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Sutormin DA, Galivondzhyan AK, Polkhovskiy AV, Kamalyan SO, Severinov KV, Dubiley SA. Diversity and Functions of Type II Topoisomerases. Acta Naturae 2021; 13:59-75. [PMID: 33959387 PMCID: PMC8084294 DOI: 10.32607/actanaturae.11058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 10/09/2020] [Indexed: 11/29/2022] Open
Abstract
The DNA double helix provides a simple and elegant way to store and copy genetic information. However, the processes requiring the DNA helix strands separation, such as transcription and replication, induce a topological side-effect - supercoiling of the molecule. Topoisomerases comprise a specific group of enzymes that disentangle the topological challenges associated with DNA supercoiling. They relax DNA supercoils and resolve catenanes and knots. Here, we review the catalytic cycles, evolution, diversity, and functional roles of type II topoisomerases in organisms from all domains of life, as well as viruses and other mobile genetic elements.
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Affiliation(s)
- D. A. Sutormin
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - A. K. Galivondzhyan
- Lomonosov Moscow State University, Moscow, 119991 Russia
- Institute of Molecular Genetics RAS, Moscow, 123182 Russia
| | - A. V. Polkhovskiy
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - S. O. Kamalyan
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
| | - K. V. Severinov
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
- Centre for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology RAS, Moscow, 119334 Russia
- Waksman Institute for Microbiology, Piscataway, New Jersey, 08854 USA
| | - S. A. Dubiley
- Institute of Gene Biology RAS, Moscow, 119334 Russia
- Centre for Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 121205 Russia
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Abstract
Topoisomerases in the type IA subfamily can catalyze change in topology for both DNA and RNA substrates. A type IA topoisomerase may have been present in a last universal common ancestor (LUCA) with an RNA genome. Type IA topoisomerases have since evolved to catalyze the resolution of topological barriers encountered by genomes that require the passing of nucleic acid strand(s) through a break on a single DNA or RNA strand. Here, based on available structural and biochemical data, we discuss how a type IA topoisomerase may recognize and bind single-stranded DNA or RNA to initiate its required catalytic function. Active site residues assist in the nucleophilic attack of a phosphodiester bond between two nucleotides to form a covalent intermediate with a 5'-phosphotyrosine linkage to the cleaved nucleic acid. A divalent ion interaction helps to position the 3'-hydroxyl group at the precise location required for the cleaved phosphodiester bond to be rejoined following the passage of another nucleic acid strand through the break. In addition to type IA topoisomerase structures observed by X-ray crystallography, we now have evidence from biophysical studies for the dynamic conformations that are required for type IA topoisomerases to catalyze the change in the topology of the nucleic acid substrates.
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Affiliation(s)
- Tumpa Dasgupta
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Shomita Ferdous
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Biochemistry PhD Program, Florida International University, Miami, FL 33199, USA
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, Miami, FL 33199, USA; (T.D.); (S.F.)
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
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Waraich NF, Jain S, Colloms SD, Stark WM, Burton NP, Maxwell A. A novel decatenation assay for DNA topoisomerases using a singly-linked catenated substrate. Biotechniques 2020; 69:356-62. [PMID: 33000631 DOI: 10.2144/btn-2020-0059] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Decatenation is a crucial in vivo reaction of DNA topoisomerases in DNA replication and is frequently used in in vitro drug screening. Usually this reaction is monitored using kinetoplast DNA as a substrate, although this assay has several limitations. Here we have engineered a substrate for Tn3 resolvase that generates a singly-linked catenane that can readily be purified from the DNA substrate after restriction enzyme digestion and centrifugation. We show that this catenated substrate can be used with high sensitivity in topoisomerase assays and drug-inhibition assays.
