sequences and structures.
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Affiliation(s)
- Alfred Pingoud
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
| | - Geoffrey G Wilson
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Wolfgang Wende
- Institute of Biochemistry, Justus-Liebig-University Giessen, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany
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Ma X, Shah S, Zhou M, Park CK, Wysocki VH, Horton NC. Structural analysis of activated SgrAI-DNA oligomers using ion mobility mass spectrometry. Biochemistry 2013; 52:4373-81. [PMID: 23742104 DOI: 10.1021/bi3013214] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/30/2022]
Abstract
SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits self-modulation of DNA cleavage activity and sequence specificity. Previous studies have shown that SgrAI forms large oligomers when bound to particular DNA sequences and under the same conditions where SgrAI exhibits accelerated DNA cleavage kinetics. However, the detailed structure and stoichiometry of the SgrAI-DNA complex as well as the basic building block of the oligomers have not been fully characterized. Ion mobility mass spectrometry (IM-MS) was employed to analyze SgrAI-DNA complexes and show that the basic building block of the oligomers is the DNA-bound SgrAI dimer (DBD) with one SgrAI dimer bound to two precleaved duplex DNA molecules each containing one-half of the SgrAI primary recognition sequence. The oligomers contain variable numbers of DBDs with as many as 19 DBDs. Observation of the large oligomers shows that nanoelectrospray ionization (nano-ESI) can preserve the proposed activated form of an enzyme. Finally, the collision cross section of the SgrAI-DNA oligomers measured by IM-MS was found to have a linear relationship with the number of DBDs in each oligomer, suggesting a regular, repeating structure.
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Affiliation(s)
- Xin Ma
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona 85721, United States
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9
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Silanskas A, Foss M, Wende W, Urbanke C, Lagunavicius A, Pingoud A, Siksnys V. Photocaged variants of the MunI and PvuII restriction enzymes. Biochemistry 2011; 50:2800-7. [PMID: 21410225 DOI: 10.1021/bi2000609] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/23/2022]
Abstract
Regulation of proteins by light is a new and promising strategy for the external control of biological processes. In this study, we demonstrate the ability to regulate the catalytic activity of the MunI and PvuII restriction endonucleases with light. We used two different approaches to attach a photoremovable caging compound, 2-nitrobenzyl bromide (NBB), to functionally important regions of the two enzymes. First, we covalently attached a caging molecule at the dimer interface of MunI to generate an inactive monomer. Second, we attached NBB at the DNA binding site of the single-chain variant of PvuII (scPvuII) to prevent binding and cleavage of the DNA substrate. Upon removal of the caging group by UV irradiation, nearly 50% of the catalytic activity of MunI and 80% of the catalytic activity of PvuII could be restored.
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Affiliation(s)
- Arunas Silanskas
- Institute of Biotechnology, Vilnius University, Graiciuno 8, LT-02241 Vilnius, Lithuania
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10
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Park CK, Joshi HK, Agrawal A, Ghare MI, Little EJ, Dunten PW, Bitinaite J, Horton NC. Domain swapping in allosteric modulation of DNA specificity. PLoS Biol 2010; 8:e1000554. [PMID: 21151881 PMCID: PMC2998434 DOI: 10.1371/journal.pbio.1000554] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 04/22/2010] [Accepted: 10/27/2010] [Indexed: 11/19/2022] Open
Abstract
SgrAI is a type IIF restriction endonuclease that cuts an unusually long recognition sequence and exhibits allosteric self-modulation of cleavage activity and sequence specificity. Previous studies have shown that DNA bound dimers of SgrAI oligomerize into an activated form with higher DNA cleavage rates, although previously determined crystal structures of SgrAI bound to DNA show only the DNA bound dimer. A new crystal structure of the type II restriction endonuclease SgrAI bound to DNA and Ca(2+) is now presented, which shows the close association of two DNA bound SgrAI dimers. This tetrameric form is unlike those of the homologous enzymes Cfr10I and NgoMIV and is formed by the swapping of the amino-terminal 24 amino acid residues. Two mutations predicted to destabilize the swapped form of SgrAI, P27W and P27G, have been made and shown to eliminate both the oligomerization of the DNA bound SgrAI dimers as well as the allosteric stimulation of DNA cleavage by SgrAI. A mechanism involving domain swapping is proposed to explain the unusual allosteric properties of SgrAI via association of the domain swapped tetramer of SgrAI bound to DNA into higher order oligomers.
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Affiliation(s)
- Chad K. Park
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Hemant K. Joshi
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Alka Agrawal
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - M. Imran Ghare
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Elizabeth J. Little
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
| | - Pete W. Dunten
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, California, United States of America
| | - Jurate Bitinaite
- New England Biolabs Inc., Ipswich, Massachusetts, United States of America
| | - Nancy C. Horton
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, Arizona, United States of America
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Prymula K, Jadczyk T, Roterman I. Catalytic residues in hydrolases: analysis of methods designed for ligand-binding site prediction. J Comput Aided Mol Des 2010; 25:117-33. [PMID: 21104192 PMCID: PMC3032897 DOI: 10.1007/s10822-010-9402-0] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 08/05/2010] [Accepted: 11/08/2010] [Indexed: 11/26/2022]
Abstract
The comparison of eight tools applicable to ligand-binding site prediction is presented. The methods examined cover three types of approaches: the geometrical (CASTp, PASS, Pocket-Finder), the physicochemical (Q-SiteFinder, FOD) and the knowledge-based (ConSurf, SuMo, WebFEATURE). The accuracy of predictions was measured in reference to the catalytic residues documented in the Catalytic Site Atlas. The test was performed on a set comprising selected chains of hydrolases. The results were analysed with regard to size, polarity, secondary structure, accessible solvent area of predicted sites as well as parameters commonly used in machine learning (F-measure, MCC). The relative accuracies of predictions are presented in the ROC space, allowing determination of the optimal methods by means of the ROC convex hull. Additionally the minimum expected cost analysis was performed. Both advantages and disadvantages of the eight methods are presented. Characterization of protein chains in respect to the level of difficulty in the active site prediction is introduced. The main reasons for failures are discussed. Overall, the best performance offers SuMo followed by FOD, while Pocket-Finder is the best method among the geometrical approaches.
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Affiliation(s)
- Katarzyna Prymula
- Faculty of Chemistry, Jagiellonian University, 3 Ingardena Street, 30-060 Krakow, Poland
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 7E Kopernika Street, 31-034 Krakow, Poland
| | - Tomasz Jadczyk
- Department of Electronics, AGH University of Science and Technology, 30 Mickiewicza Avenue, 30-059 Krakow, Poland
| | - Irena Roterman
- Department of Bioinformatics and Telemedicine, Medical College, Jagiellonian University, 16 Lazarza Street, 31-530 Krakow, Poland
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12
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Zaremba M, Owsicka A, Tamulaitis G, Sasnauskas G, Shlyakhtenko LS, Lushnikov AY, Lyubchenko YL, Laurens N, van den Broek B, Wuite GJL, Siksnys V. DNA synapsis through transient tetramerization triggers cleavage by Ecl18kI restriction enzyme. Nucleic Acids Res 2010; 38:7142-54. [PMID: 20571089 PMCID: PMC2978343 DOI: 10.1093/nar/gkq560] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/29/2023] Open
Abstract
To cut DNA at their target sites, restriction enzymes assemble into different oligomeric structures. The Ecl18kI endonuclease in the crystal is arranged as a tetramer made of two dimers each bound to a DNA copy. However, free in solution Ecl18kI is a dimer. To find out whether the Ecl18kI dimer or tetramer represents the functionally important assembly, we generated mutants aimed at disrupting the putative dimer–dimer interface and analysed the functional properties of Ecl18kI and mutant variants. We show by atomic force microscopy that on two-site DNA, Ecl18kI loops out an intervening DNA fragment and forms a tetramer. Using the tethered particle motion technique, we demonstrate that in solution DNA looping is highly dynamic and involves a transient interaction between the two DNA-bound dimers. Furthermore, we show that Ecl18kI cleaves DNA in the synaptic complex much faster than when acting on a single recognition site. Contrary to Ecl18kI, the tetramerization interface mutant R174A binds DNA as a dimer, shows no DNA looping and is virtually inactive. We conclude that Ecl18kI follows the association model for the synaptic complex assembly in which it binds to the target site as a dimer and then associates into a transient tetrameric form to accomplish the cleavage reaction.
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Affiliation(s)
- Mindaugas Zaremba
- Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania
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13
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Khan F, Furuta Y, Kawai M, Kaminska KH, Ishikawa K, Bujnicki JM, Kobayashi I. A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI). Nucleic Acids Res 2010; 38:3019-30. [PMID: 20071747 PMCID: PMC2875022 DOI: 10.1093/nar/gkp1221] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 01/24/2023] Open
Abstract
Genome comparison and genome context analysis were used to find a putative mobile element in the genome of Photorhabdus luminescens, an entomopathogenic bacterium. The element is composed of 16-bp direct repeats in the terminal regions, which are identical to a part of insertion sequences (ISs), a DNA methyltransferase gene homolog, two genes of unknown functions and an open reading frame (ORF) (plu0599) encoding a protein with no detectable sequence similarity to any known protein. The ORF (plu0599) product showed DNA endonuclease activity, when expressed in a cell-free expression system. Subsequently, the protein, named R.PluTI, was expressed in vivo, purified and found to be a novel type IIF restriction enzyme that recognizes 5′-GGCGC/C-3′ (/ indicates position of cleavage). R.PluTI cleaves a two-site supercoiled substrate at both the sites faster than a one-site supercoiled substrate. The modification enzyme homolog encoded by plu0600, named M.PluTI, was expressed in Escherichia coli and shown to protect DNA from R.PluTI cleavage in vitro, and to suppress the lethal effects of R.PluTI expression in vivo. These results suggested that they constitute a restriction–modification system, present on the putative mobile element. Our approach thus allowed detection of a previously uncharacterized family of DNA-interacting proteins.
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Affiliation(s)
- Feroz Khan
- Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Japan
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14
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Laurens N, Bellamy SRW, Harms AF, Kovacheva YS, Halford SE, Wuite GJL. Dissecting protein-induced DNA looping dynamics in real time. Nucleic Acids Res 2009; 37:5454-64. [PMID: 19586932 PMCID: PMC2760800 DOI: 10.1093/nar/gkp570] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/14/2022] Open
Abstract
Many proteins that interact with DNA perform or enhance their specific functions by binding simultaneously to multiple target sites, thereby inducing a loop in the DNA. The dynamics and energies involved in this loop formation influence the reaction mechanism. Tethered particle motion has proven a powerful technique to study in real time protein-induced DNA looping dynamics while minimally perturbing the DNA-protein interactions. In addition, it permits many single-molecule experiments to be performed in parallel. Using as a model system the tetrameric Type II restriction enzyme SfiI, that binds two copies of its recognition site, we show here that we can determine the DNA-protein association and dissociation steps as well as the actual process of protein-induced loop capture and release on a single DNA molecule. The result of these experiments is a quantitative reaction scheme for DNA looping by SfiI that is rigorously compared to detailed biochemical studies of SfiI looping dynamics. We also present novel methods for data analysis and compare and discuss these with existing methods. The general applicability of the introduced techniques will further enhance tethered particle motion as a tool to follow DNA-protein dynamics in real time.
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Affiliation(s)
- Niels Laurens
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stuart R. W. Bellamy
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - August F. Harms
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Yana S. Kovacheva
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Stephen E. Halford
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
| | - Gijs J. L. Wuite
- Department of Physics and Astronomy and Laser Centre, VU University, De Boelelaan 1081, 1081 HV, Amsterdam, the Netherlands and The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
- *To whom correspondence should be addressed. Tel: +31 20 5987987; Fax: +31 205987991;
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15
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Ibryashkina EM, Sasnauskas G, Solonin AS, Zakharova MV, Siksnys V. Oligomeric structure diversity within the GIY-YIG nuclease family. J Mol Biol 2009; 387:10-6. [PMID: 19361436 DOI: 10.1016/j.jmb.2009.01.048] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/10/2008] [Revised: 12/30/2008] [Accepted: 01/23/2009] [Indexed: 10/21/2022]
Abstract
The GIY-YIG nuclease domain has been identified in homing endonucleases, DNA repair and recombination enzymes, and restriction endonucleases. The Type II restriction enzyme Eco29kI belongs to the GIY-YIG nuclease superfamily and, like most of other family members, including the homing endonuclease I-TevI, is a monomer. It recognizes the palindromic sequence 5'-CCGC/GG-3' ("/" marks the cleavage position) and cuts it to generate 3'-staggered ends. The Eco29kI monomer, which contains a single active site, either has to nick sequentially individual DNA strands or has to form dimers or even higher-order oligomers upon DNA binding to make a double-strand break at its target site. Here, we provide experimental evidence that Eco29kI monomers dimerize on a single cognate DNA molecule forming the catalytically active complex. The mechanism described here for Eco29kI differs from that of Cfr42I isoschisomer, which also belongs to the GIY-YIG family but is functional as a tetramer. This novel mechanism may have implications for the function of homing endonucleases and other enzymes of the GIY-YIG family.
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Affiliation(s)
- Elena M Ibryashkina
- Institute of Biochemistry and Physiology of Microorganisms, Russian Academy of Sciences, Pushchino, Moscow Region, Russia
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16
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Dunten PW, Little EJ, Gregory MT, Manohar VM, Dalton M, Hough D, Bitinaite J, Horton NC. The structure of SgrAI bound to DNA; recognition of an 8 base pair target. Nucleic Acids Res 2008; 36:5405-16. [PMID: 18701646 PMCID: PMC2532715 DOI: 10.1093/nar/gkn510] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/03/2008] [Revised: 07/19/2008] [Accepted: 07/24/2008] [Indexed: 11/14/2022] Open
Abstract
The three-dimensional X-ray crystal structure of the 'rare cutting' type II restriction endonuclease SgrAI bound to cognate DNA is presented. SgrAI forms a dimer bound to one duplex of DNA. Two Ca(2+) bind in the enzyme active site, with one ion at the interface between the protein and DNA, and the second bound distal from the DNA. These sites are differentially occupied by Mn(2+), with strong binding at the protein-DNA interface, but only partial occupancy of the distal site. The DNA remains uncleaved in the structures from crystals grown in the presence of either divalent cation. The structure of the dimer of SgrAI is similar to those of Cfr10I, Bse634I and NgoMIV, however no tetrameric structure of SgrAI is observed. DNA contacts to the central CCGG base pairs of the SgrAI canonical target sequence (CR|CCGGYG, | marks the site of cleavage) are found to be very similar to those in the NgoMIV/DNA structure (target sequence G|CCGGC). Specificity at the degenerate YR base pairs of the SgrAI sequence may occur via indirect readout using DNA distortion. Recognition of the outer GC base pairs occurs through a single contact to the G from an arginine side chain located in a region unique to SgrAI.
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Affiliation(s)
- Pete W. Dunten
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - Elizabeth J. Little
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - Mark T. Gregory
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - Veena M. Manohar
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - Michael Dalton
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - David Hough
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - Jurate Bitinaite
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
| | - Nancy C. Horton
- Stanford Synchrotron Radiation Laboratory, Stanford University, Menlo Park, CA 94025, Department of Biochemistry and Molecular Biophysics, University of Arizona, Tucson, AZ 85721 and New England Biolabs, 240 County Road Ipswich, MA 01938-2723, USA
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17
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Takahashi S, Matsuno H, Furusawa H, Okahata Y. Direct monitoring of allosteric recognition of type IIE restriction endonuclease EcoRII. J Biol Chem 2008; 283:15023-30. [PMID: 18367450 PMCID: PMC3258892 DOI: 10.1074/jbc.m800334200] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/14/2008] [Revised: 03/13/2008] [Indexed: 11/06/2022] Open
Abstract
EcoRII is a homodimer with two domains consisting of a DNA-binding N terminus and a catalytic C terminus and recognizes two specific sequences on DNA. It shows a relatively complicated cleavage reaction in bulk solution. After binding to either recognition site, EcoRII cleaves the other recognition site of the same DNA (cis-binding) strand and/or the recognition site of the other DNA (trans-binding) strand. Although it is difficult to separate these two reactions in bulk solution, we could simply obtain the binding and cleavage kinetics of only the cis-binding by following the frequency (mass) changes of a DNA-immobilized quartz-crystal microbalance (QCM) responding to the addition of EcoRII in aqueous solution. We obtained the maximum binding amounts (Deltam(max)), the dissociation constants (K(d)), the binding and dissociation rate constants (k(on) and k(off)), and the catalytic cleavage reaction rate constants (k(cat)) for wild-type EcoRII, the N-terminal-truncated form (EcoRII N-domain), and the mutant derivatives in its C-terminal domain (K263A and R330A). It was determined from the kinetic analyses that the N-domain, which covers the catalytic C-domain in the absence of DNA, preferentially binds to the one DNA recognition site while transforming EcoRII into an active form allosterically, and then the secondary C-domain binds to and cleaves the other recognition site of the DNA strand.
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Affiliation(s)
| | | | | | - Yoshio Okahata
- Frontier Research Center, Department of Biomolecular Engineering, Tokyo Institute of Technology, B-53 4259 Nagatsuda, Midori-ku, Yokohama, Japan
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18
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Nakonieczna J, Zmijewski JW, Banecki B, Podhajska AJ. Binding of MmeI restriction-modification enzyme to its specific recognition sequence is stimulated by S-adenosyl-L-methionine. Mol Biotechnol 2008; 37:127-35. [PMID: 17914173 DOI: 10.1007/s12033-007-0034-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 11/30/1999] [Revised: 11/30/1999] [Accepted: 11/30/1999] [Indexed: 11/29/2022]
Abstract
Restriction endonucleases serve as a very good model for studying specific protein-DNA interaction. MmeI is a very interesting restriction endonuclease, but although it is useful in Serial Analysis of Gene Expression, still very little is known about the mechanism of its interaction with DNA. MmeI is a unique enzyme as besides cleaving DNA it also methylates specific sequence. For endonucleolytic activity MmeI requires Mg(II) and S-adenosyl-l-methionine (AdoMet). AdoMet is a methyl donor in the methylation reaction, but its requirement for DNA cleavage remains unclear. In the present article we investigated MmeI interaction with DNA with the use of numerous methods. Our electrophoretic mobility shift assay revealed formation of two types of specific protein-DNA complexes. We speculate that faster migrating complex consists of one protein molecule and one DNA fragment whereas, slower migrating complex, which appears in the presence of AdoMet, may be a dimer or multimer form of MmeI interacting with specific DNA. Additionally, using spectrophotometric measurements we showed that in the presence of AdoMet, MmeI protein undergoes conformational changes. We think that such change in the enzyme structure, upon addition of AdoMet, may enhance its specific binding to DNA. In the absence of AdoMet MmeI binds DNA to the much lower extent.