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Jolly SM, Gainetdinov I, Jouravleva K, Zhang H, Strittmatter L, Bailey SM, Hendricks GM, Dhabaria A, Ueberheide B, Zamore PD. Thermus thermophilus Argonaute Functions in the Completion of DNA Replication. Cell 2020; 182:1545-1559.e18. [PMID: 32846159 PMCID: PMC7502556 DOI: 10.1016/j.cell.2020.07.036] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/25/2020] [Accepted: 07/24/2020] [Indexed: 01/06/2023]
Abstract
In many eukaryotes, Argonaute proteins, guided by short RNA sequences, defend cells against transposons and viruses. In the eubacterium Thermus thermophilus, the DNA-guided Argonaute TtAgo defends against transformation by DNA plasmids. Here, we report that TtAgo also participates in DNA replication. In vivo, TtAgo binds 15- to 18-nt DNA guides derived from the chromosomal region where replication terminates and associates with proteins known to act in DNA replication. When gyrase, the sole T. thermophilus type II topoisomerase, is inhibited, TtAgo allows the bacterium to finish replicating its circular genome. In contrast, loss of gyrase and TtAgo activity slows growth and produces long sausage-like filaments in which the individual bacteria are linked by DNA. Finally, wild-type T. thermophilus outcompetes an otherwise isogenic strain lacking TtAgo. We propose that the primary role of TtAgo is to help T. thermophilus disentangle the catenated circular chromosomes generated by DNA replication.
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Affiliation(s)
- Samson M Jolly
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA; Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Ildar Gainetdinov
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Karina Jouravleva
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Han Zhang
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Lara Strittmatter
- Department of Radiology, Division of Cell Biology and Imaging, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Shannon M Bailey
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Gregory M Hendricks
- Department of Radiology, Division of Cell Biology and Imaging, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Avantika Dhabaria
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, NY 10016, USA
| | - Beatrix Ueberheide
- Proteomics Laboratory, Division of Advanced Research Technologies, New York University School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Center for Cognitive Neurology, Department of Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Phillip D Zamore
- Howard Hughes Medical Institute and RNA Therapeutics Institute, University of Massachusetts Medical School, Worcester, MA 01605, USA.
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Weidlich D, Klostermeier D. Functional interactions between gyrase subunits are optimized in a species-specific manner. J Biol Chem 2020; 295:2299-2312. [PMID: 31953321 DOI: 10.1074/jbc.ra119.010245] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 01/03/2020] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase is a bacterial DNA topoisomerase that catalyzes ATP-dependent negative DNA supercoiling and DNA decatenation. The enzyme is a heterotetramer comprising two GyrA and two GyrB subunits. Its overall architecture is conserved, but species-specific elements in the two subunits are thought to optimize subunit interaction and enzyme function. Toward understanding the roles of these different elements, we compared the activities of Bacillus subtilis, Escherichia coli, and Mycobacterium tuberculosis gyrases and of heterologous enzymes reconstituted from subunits of two different species. We show that B. subtilis and E. coli gyrases are proficient DNA-stimulated ATPases and efficiently supercoil and decatenate DNA. In contrast, M. tuberculosis gyrase hydrolyzes ATP only slowly and is a poor supercoiling enzyme and decatenase. The heterologous enzymes are generally less active than their homologous counterparts. The only exception is a gyrase reconstituted from mycobacterial GyrA and B. subtilis GyrB, which exceeds the activity of M. tuberculosis gyrase and reaches the activity of the B. subtilis gyrase, indicating that the activities of enzymes containing mycobacterial GyrB are limited by ATP hydrolysis. The activity pattern of heterologous gyrases is in agreement with structural features present: B. subtilis gyrase is a minimal enzyme, and its subunits can functionally interact with subunits from other bacteria. In contrast, the specific insertions in E. coli and mycobacterial gyrase subunits appear to prevent efficient functional interactions with heterologous subunits. Understanding the molecular details of gyrase adaptations to the specific physiological requirements of the respective organism might aid in the development of species-specific gyrase inhibitors.
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Affiliation(s)
- Daniela Weidlich
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany
| | - Dagmar Klostermeier
- Institute for Physical Chemistry, University of Muenster, Corrensstrasse 30, D-48149 Muenster, Germany.