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Affiliation(s)
- Joanna Nakonieczna
- Intercollegiate Faculty of Biotechnology, Department of Biotechnology, University of Gdansk and Medical University of Gdansk, Kladki 24, Gdansk, 80-822, Poland.
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19
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Gasiunas G, Sasnauskas G, Tamulaitis G, Urbanke C, Razaniene D, Siksnys V. Tetrameric restriction enzymes: expansion to the GIY-YIG nuclease family. Nucleic Acids Res 2007; 36:938-49. [PMID: 18086711 PMCID: PMC2241918 DOI: 10.1093/nar/gkm1090] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/13/2022] Open
Abstract
The GIY-YIG nuclease domain was originally identified in homing endonucleases and enzymes involved in DNA repair and recombination. Many of the GIY-YIG family enzymes are functional as monomers. We show here that the Cfr42I restriction endonuclease which belongs to the GIY-YIG family and recognizes the symmetric sequence 5′-CCGC/GG-3′ (‘/’ indicates the cleavage site) is a tetramer in solution. Moreover, biochemical and kinetic studies provided here demonstrate that the Cfr42I tetramer is catalytically active only upon simultaneous binding of two copies of its recognition sequence. In that respect Cfr42I resembles the homotetrameric Type IIF restriction enzymes that belong to the distinct PD-(E/D)XK nuclease superfamily. Unlike the PD-(E/D)XK enzymes, the GIY-YIG nuclease Cfr42I accommodates an extremely wide selection of metal-ion cofactors, including Mg2+, Mn2+, Co2+, Zn2+, Ni2+, Cu2+ and Ca2+. To our knowledge, Cfr42I is the first tetrameric GIY-YIG family enzyme. Similar structural arrangement and phenotypes displayed by restriction enzymes of the PD-(E/D)XK and GIY-YIG nuclease families point to the functional significance of tetramerization.
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Affiliation(s)
- Giedrius Gasiunas
- Institute of Biotechnology, Graiciuno 8, LT-02241 Vilnius, Lithuania
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20
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Kwiatek A, Piekarowicz A. The restriction endonuclease R.NmeDI from Neisseria meningitidis that recognizes a palindromic sequence and cuts the DNA on both sides of the recognition sequence. Nucleic Acids Res 2007; 35:6539-46. [PMID: 17897964 PMCID: PMC2095814 DOI: 10.1093/nar/gkm702] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 12/01/2022] Open
Abstract
The restriction endonuclease Type II R.NmeDI from Neisseria meningitidis 2120 (serogroup C, ST-11 complex) was characterized. The cloned nmeDIR gene was expressed in Escherichia coli cells, and the endonucleolytic and restriction activities of R.NmeDI were then observed in vitro and in vivo. The nmeDIR gene consists of 1056 bp coding 351 aa protein with a calculated molecular weight of M(r) = 39 000 ± 1000 Da. The R.NmeDI enzyme was purified to apparent homogeneity following overexpression, using metal affinity chromatography. This enzyme recognizes a palindrome sequence and cleaves double-stranded DNA upstream and downstream of its recognition sequence (12/7) RCCGGY (7/12) (R = A/G, Y = C/T) cutting out a 25-bp fragment. R.NmeDI cleaves in two steps. The enzyme cleaves the first strand randomly on either side of the recognition sequence generating an intermediate, and the second cleavage occurs more slowly and results in the production of a final reaction product. The R.NmeDI endonuclease requires two recognition sequences for effective cleavage. The tetramer is an active form of the R.NmeDI enzyme.
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Affiliation(s)
- Agnieszka Kwiatek
- *To whom the correspondence should be addressed. +48 22 5541521+48 22 5541402
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21
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Bellamy SRW, Milsom SE, Kovacheva YS, Sessions RB, Halford SE. A switch in the mechanism of communication between the two DNA-binding sites in the SfiI restriction endonuclease. J Mol Biol 2007; 373:1169-83. [PMID: 17870087 PMCID: PMC2082129 DOI: 10.1016/j.jmb.2007.08.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/12/2007] [Revised: 08/10/2007] [Accepted: 08/14/2007] [Indexed: 11/29/2022]
Abstract
While many Type II restriction enzymes are dimers with a single DNA-binding cleft between the subunits, SfiI is a tetramer of identical subunits. Two of its subunits (a dimeric unit) create one DNA-binding cleft, and the other two create a second cleft on the opposite side of the protein. The two clefts bind specific DNA cooperatively to give a complex of SfiI with two recognition sites. This complex is responsible for essentially all of the DNA-cleavage reactions by SfiI: virtually none is due to the complex with one site. The communication between the DNA-binding clefts was examined by disrupting one of the very few polar interactions in the otherwise hydrophobic interface between the dimeric units: a tyrosine hydroxyl was removed by mutation to phenylalanine. The mutant protein remained tetrameric in solution and could bind two DNA sites. But instead of being activated by binding two sites, like wild-type SfiI, it showed maximal activity when bound to a single site and had a lower activity when bound to two sites. This interaction across the dimer interface thus enforces in wild-type SfiI a cooperative transition between inactive and active states in both dimers, but without this interaction as in the mutant protein, a single dimer can undergo the transition to give a stable intermediate with one inactive dimer and one active dimer.
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Affiliation(s)
- Stuart R W Bellamy
- The DNA-Protein Interactions Unit, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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22
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Sokolowska M, Kaus-Drobek M, Czapinska H, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M. Monomeric restriction endonuclease BcnI in the apo form and in an asymmetric complex with target DNA. J Mol Biol 2007; 369:722-34. [PMID: 17445830 DOI: 10.1016/j.jmb.2007.03.018] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/15/2007] [Revised: 03/01/2007] [Accepted: 03/06/2007] [Indexed: 11/20/2022]
Abstract
Restriction endonuclease BcnI cleaves duplex DNA containing the sequence CC/SGG (S stands for C or G, / designates a cleavage position) to generate staggered products with single nucleotide 5'-overhangs. Here, we show that BcnI functions as a monomer that interacts with its target DNA in 1:1 molar ratio and report crystal structures of BcnI in the absence and in the presence of DNA. In the complex with DNA, BcnI makes specific contacts with all five bases of the target sequence and not just with a half-site, as the protomer of a typical dimeric restriction endonuclease. Our data are inconsistent with BcnI dimerization and suggest that the enzyme introduces double-strand breaks by sequentially nicking individual DNA strands, although this remains to be confirmed by kinetic experiments. BcnI is remotely similar to the DNA repair protein MutH and shares approximately 20% sequence identity with the restriction endonuclease MvaI, which is specific for the related sequence CC/WGG (W stands for A or T). As expected, BcnI is structurally similar to MvaI and recognizes conserved bases in the target sequence similarly but not identically. BcnI has a unique machinery for the recognition of the central base-pair.
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Affiliation(s)
- Monika Sokolowska
- International Institute of Molecular and Cell Biology, Warsaw, Poland
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23
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Kaus-Drobek M, Czapinska H, Sokołowska M, Tamulaitis G, Szczepanowski RH, Urbanke C, Siksnys V, Bochtler M. Restriction endonuclease MvaI is a monomer that recognizes its target sequence asymmetrically. Nucleic Acids Res 2007; 35:2035-46. [PMID: 17344322 PMCID: PMC1874612 DOI: 10.1093/nar/gkm064] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/12/2022] Open
Abstract
Restriction endonuclease MvaI recognizes the sequence CC/WGG (W stands for A or T, '/' designates the cleavage site) and generates products with single nucleotide 5'-overhangs. The enzyme has been noted for its tolerance towards DNA modifications. Here, we report a biochemical characterization and crystal structures of MvaI in an apo-form and in a complex with target DNA at 1.5 A resolution. Our results show that MvaI is a monomer and recognizes its pseudosymmetric target sequence asymmetrically. The enzyme consists of two lobes. The catalytic lobe anchors the active site residues Glu36, Asp50, Glu55 and Lys57 and contacts the bases from the minor grove side. The recognition lobe mediates all major grove interactions with the bases. The enzyme in the crystal is bound to the strand with T at the center of the recognition sequence. The crystal structure with calcium ions and DNA mimics the prereactive state. MvaI shows structural similarities to BcnI, which cleaves the related sequence CC/SGG and to MutH enzyme, which is a component of the DNA repair machinery, and nicks one DNA strand instead of making a double-strand break.