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Lee JH, Berger JM. Cell Cycle-Dependent Control and Roles of DNA Topoisomerase II. Genes (Basel) 2019; 10:E859. [PMID: 31671531 DOI: 10.3390/genes10110859] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/25/2019] [Accepted: 10/28/2019] [Indexed: 12/13/2022] Open
Abstract
Type II topoisomerases are ubiquitous enzymes in all branches of life that can alter DNA superhelicity and unlink double-stranded DNA segments during processes such as replication and transcription. In cells, type II topoisomerases are particularly useful for their ability to disentangle newly-replicated sister chromosomes. Growing lines of evidence indicate that eukaryotic topoisomerase II (topo II) activity is monitored and regulated throughout the cell cycle. Here, we discuss the various roles of topo II throughout the cell cycle, as well as mechanisms that have been found to govern and/or respond to topo II function and dysfunction. Knowledge of how topo II activity is controlled during cell cycle progression is important for understanding how its misregulation can contribute to genetic instability and how modulatory pathways may be exploited to advance chemotherapeutic development.
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Kratz AS, Richter KT, Schlosser YT, Schmitt M, Shumilov A, Delecluse HJ, Hoffmann I. Fbxo28 promotes mitotic progression and regulates topoisomerase IIα-dependent DNA decatenation. Cell Cycle 2016; 15:3419-3431. [PMID: 27754753 DOI: 10.1080/15384101.2016.1246093] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Topoisomerase IIα is an essential enzyme that resolves topological constraints in genomic DNA. It functions in disentangling intertwined chromosomes during anaphase leading to chromosome segregation thus preserving genomic stability. Here we describe a previously unrecognized mechanism regulating topoisomerase IIα activity that is dependent on the F-box protein Fbxo28. We find that Fbxo28, an evolutionarily conserved protein, is required for proper mitotic progression. Interfering with Fbxo28 function leads to a delay in metaphase-to-anaphase progression resulting in mitotic defects as lagging chromosomes, multipolar spindles and multinucleation. Furthermore, we find that Fbxo28 interacts and colocalizes with topoisomerase IIα throughout the cell cycle. Depletion of Fbxo28 results in an increase in topoisomerase IIα-dependent DNA decatenation activity. Interestingly, blocking the interaction between Fbxo28 and topoisomerase IIα also results in multinucleated cells. Our findings suggest that Fbxo28 regulates topoisomerase IIα decatenation activity and plays an important role in maintaining genomic stability.
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Affiliation(s)
- Anne-Sophie Kratz
- a Cell Cycle Control and Carcinogenesis, F045, German Cancer Research Center , Heidelberg , Germany
| | - Kai T Richter
- a Cell Cycle Control and Carcinogenesis, F045, German Cancer Research Center , Heidelberg , Germany
| | - Yvonne T Schlosser
- a Cell Cycle Control and Carcinogenesis, F045, German Cancer Research Center , Heidelberg , Germany
| | - Miriam Schmitt
- a Cell Cycle Control and Carcinogenesis, F045, German Cancer Research Center , Heidelberg , Germany
| | - Anatoliy Shumilov
- b Pathogenesis of Virus Associated Tumors, F100, German Cancer Research Center , Heidelberg , Germany
| | - Henri-Jacques Delecluse
- b Pathogenesis of Virus Associated Tumors, F100, German Cancer Research Center , Heidelberg , Germany
| | - Ingrid Hoffmann
- a Cell Cycle Control and Carcinogenesis, F045, German Cancer Research Center , Heidelberg , Germany
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Martin CA, Murray JE, Carroll P, Leitch A, Mackenzie KJ, Halachev M, Fetit AE, Keith C, Bicknell LS, Fluteau A, Gautier P, Hall EA, Joss S, Soares G, Silva J, Bober MB, Duker A, Wise CA, Quigley AJ, Phadke SR, Wood AJ, Vagnarelli P, Jackson AP. Mutations in genes encoding condensin complex proteins cause microcephaly through decatenation failure at mitosis. Genes Dev 2016; 30:2158-2172. [PMID: 27737959 PMCID: PMC5088565 DOI: 10.1101/gad.286351.116] [Citation(s) in RCA: 85] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2016] [Accepted: 09/09/2016] [Indexed: 11/24/2022]
Abstract
Martin et al. report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of condensin complexes, cause microcephaly. Frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis are the consequence of failed sister chromatid disentanglement during chromosome compaction. Compaction of chromosomes is essential for accurate segregation of the genome during mitosis. In vertebrates, two condensin complexes ensure timely chromosome condensation, sister chromatid disentanglement, and maintenance of mitotic chromosome structure. Here, we report that biallelic mutations in NCAPD2, NCAPH, or NCAPD3, encoding subunits of these complexes, cause microcephaly. In addition, hypomorphic Ncaph2 mice have significantly reduced brain size, with frequent anaphase chromatin bridge formation observed in apical neural progenitors during neurogenesis. Such DNA bridges also arise in condensin-deficient patient cells, where they are the consequence of failed sister chromatid disentanglement during chromosome compaction. This results in chromosome segregation errors, leading to micronucleus formation and increased aneuploidy in daughter cells. These findings establish “condensinopathies” as microcephalic disorders, with decatenation failure as an additional disease mechanism for microcephaly, implicating mitotic chromosome condensation as a key process ensuring mammalian cerebral cortex size.