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Affiliation(s)
- Magdalena Kaus-Drobek
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Honorata Czapinska
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Monika Sokołowska
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Gintautas Tamulaitis
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Roman H. Szczepanowski
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Claus Urbanke
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Virginijus Siksnys
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
| | - Matthias Bochtler
- International Institute of Molecular and Cell Biology, ul. Trojdena 4, 02-109 Warsaw, Poland, Max-Planck-Institute for Molecular Cell Biology and Genetics, Pfotenhauerstr. 108, 01309 Dresden, Germany, Institute of Biotechnology, Graiciuno 8, LT-02241, Vilnius, Lithuania and Medizinische Hochschule, Abteilung Strukturanalyse OE 8830, Carl Neuberg Str. 1, 30625 Hannover, Germany
- *To whom correspondence should be addressed. 0048 22 59707320048 22 5970715
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24
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Okorokov AL, Sherman MB, Plisson C, Grinkevich V, Sigmundsson K, Selivanova G, Milner J, Orlova EV. The structure of p53 tumour suppressor protein reveals the basis for its functional plasticity. EMBO J 2006; 25:5191-200. [PMID: 17053786 PMCID: PMC1630404 DOI: 10.1038/sj.emboj.7601382] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 04/10/2006] [Accepted: 09/13/2006] [Indexed: 01/11/2023] Open
Abstract
p53 major tumour suppressor protein has presented a challenge for structural biology for two decades. The intact and complete p53 molecule has eluded previous attempts to obtain its structure, largely due to the intrinsic flexibility of the protein. Using ATP-stabilised p53, we have employed cryoelectron microscopy and single particle analysis to solve the first three-dimensional structure of the full-length p53 tetramer (resolution 13.7 A). The p53 molecule is a D2 tetramer, resembling a hollow skewed cube with node-like vertices of two sizes. Four larger nodes accommodate central core domains, as was demonstrated by fitting of its X-ray structure. The p53 monomers are connected via their juxtaposed N- and C-termini within smaller N/C nodes to form dimers. The dimers form tetramers through the contacts between core nodes and N/C nodes. This structure revolutionises existing concepts of p53's molecular organisation and resolves conflicting data relating to its biochemical properties. This architecture of p53 in toto suggests novel mechanisms for structural plasticity, which enables the protein to bind variably spaced DNA target sequences, essential for p53 transactivation and tumour suppressor functions.
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Affiliation(s)
- Andrei L Okorokov
- Department of Pathology, Royal Free and University College Medical School, University College London, London, UK
- Wolfson Institute for Biomedical Research, University College London, London, UK
- Department of Pathology, Royal Free and University College Medical School, University College London, London WCIE 6JJ, UK. Tel.: +44 20 7679 0959; Fax: +44 20 7388 4408; E-mail:
| | - Michael B Sherman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - Celia Plisson
- School of Crystallography, Birkbeck College, London, UK
| | - Vera Grinkevich
- Microbiology and Tumor Biology Center, Karolinska Institutet, Stockholm, Sweden
| | | | - Galina Selivanova
- Microbiology and Tumor Biology Center, Karolinska Institutet, Stockholm, Sweden
| | - Jo Milner
- YCR p53 Laboratory, Department of Biology, University of York, York, UK
| | - Elena V Orlova
- School of Crystallography, Birkbeck College, London, UK
- Department of Crystallography, Birkbeck College, Malet Street, London WC1E 7HX, UK. Tel.: +44 20 7631 6845; Fax: +44 20 7631 6803; E-mail:
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Tamulaitiene G, Jakubauskas A, Urbanke C, Huber R, Grazulis S, Siksnys V. The crystal structure of the rare-cutting restriction enzyme SdaI reveals unexpected domain architecture. Structure 2006; 14:1389-400. [PMID: 16962970 DOI: 10.1016/j.str.2006.07.002] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 04/24/2006] [Revised: 07/04/2006] [Accepted: 07/05/2006] [Indexed: 01/31/2023]
Abstract
Rare-cutting restriction enzymes are important tools in genome analysis. We report here the crystal structure of SdaI restriction endonuclease, which is specific for the 8 bp sequence CCTGCA/GG ("/" designates the cleavage site). Unlike orthodox Type IIP enzymes, which are single domain proteins, the SdaI monomer is composed of two structural domains. The N domain contains a classical winged helix-turn-helix (wHTH) DNA binding motif, while the C domain shows a typical restriction endonuclease fold. The active site of SdaI is located within the C domain and represents a variant of the canonical PD-(D/E)XK motif. SdaI determinants of sequence specificity are clustered on the recognition helix of the wHTH motif at the N domain. The modular architecture of SdaI, wherein one domain mediates DNA binding while the other domain is predicted to catalyze hydrolysis, distinguishes SdaI from previously characterized restriction enzymes interacting with symmetric recognition sequences.
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26
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Zaremba M, Sasnauskas G, Urbanke C, Siksnys V. Allosteric communication network in the tetrameric restriction endonuclease Bse634I. J Mol Biol 2006; 363:800-12. [PMID: 16987525 DOI: 10.1016/j.jmb.2006.08.050] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 07/03/2006] [Revised: 08/03/2006] [Accepted: 08/17/2006] [Indexed: 11/20/2022]
Abstract
Restriction endonuclease Bse634I is a homotetramer arranged as a dimer of two primary dimers. Bse634I displays its maximum catalytic efficiency upon binding of two copies of cognate DNA, one per each primary dimer. The catalytic activity of Bse634I on a single DNA copy is down-regulated due to the cross-talking interactions between the primary dimers. The mechanism of signal propagation between the individual active sites of Bse634I remains unclear. To identify communication pathways involved in the catalytic activity regulation of Bse634I tetramer we mutated a selected set of amino acid residues at the dimer-dimer interface and analysed the oligomeric state and catalytic properties of the mutant proteins. We demonstrate that alanine replacement of N262 and V263 residues located in the loop at the tetramerisation interface did not inhibit tetramer assembly but dramatically altered the catalytic properties of Bse634I despite of the distal location from the active site. Kinetic analysis using cognate hairpin oligonucleotide and one and two-site plasmids as substrates allowed us to identify two types of communication signals propagated through the dimer-dimer interface in the Bse634I tetramer: the inhibitory, or "stopper" and the activating, or "sync" signal. We suggest that the interplay between the two signals determines the catalytic and regulatory properties of the Bse634I and mutant proteins.
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Affiliation(s)
- Mindaugas Zaremba
- Institute of Biotechnology, Graiciuno 8, Vilnius, LT-02241, Lithuania
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27
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Gemmen GJ, Millin R, Smith DE. Tension-dependent DNA cleavage by restriction endonucleases: two-site enzymes are "switched off" at low force. Proc Natl Acad Sci U S A 2006; 103:11555-60. [PMID: 16868081 PMCID: PMC1520314 DOI: 10.1073/pnas.0604463103] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/18/2022] Open
Abstract
DNA looping occurs in many important protein-DNA interactions, including those regulating replication, transcription, and recombination. Recent theoretical studies predict that tension of only a few piconewtons acting on DNA would almost completely inhibit DNA looping. Here, we study restriction endonucleases that require interaction at two separated sites for efficient cleavage. Using optical tweezers we measured the dependence of cleavage activity on DNA tension with 15 known or suspected two-site enzymes (BfiI, BpmI, BsgI, BspMI, Cfr9I, Cfr10I, Eco57I, EcoRII, FokI, HpaII, MboII, NarI, SacII, Sau3AI, and SgrAI) and six one-site enzymes (BamHI, EcoRI, EcoRV, HaeIII, HindIII, and DNaseI). All of the one-site enzymes were virtually unaffected by 5 pN of tension, whereas all of the two-site enzymes were completely inhibited. These enzymes thus constitute a remarkable example of a tension sensing "molecular switch." A detailed study of one enzyme, Sau3AI, indicated that the activity decreased exponentially with tension and the decrease was approximately 10-fold at 0.7 pN. At higher forces (approximately 20-40 pN) cleavage by the one-site enzymes EcoRV and HaeIII was partly inhibited and cleavage by HindIII was enhanced, whereas BamHI, EcoRI, and DNaseI were largely unaffected. These findings correlate with structural data showing that EcoRV bends DNA sharply, whereas BamHI, EcoRI, and DNaseI do not. Thus, DNA-directed enzyme activity involving either DNA looping or bending can be modulated by tension, a mechanism that could facilitate mechanosensory transduction in vivo.
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Affiliation(s)
- Gregory J. Gemmen
- Department of Physics, University of California at San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093
| | - Rachel Millin
- Department of Physics, University of California at San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093
| | - Douglas E. Smith
- Department of Physics, University of California at San Diego, Mail Code 0379, 9500 Gilman Drive, La Jolla, CA 92093
- To whom correspondence should be addressed. E-mail:
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28
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Gemmen GJ, Millin R, Smith DE. DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force. Nucleic Acids Res 2006; 34:2864-77. [PMID: 16723432 PMCID: PMC1474071 DOI: 10.1093/nar/gkl382] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/12/2022] Open
Abstract
Proteins interacting at multiple sites on DNA via looping play an important role in many fundamental biochemical processes. Restriction endonucleases that must bind at two recognition sites for efficient activity are a useful model system for studying such interactions. Here we used single DNA manipulation to study sixteen known or suspected two-site endonucleases. In eleven cases (BpmI, BsgI, BspMI, Cfr10I, Eco57I, EcoRII, FokI, HpaII, NarI, Sau3AI and SgrAI) we found that substitution of Ca2+ for Mg2+ blocked cleavage and enabled us to observe stable DNA looping. Forced disruption of these loops allowed us to measure the frequency of looping and probability distributions for loop size and unbinding force for each enzyme. In four cases we observed bimodal unbinding force distributions, indicating conformational heterogeneity and/or complex binding energy landscapes. Measured unlooping events ranged in size from 7 to 7500 bp and the most probable size ranged from less than 75 bp to nearly 500 bp, depending on the enzyme. In most cases the size distributions were in much closer agreement with theoretical models that postulate sharp DNA kinking than with classical models of DNA elasticity. Our findings indicate that DNA looping is highly variable depending on the specific protein and does not depend solely on the mechanical properties of DNA.
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Affiliation(s)
| | | | - Douglas E. Smith
- To whom correspondence should be addressed. Tel: +1 858 534 5241;
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29
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Lushnikov AY, Potaman VN, Oussatcheva EA, Sinden RR, Lyubchenko YL. DNA strand arrangement within the SfiI-DNA complex: atomic force microscopy analysis. Biochemistry 2006; 45:152-8. [PMID: 16388590 PMCID: PMC1352315 DOI: 10.1021/bi051767c] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/28/2022]
Abstract
The SfiI restriction enzyme binds to DNA as a tetramer holding two usually distant DNA recognition sites together before cleavage of the four DNA strands. To elucidate structural properties of the SfiI-DNA complex, atomic force microscopy (AFM) imaging of the complexes under noncleaving conditions (Ca2+ instead of Mg2+ in the reaction buffer) was performed. Intramolecular complexes formed by protein interaction between two binding sites in one DNA molecule (cis interaction) as well as complexes formed by the interaction of two sites in different molecules (trans interaction) were analyzed. Complexes were identified unambiguously by the presence of a tall spherical blob at the DNA intersections. To characterize the path of DNA within the complex, the angles between the DNA helices in the proximity of the complex were systematically analyzed. All the data show clear-cut bimodal distributions centered around peak values corresponding to 60 degrees and 120 degrees. To unambiguously distinguish between the crossed and bent models for the DNA orientation within the complex, DNA molecules with different arm lengths flanking the SfiI binding site were designed. The analysis of the AFM images for complexes of this type led to the conclusion that the DNA recognition sites within the complex are crossed. The angles of 60 degrees or 120 degrees between the DNA helices correspond to a complex in which one of the helices is flipped with respect to the orientation of the other. Complexes formed by five different recognition sequences (5'-GGCCNNNNNGGCC-3'), with different central base pairs, were also analyzed. Our results showed that complexes containing the two possible orientations of the helices were formed almost equally. This suggests no preferential orientation of the DNA cognate site within the complex, suggesting that the central part of the DNA binding site does not form strong sequence specific contacts with the protein.
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Affiliation(s)
- Alexander Y. Lushnikov
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, and
| | - Vladimir N. Potaman
- Institute of Biosciences and Technology, Texas A&M University Health Sciences Center, 2121 W. Holcombe Blvd., Houston, TX 77030
| | - Elena A. Oussatcheva
- Institute of Biosciences and Technology, Texas A&M University Health Sciences Center, 2121 W. Holcombe Blvd., Houston, TX 77030
| | - Richard R. Sinden
- Institute of Biosciences and Technology, Texas A&M University Health Sciences Center, 2121 W. Holcombe Blvd., Houston, TX 77030
| | - Yuri L. Lyubchenko
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, and
- *Corresponding author: Yuri Lyubchenko, Department of Pharmaceutical Sciences, College of Pharmacy, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, Phone: 402-559-1971, Fax: 402-559-9543, E-mail:
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30
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Catto LE, Ganguly S, Milsom SE, Welsh AJ, Halford SE. Protein assembly and DNA looping by the FokI restriction endonuclease. Nucleic Acids Res 2006; 34:1711-20. [PMID: 16556912 PMCID: PMC1410913 DOI: 10.1093/nar/gkl076] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/14/2022] Open
Abstract
The FokI restriction endonuclease recognizes an asymmetric DNA sequence and cuts both strands at fixed positions upstream of the site. The sequence is contacted by a single monomer of the protein, but the monomer has only one catalytic centre and forms a dimer to cut both strands. FokI is also known to cleave DNA with two copies of its site more rapidly than DNA with one copy. To discover how FokI acts at a single site and how it acts at two sites, its reactions were examined on a series of plasmids with either one recognition site or with two sites separated by varied distances, sometimes in the presence of a DNA-binding defective mutant of FokI. These experiments showed that, to cleave DNA with one site, the monomer bound to that site associates via a weak protein–protein interaction with a second monomer that remains detached from the recognition sequence. Nevertheless, the second monomer catalyses phosphodiester bond hydrolysis at the same rate as the DNA-bound monomer. On DNA with two sites, two monomers of FokI interact strongly, as a result of being tethered to the same molecule of DNA, and sequester the intervening DNA in a loop.
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Affiliation(s)
| | | | | | | | - Stephen E. Halford
- To whom correspondence should be addressed. Tel: +44 117 928 7429; Fax: +44 117 928 8274;
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31
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Tamulaitis G, Sasnauskas G, Mucke M, Siksnys V. Simultaneous binding of three recognition sites is necessary for a concerted plasmid DNA cleavage by EcoRII restriction endonuclease. J Mol Biol 2006; 358:406-19. [PMID: 16529772 DOI: 10.1016/j.jmb.2006.02.024] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 10/29/2005] [Revised: 02/08/2006] [Accepted: 02/09/2006] [Indexed: 11/28/2022]
Abstract
According to the current paradigm type IIE restriction endonucleases are homodimeric proteins that simultaneously bind to two recognition sites but cleave DNA at only one site per turnover: the other site acts as an allosteric locus, activating the enzyme to cleave DNA at the first. Structural and biochemical analysis of the archetypal type IIE restriction enzyme EcoRII suggests that it has three possible DNA binding interfaces enabling simultaneous binding of three recognition sites. To test if putative synapsis of three binding sites has any functional significance, we have studied EcoRII cleavage of plasmids containing a single, two and three recognition sites under both single turnover and steady state conditions. EcoRII displays distinct reaction patterns on different substrates: (i) it shows virtually no activity on a single site plasmid; (ii) it yields open-circular DNA form nicked at one strand as an obligatory intermediate acting on a two-site plasmid; (iii) it cleaves concertedly both DNA strands at a single site during a single turnover on a three site plasmid to yield linear DNA. Cognate oligonucleotide added in trans increases the reaction velocity and changes the reaction pattern for the EcoRII cleavage of one and two-site plasmids but has little effect on the three-site plasmid. Taken together the data indicate that EcoRII requires simultaneous binding of three rather than two recognition sites in cis to achieve concerted DNA cleavage at a single site. We show that the orthodox type IIP enzyme PspGI which is an isoschisomer of EcoRII, cleaves different plasmid substrates with equal rates. Data provided here indicate that type IIE restriction enzymes EcoRII and NaeI follow different mechanisms. We propose that other type IIE restriction enzymes may employ the mechanism suggested here for EcoRII.
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32
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Tamulaitis G, Mucke M, Siksnys V. Biochemical and mutational analysis ofEcoRII functional domains reveals evolutionary links between restriction enzymes. FEBS Lett 2006; 580:1665-71. [PMID: 16497303 DOI: 10.1016/j.febslet.2006.02.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 12/12/2005] [Revised: 01/16/2006] [Accepted: 02/07/2006] [Indexed: 11/23/2022]
Abstract
The archetypal Type IIE restriction endonuclease EcoRII is a dimer that has a modular structure. DNA binding studies indicate that the isolated C-terminal domain dimer has an interface that binds a single cognate DNA molecule whereas the N-terminal domain is a monomer that also binds a single copy of cognate DNA. Hence, the full-length EcoRII contains three putative DNA binding interfaces: one at the C-terminal domain dimer and two at each of the N-terminal domains. Mutational analysis indicates that the C-terminal domain shares conserved active site architecture and DNA binding elements with the tetrameric restriction enzyme NgoMIV. Data provided here suggest possible evolutionary relationships between different subfamilies of restriction enzymes.