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Affiliation(s)
- Carol-Anne Martin
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Jennie E Murray
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paula Carroll
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Andrea Leitch
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Karen J Mackenzie
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Mihail Halachev
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Ahmed E Fetit
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Charlotte Keith
- South East Scotland Cytogenetics Service, Western General Hospital, Edinburgh EH4 2XU, United Kingdom
| | - Louise S Bicknell
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom.,Department of Pathology, Dunedin School of Medicine, University of Otago, Dunedin 9054, New Zealand
| | - Adeline Fluteau
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Philippe Gautier
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Emma A Hall
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Shelagh Joss
- West of Scotland Genetic Service, Southern General Hospital, Glasgow G51 4TF, United Kingdom
| | - Gabriela Soares
- Centro de Genética Médica Doutor Jacinto Magalhães, Centro Hospitalar do Porto, 4099-028 Porto, Portugal
| | - João Silva
- Instituto de Biologia Molecular e Celular (IBMC), 4150 Porto, Portugal.,Instituto de Investigação e Inovação em Saúde (I3S), Universidade do Porto, 4200-135 Porto, Portugal
| | - Michael B Bober
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Angela Duker
- Division of Genetics, Department of Pediatrics, A.I. duPont Hospital for Children, Wilmington, Delaware 19803, USA
| | - Carol A Wise
- Sarah M. and Charles E. Seay Center for Musculoskeletal Research, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Orthopedic Surgery, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,Department of Pediatrics, Texas Scottish Rite Hospital for Children, Dallas, Texas 75219, USA.,McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, Texas 75350, USA
| | - Alan J Quigley
- Department of Radiology, Royal Hospital for Sick Children, Edinburgh EH9 1LF, United Kingdom
| | - Shubha R Phadke
- Sanjay Gandhi Postgraduate Institute of Medical Sciences, Lucknow, Uttar Pradesh 226014, India
| | | | - Andrew J Wood
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
| | - Paola Vagnarelli
- Biosciences, Research Institute for Health and Environment, Brunel University, London UB8 3PH, United Kingdom
| | - Andrew P Jackson
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom
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Affiliation(s)
- Makoto M Yoshida
- a Department of Molecular Biosciences , University of Kansas , Lawrence , KS , USA
| | - Yoshiaki Azuma
- a Department of Molecular Biosciences , University of Kansas , Lawrence , KS , USA
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Abstract
DNA gyrase is unique among topoisomerases in its ability to introduce negative supercoils into closed-circular DNA. We have demonstrated that deletion of the C-terminal DNA-binding domain of the A subunit of gyrase gives rise to an enzyme that cannot supercoil DNA but relaxes DNA in an ATP-dependent manner. Novobiocin, a competitive inhibitor of ATP binding by gyrase, inhibits this reaction. The truncated enzyme, unlike gyrase, does not introduce a right-handed wrap when bound to DNA and stabilizes DNA crossovers; characteristics reminiscent of conventional type II topoisomerases. This new enzyme form can decatenate DNA circles with increased efficiency compared with intact gyrase and, as a result, can complement the temperature-sensitive phenotype of a parCts mutant. Thus these results suggest that the unique properties of DNA gyrase are attributable to the wrapping of DNA around the C-terminal DNA-binding domains of the A subunits and provide an insight into the mechanism of type II topoisomerases.
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Affiliation(s)
- S C Kampranis
- Department of Biochemistry, University of Leicester, United Kingdom
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