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33
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van den Broek B, Vanzi F, Normanno D, Pavone FS, Wuite GJ. Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI. Nucleic Acids Res 2006; 34:167-74. [PMID: 16407332 PMCID: PMC1326248 DOI: 10.1093/nar/gkj432] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/13/2022] Open
Abstract
Many restriction enzymes require binding of two copies of a recognition sequence for DNA cleavage, thereby introducing a loop in the DNA. We investigated looping dynamics of Type IIE restriction enzymes NaeI and NarI by tracking the Brownian motion of single tethered DNA molecules. DNA containing two endonuclease recognition sites spaced a few 100 bp apart connect small polystyrene beads to a glass surface. The position of a bead is tracked through video microscopy. Protein-mediated looping and unlooping is then observed as a sudden specific change in Brownian motion of the bead. With this method we are able to directly follow DNA looping kinetics of single protein–DNA complexes to obtain loop stability and loop formation times. We show that, in the absence of divalent cations, NaeI induces DNA loops of specific size. In contrast, under these conditions NarI mainly creates non-specific loops, resulting in effective DNA compaction for higher enzyme concentrations. Addition of Ca2+ increases the NaeI-DNA loop lifetime by two orders of magnitude and stimulates specific binding by NarI. Finally, for both enzymes we observe exponentially distributed loop formation times, indicating that looping is dominated by (re)binding the second recognition site.
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Affiliation(s)
| | - Francesco Vanzi
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 150019 Sesto Fiorentino (Firenze), Italy
| | - Davide Normanno
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 150019 Sesto Fiorentino (Firenze), Italy
| | - Francesco S. Pavone
- European Laboratory for Non-linear Spectroscopy (LENS), Via Nello Carrara 150019 Sesto Fiorentino (Firenze), Italy
| | - Gijs J.L. Wuite
- To whom correspondence should be addressed. Tel: +31205987987; Fax: +31205987991;
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34
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Wood KM, Daniels LE, Halford SE. Long-range communications between DNA sites by the dimeric restriction endonuclease SgrAI. J Mol Biol 2005; 350:240-53. [PMID: 15923010 DOI: 10.1016/j.jmb.2005.04.053] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 03/09/2005] [Revised: 04/21/2005] [Accepted: 04/25/2005] [Indexed: 10/25/2022]
Abstract
The SgrAI endonuclease displays its maximal activity on DNA with two copies of its recognition sequence, cleaving both sites concertedly. While most restriction enzymes that act concurrently at two sites are tetramers, SgrAI is a dimer in solution. Its reaction at two cognate sites involves the association of two DNA-bound dimers. SgrAI can also bridge cognate and secondary sites, the latter being certain sequences that differ from the cognate by one base-pair. The mechanisms for cognate-cognate and cognate-secondary communications were examined for sites in the following topological relationships: in cis, on plasmids with two sites in a single DNA molecule; on catenanes containing two interlinked rings of DNA with one site in each ring; and in trans, on oligoduplexes carrying either a single site or the DNA termini generated by SgrAI. Both cognate-cognate and cognate-secondary interactions occur through 3-D space and not by 1-D tracking along the DNA. Both sorts of communication arise more readily when the sites are tethered to each other, either in cis on the same molecule of DNA or by the interlinking of catenane rings, than when released from the tether. However, the dimer bound to an oligoduplex carrying either a cognate or a secondary site could be activated to cleave that duplex by interacting with a second dimer bound to the recognition site, provided both duplexes are at least 30 base-pairs long: the second dimer could alternatively be bound to the two duplexes that correspond to the products of DNA cleavage by SgrAI.
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Affiliation(s)
- Katie M Wood
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
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35
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Yang Z, Horton JR, Maunus R, Wilson GG, Roberts RJ, Cheng X. Structure of HinP1I endonuclease reveals a striking similarity to the monomeric restriction enzyme MspI. Nucleic Acids Res 2005; 33:1892-901. [PMID: 15805123 PMCID: PMC1074309 DOI: 10.1093/nar/gki337] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/13/2022] Open
Abstract
HinP1I, a type II restriction endonuclease, recognizes and cleaves a palindromic tetranucleotide sequence (G↓CGC) in double-stranded DNA, producing 2 nt 5′ overhanging ends. Here, we report the structure of HinP1I crystallized as one protein monomer in the crystallographic asymmetric unit. HinP1I displays an elongated shape, with a conserved catalytic core domain containing an active-site motif of SDX18QXK and a putative DNA-binding domain. Without significant sequence homology, HinP1I displays striking structural similarity to MspI, an endonuclease that cleaves a similar palindromic DNA sequence (C↓CGG) and binds to that sequence crystallographically as a monomer. Almost all the structural elements of MspI can be matched in HinP1I, including both the DNA recognition and catalytic elements. Examining the protein–protein interactions in the crystal lattice, HinP1I could be dimerized through two helices located on the opposite side of the protein to the active site, generating a molecule with two active sites and two DNA-binding surfaces opposite one another on the outer surfaces of the dimer. A possible functional link between this unusual dimerization mode and the tetrameric restriction enzymes is discussed.
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Affiliation(s)
| | | | - Robert Maunus
- New England Biolabs32 Tozer Road, Beverly, MA 01915, USA
| | | | | | - Xiaodong Cheng
- To whom correspondence should be addressed. Tel: +1 404 727 8491; Fax: +1 404 727 3746;
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36
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Zaremba M, Sasnauskas G, Urbanke C, Siksnys V. Conversion of the Tetrameric Restriction Endonuclease Bse634I into a Dimer: Oligomeric Structure–Stability–Function Correlations. J Mol Biol 2005; 348:459-78. [PMID: 15811381 DOI: 10.1016/j.jmb.2005.02.037] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 12/15/2004] [Revised: 02/02/2005] [Accepted: 02/20/2005] [Indexed: 11/30/2022]
Abstract
The Bse634I restriction endonuclease is a tetramer and belongs to the type IIF subtype of restriction enzymes. It requires two recognition sites for its optimal activity and cleaves plasmid DNA with two sites much faster than a single-site DNA. We show that disruption of the tetramerisation interface of Bse634I by site-directed mutagenesis converts the tetrameric enzyme into a dimer. Dimeric W228A mutant cleaves plasmid DNA containing one or two sites with the same efficiency as the tetramer cleaves the two-site plasmid. Hence, the catalytic activity of the Bse634I tetramer on a single-site DNA is down-regulated due to the cross-talking interactions between the individual dimers. The autoinhibition within the Bse634I tetramer is relieved by bridging two DNA copies into the synaptic complex that promotes fast and concerted cleavage at both sites. Cleavage analysis of the oligonucleotide attached to the solid support revealed that Bse634I is able to form catalytically competent synaptic complexes by bridging two molecules of the cognate DNA, cognate DNA-miscognate DNA and cognate DNA-product DNA. Taken together, our data demonstrate that a single W228A mutation converts a tetrameric type IIF restriction enzyme Bse634I into the orthodox dimeric type IIP restriction endonuclease. However, the stability of the dimer towards chemical denaturants, thermal inactivation and proteolytic degradation are compromised.
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Affiliation(s)
- M Zaremba
- Institute of Biotechnology, Graiciuno 8, Vilnius LT-02241, Lithuania
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37
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Chmiel AA, Bujnicki JM, Skowronek KJ. A homology model of restriction endonuclease SfiI in complex with DNA. BMC STRUCTURAL BIOLOGY 2005; 5:2. [PMID: 15667656 PMCID: PMC548270 DOI: 10.1186/1472-6807-5-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Academic Contribution Register] [Received: 10/08/2004] [Accepted: 01/24/2005] [Indexed: 11/10/2022]
Abstract
Background Restriction enzymes (REases) are commercial reagents commonly used in recombinant DNA technologies. They are attractive models for studying protein-DNA interactions and valuable targets for protein engineering. They are, however, extremely divergent: the amino acid sequence of a typical REase usually shows no detectable similarities to any other proteins, with rare exceptions of other REases that recognize identical or very similar sequences. From structural analyses and bioinformatics studies it has been learned that some REases belong to at least four unrelated and structurally distinct superfamilies of nucleases, PD-DxK, PLD, HNH, and GIY-YIG. Hence, they are extremely hard targets for structure prediction and homology-based inference of sequence-function relationships and the great majority of REases remain structurally and evolutionarily unclassified. Results SfiI is a REase which recognizes the interrupted palindromic sequence 5'GGCCNNNN^NGGCC3' and generates 3 nt long 3' overhangs upon cleavage. SfiI is an archetypal Type IIF enzyme, which functions as a tetramer and cleaves two copies of the recognition site in a concerted manner. Its sequence shows no similarity to other proteins and nothing is known about the localization of its active site or residues important for oligomerization. Using the threading approach for protein fold-recognition, we identified a remote relationship between SfiI and BglI, a dimeric Type IIP restriction enzyme from the PD-DxK superfamily of nucleases, which recognizes the 5'GCCNNNN^NGGC3' sequence and whose structure in complex with the substrate DNA is available. We constructed a homology model of SfiI in complex with its target sequence and used it to predict residues important for dimerization, tetramerization, DNA binding and catalysis. Conclusions The bioinformatics analysis suggest that SfiI, a Type IIF enzyme, is more closely related to BglI, an "orthodox" Type IIP restriction enzyme, than to any other REase, including other Type IIF REases with known structures, such as NgoMIV. NgoMIV and BglI belong to two different, very remotely related branches of the PD-DxK superfamily: the α-class (EcoRI-like), and the β-class (EcoRV-like), respectively. Thus, our analysis provides evidence that the ability to tetramerize and cut the two DNA sequences in a concerted manner was developed independently at least two times in the evolution of the PD-DxK superfamily of REases. The model of SfiI will also serve as a convenient platform for further experimental analyses.
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Affiliation(s)
- Agnieszka A Chmiel
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Janusz M Bujnicki
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
| | - Krzysztof J Skowronek
- Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, 02-109 Warsaw, Poland
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38
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Xu QS, Kucera RB, Roberts RJ, Guo HC. An Asymmetric Complex of Restriction Endonuclease MspI on Its Palindromic DNA Recognition Site. Structure 2004; 12:1741-7. [PMID: 15341737 DOI: 10.1016/j.str.2004.07.014] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 05/10/2004] [Revised: 06/28/2004] [Accepted: 07/06/2004] [Indexed: 11/30/2022]
Abstract
Most well-known restriction endonucleases recognize palindromic DNA sequences and are classified as Type IIP. Due to the recognition and cleavage symmetry, Type IIP enzymes are usually found to act as homodimers in forming 2-fold symmetric enzyme-DNA complexes. Here we report an asymmetric complex of the Type IIP restriction enzyme MspI in complex with its cognate recognition sequence. Unlike any other Type IIP enzyme reported to date, an MspI monomer and not a dimer binds to a palindromic DNA sequence. The enzyme makes specific contacts with all 4 base pairs in the recognition sequence, by six direct and five water-mediated hydrogen bonds and numerous van der Waal contacts. This MspI-DNA structure represents the first example of asymmetric recognition of a palindromic DNA sequence by two different structural motifs in one polypeptide. A few possible pathways are discussed for MspI to cut both strands of DNA, either as a monomer or dimer.
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Affiliation(s)
- Qian Steven Xu
- Department of Physiology and Biophysics, Boston University School of Medicine, 715 Albany Street, MA 02118, USA
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39
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Peakman LJ, Szczelkun MD. DNA communications by Type III restriction endonucleases--confirmation of 1D translocation over 3D looping. Nucleic Acids Res 2004; 32:4166-74. [PMID: 15302916 PMCID: PMC514383 DOI: 10.1093/nar/gkh762] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/15/2022] Open
Abstract
DNA cleavage by Type III restriction enzymes is governed strictly by the relative arrangement of recognition sites on a DNA substrate--endonuclease activity is usually only triggered by sequences in head-to-head orientation. Tens to thousands of base pairs can separate these sites. Long distance communication over such distances could occur by either one-dimensional (1D) DNA translocation or 3D DNA looping. To distinguish between these alternatives, we analysed the activity of EcoPI and EcoP15I on DNA catenanes in which the recognition sites were either on the same or separate rings. While substrates with a pair of sites located on the same ring were cleaved efficiently, catenanes with sites on separate rings were not cleaved. These results exclude a simple 3D DNA-looping activity. To characterize the interactions further, EcoPI was incubated with plasmids carrying two recognition sites interspersed with two 21res sites for site-specific recombination by Tn21 resolvase; inhibition of recombination would indicate the formation of stable DNA loops. No inhibition was observed, even under conditions where EcoPI translocation could also occur.
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Affiliation(s)
- Luke J Peakman
- DNA-Protein Interactions Group, Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
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40
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Abstract
Most reactions on DNA are carried out by multimeric protein complexes that interact with two or more sites in the DNA and thus loop out the DNA between the sites. The enzymes that catalyze these reactions usually have no activity until they interact with both sites. This review examines the mechanisms for the assembly of protein complexes spanning two DNA sites and the resultant triggering of enzyme activity. There are two main routes for bringing together distant DNA sites in an enzyme complex: either the proteins bind concurrently to both sites and capture the intervening DNA in a loop, or they translocate the DNA between one site and another into an expanding loop, by an energy-dependent translocation mechanism. Both capture and translocation mechanisms are discussed here, with reference to the various types of restriction endonuclease that interact with two recognition sites before cleaving DNA.
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Affiliation(s)
- Stephen E Halford
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University walk, Bristol BS8 1TD, United Kingdom.
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Gowers DM, Bellamy SRW, Halford SE. One recognition sequence, seven restriction enzymes, five reaction mechanisms. Nucleic Acids Res 2004; 32:3469-79. [PMID: 15226412 PMCID: PMC443551 DOI: 10.1093/nar/gkh685] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/13/2022] Open
Abstract
The diversity of reaction mechanisms employed by Type II restriction enzymes was investigated by analysing the reactions of seven endonucleases at the same DNA sequence. NarI, KasI, Mly113I, SfoI, EgeI, EheI and BbeI cleave DNA at several different positions in the sequence 5'-GGCGCC-3'. Their reactions on plasmids with one or two copies of this sequence revealed five distinct mechanisms. These differ in terms of the number of sites the enzyme binds, and the number of phosphodiester bonds cleaved per turnover. NarI binds two sites, but cleaves only one bond per DNA-binding event. KasI also cuts only one bond per turnover but acts at individual sites, preferring intact to nicked sites. Mly113I cuts both strands of its recognition sites, but shows full activity only when bound to two sites, which are then cleaved concertedly. SfoI, EgeI and EheI cut both strands at individual sites, in the manner historically considered as normal for Type II enzymes. Finally, BbeI displays an absolute requirement for two sites in close physical proximity, which are cleaved concertedly. The range of reaction mechanisms for restriction enzymes is thus larger than commonly imagined, as is the number of enzymes needing two recognition sites.
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Affiliation(s)
- Darren M Gowers
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK.
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42
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Embleton ML, Vologodskii AV, Halford SE. Dynamics of DNA loop capture by the SfiI restriction endonuclease on supercoiled and relaxed DNA. J Mol Biol 2004; 339:53-66. [PMID: 15123420 DOI: 10.1016/j.jmb.2004.03.046] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Received: 01/05/2004] [Revised: 03/11/2004] [Accepted: 03/18/2004] [Indexed: 11/18/2022]
Abstract
The SfiI endonuclease is a prototype for DNA looping. It binds two copies of its recognition sequence and, if Mg(2+) is present, cuts both concertedly. Looping was examined here on supercoiled and relaxed forms of a 5.5 kb plasmid with three SfiI sites: sites 1 and 2 were separated by 0.4 kb, and sites 2 and 3 by 2.0 kb. SfiI converted this plasmid directly to the products cut at all three sites, though DNA species cleaved at one or two sites were formed transiently during a burst phase. The burst revealed three sets of doubly cut products, corresponding to the three possible pairings of sites. The equilibrium distribution between the different loops was evaluated from the burst phases of reactions initiated by adding MgCl(2) to SfiI bound to the plasmid. The short loop was favored over the longer loops, particularly on supercoiled DNA. The relative rates for loop capture were assessed after adding SfiI to solutions containing the plasmid and MgCl(2). On both supercoiled and relaxed DNA, the rate of loop capture across 0.4 kb was only marginally faster than over 2.0 kb or 2.4 kb. The relative strengths and rates of looping were compared to computer simulations of conformational fluctuations in DNA. The simulations concurred broadly with the experimental data, though they predicted that increasing site separations should cause a shallower decline in the equilibrium constants than was observed but a slightly steeper decline in the rates for loop capture. Possible reasons for these discrepancies are discussed.
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Affiliation(s)
- Michelle L Embleton
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, Bristol BS8 1TD, UK
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Zaremba M, Urbanke C, Halford SE, Siksnys V. Generation of the BfiI restriction endonuclease from the fusion of a DNA recognition domain to a non-specific nuclease from the phospholipase D superfamily. J Mol Biol 2004; 336:81-92. [PMID: 14741205 DOI: 10.1016/j.jmb.2003.12.012] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 10/26/2022]
Abstract
The BfiI endonuclease cleaves DNA at fixed positions downstream of an asymmetric sequence. Unlike other restriction enzymes, it functions without metal ions. The N-terminal half of BfiI is similar to Nuc, an EDTA-resistant nuclease from Salmonella typhimurium that belongs to the phosphoplipase D superfamily. Nuc is a dimer with one active site at its subunit interface, as is BfiI, but it cuts DNA non-specifically. BfiI was cleaved by thermolysin into an N-terminal domain, which forms a dimer with non-specific nuclease activity, and a C-terminal domain, which lacks catalytic activity but binds specifically to the recognition sequence as a monomer. On denaturation with guanidinium, BfiI underwent two unfolding transitions: one at a relatively low concentration of guanidinium, to a dimeric non-specific nuclease; a second at a higher concentration, to an inactive monomer. The isolated C-terminal domain unfolded at the first (relatively low) concentration, the isolated N-terminal at the second. Hence, BfiI consists of two physically separate domains, with catalytic and dimerisation functions in the N terminus and DNA recognition functions in the C terminus. It is the first example of a restriction enzyme generated by the evolutionary fusion of a DNA recognition domain to a phosphodiesterase from the phospholipase D superfamily. BfiI may consist of three structural units: a stable central core with the active site, made from two copies of the N-terminal domain, flanked by relatively unstable C-terminal domains, that each bind a copy of the recognition sequence.
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Zhou XE, Wang Y, Reuter M, Mücke M, Krüger DH, Meehan EJ, Chen L. Crystal Structure of Type IIE Restriction Endonuclease EcoRII Reveals an Autoinhibition Mechanism by a Novel Effector-binding Fold. J Mol Biol 2004; 335:307-19. [PMID: 14659759 DOI: 10.1016/j.jmb.2003.10.030] [Citation(s) in RCA: 55] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/29/2022]
Abstract
EcoRII is a type IIE restriction endonuclease that interacts with two copies of the DNA recognition sequence 5'CCWGG, one being the actual target of cleavage, the other serving as the allosteric effector. The mode of enzyme activation by effector binding is unknown. To investigate the molecular basis of activation and cleavage mechanisms by EcoRII, the crystal structure of EcoRII mutant R88A has been solved at 2.1A resolution. The EcoRII monomer has two domains linked through a hinge loop. The N-terminal effector-binding domain has a novel DNA recognition fold with a prominent cleft. The C-terminal catalytic domain has a restriction endonuclease-like fold. Structure-based sequence alignment identified the putative catalytic site of EcoRII that is spatially blocked by the N-terminal domain. The structure together with the earlier characterized EcoRII enzyme activity enhancement in the absence of its N-terminal domain reveal an autoinhibition/activation mechanism of enzyme activity mediated by a novel effector-binding fold. This is the first case of autoinhibition, a mechanism described for many transcription factors and signal transducing proteins, of a restriction endonuclease.
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Affiliation(s)
- Xiaoyin E Zhou
- Laboratory for Structural Biology, Department of Chemistry, Graduate Programs of Biotechnology, Chemistry and Materials Science, University of Alabama in Huntsville, Huntsville, AL 35899, USA
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Mucke M, Kruger DH, Reuter M. Diversity of type II restriction endonucleases that require two DNA recognition sites. Nucleic Acids Res 2003; 31:6079-84. [PMID: 14576294 PMCID: PMC275478 DOI: 10.1093/nar/gkg836] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/12/2022] Open
Abstract
Orthodox Type IIP restriction endonucleases, which are commonly used in molecular biological work, recognize a single palindromic DNA recognition sequence and cleave within or near this sequence. Several new studies have reported on structural and biochemical peculiarities of restriction endonucleases that differ from the orthodox in that they require two copies of a particular DNA recognition sequence to cleave the DNA. These two sites requiring restriction endonucleases belong to different subtypes of Type II restriction endonucleases, namely Types IIE, IIF and IIS. We compare enzymes of these three types with regard to their DNA recognition and cleavage properties. The simultaneous recognition of two identical DNA sites by these restriction endonucleases ensures that single unmethylated recognition sites do not lead to chromosomal DNA cleavage, and might reflect evolutionary connections to other DNA processing proteins that specifically function with two sites.
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Affiliation(s)
- Merlind Mucke
- Institut für Virologie, Medizinische Fakultät (Charité) der Humboldt-Universität zu Berlin, D-10098 Berlin, Germany
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47
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Hingorani-Varma K, Bitinaite J. Kinetic analysis of the coordinated interaction of SgrAI restriction endonuclease with different DNA targets. J Biol Chem 2003; 278:40392-9. [PMID: 12851384 DOI: 10.1074/jbc.m304603200] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/06/2022] Open
Abstract
SgrAI restriction endonuclease cooperatively interacts and cleaves two target sites that include both the canonical sites, CPuCCGGPyG, and the secondary sites, CPuCCGGPy(A/T/C). It has been observed that the cleaved canonical sites stimulate SgrAI cleavage at the secondary sites. Equilibrium binding studies show that SgrAI binds to its canonical sites with a high affinity (Ka = 4-8 x 10(10) M-1) and that it has a 15-fold lower affinity for the cleaved canonical sites and a 30-fold lower affinity for the secondary sites. Steady-state kinetics reveals substrate cooperativity for SgrAI cleavage on both canonical and secondary sites. The specificity of SgrAI for the secondary site CACCGGCT, as measured by kcat/K is about 500-fold lower than that for the canonical site CACCGGCG, but this difference is reduced to 10-fold in the presence of the cleaved canonical sites. The efficiency of canonical site cleavage also increases by 3-fold when the cleaved canonical sites are present in the reaction. Furthermore, the substrate cooperativity for SgrAI cleavage is abolished for both types of sites in the presence of cleaved canonical sites. These results indicate that target site cleavage occurs via a coordinated interaction of two SgrAI protein subunits, where the subunit bound to the cleaved site stimulates the cleavage of the uncut site bound by the other subunit. The free subunits of SgrAI have the flexibility to bind different target sites and, consequently, assemble into various catalytically active complexes, which differ in their catalytic efficiencies.
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Pingoud V, Conzelmann C, Kinzebach S, Sudina A, Metelev V, Kubareva E, Bujnicki JM, Lurz R, Lüder G, Xu SY, Pingoud A. PspGI, a type II restriction endonuclease from the extreme thermophile Pyrococcus sp.: structural and functional studies to investigate an evolutionary relationship with several mesophilic restriction enzymes. J Mol Biol 2003; 329:913-29. [PMID: 12798682 DOI: 10.1016/s0022-2836(03)00523-0] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Academic Contribution Register] [Indexed: 11/17/2022]
Abstract
We present here the first detailed biochemical analysis of an archaeal restriction enzyme. PspGI shows sequence similarity to SsoII, EcoRII, NgoMIV and Cfr10I, which recognize related DNA sequences. We demonstrate here that PspGI, like SsoII and unlike EcoRII or NgoMIV and Cfr10I, interacts with and cleaves DNA as a homodimer and is not stimulated by simultaneous binding to two recognition sites. PspGI and SsoII differ in their basic biochemical properties, viz. stability against chemical denaturation and proteolytic digestion, DNA binding and the pH, MgCl(2) and salt-dependence of their DNA cleavage activity. In contrast, the results of mutational analyses and cross-link experiments show that PspGI and SsoII have a very similar DNA binding site and catalytic center as NgoMIV and Cfr10I (whose crystal structures are known), and presumably also as EcoRII, in spite of the fact that these enzymes, which all recognize variants of the sequence -/CC-GG- (/ denotes the site of cleavage), are representatives of different subgroups of type II restriction endonucleases. A sequence comparison of all known restriction endonuclease sequences, furthermore, suggests that several enzymes recognizing other DNA sequences also share amino acid sequence similarities with PspGI, SsoII and EcoRII in the region of the presumptive active site. These results are discussed in an evolutionary context.
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Affiliation(s)
- Vera Pingoud
- Institut für Biochemie, Justus-Liebig-Universität, Heinrich-Buff-Ring 58, D-35392 Giessen, Germany.
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Abstract
Single molecule fluorescence resonance energy transfer (FRET) and fluorescence correlation spectroscopy were used to investigate DNA looping by NgoMIV restriction endonuclease. Using a linear double-stranded DNA (dsDNA) molecule labeled with a fluorescence donor molecule, Cy3, and fluorescence acceptor molecule, Cy5, and by varying the concentration of NgoMIV endonuclease from 0 to 3 x 10(-6) M, it was possible to detect and determine diffusion properties of looped DNA/protein complexes. FRET efficiency distributions revealed a subpopulation of complexes with an energy transfer efficiency of 30%, which appeared upon addition of enzyme in the picomolar to nanomolar concentration range (using 10(-11) M dsDNA). The concentration dependence, fluorescence burst size analysis, and fluorescence correlation analysis were all consistent with this subpopulation arising from a sequence specific interaction between an individual enzyme and a DNA molecule. A 30% FRET efficiency corresponds to a distance of approximately 65 A, which correlates well with the distance between the ends of the dsDNA molecule when bound to NgoMIV according to the crystal structure of this complex. Formation of the looped complexes was also evident in measurements of the diffusion times of freely diffusing DNA molecules with and without NgoMIV. At very high protein concentrations compared to the DNA concentration, FRET and fluorescence correlation spectroscopy results revealed the formation of larger DNA/protein complexes.
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Affiliation(s)
- Zivile Katiliene
- Department of Chemistry and Biochemistry and the Center for the Study of Early Events in Photosynthesis, Arizona State University, Tempe, Arizona 85287-1604, USA.
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50
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Abstract
The SgrAI endonuclease usually cleaves DNA with two recognition sites more rapidly than DNA with one site, often converting the former directly to the products cut at both sites. In this respect, SgrAI acts like the tetrameric restriction enzymes that bind two copies of their target sites before cleaving both sites concertedly. However, by analytical ultracentrifugation, SgrAI is a dimer in solution though it aggregates to high molecular mass species when bound to its specific DNA sequence. Its reaction kinetics indicate that it uses different mechanisms to cleave DNA with one and with two SgrAI sites. It cleaves the one-site DNA in the style of a dimeric restriction enzyme acting at an individual site, mediating neither interactions in trans, as seen with the tetrameric enzymes, nor subunit associations, as seen with the monomeric enzymes. In contrast, its optimal reaction on DNA with two sites involves an association of protein subunits: two dimers bound to sites in cis may associate to form a tetramer that has enhanced activity, which then cleaves both sites concurrently. The mode of action of SgrAI differs from all restriction enzymes characterised previously, so this study extends the range of mechanisms known for restriction endonucleases.
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Affiliation(s)
- Lucy E Daniels
- Department of Biochemistry, School of Medical Sciences, University of Bristol, University Walk, BS8 1TD, Bristol, UK
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