Structure of the Topoisomerase IV C-terminal Domain

Hsieh, T.J.; Farh, Lynn; Huang, Wai Mun; Chan, Nei-Li

doi:10.1074/jbc.m408934200

Cited by 46 publications

(45 citation statements)

References 54 publications

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“…One is the presence of a GyrA-box, QRRGGKG (19), and the other is the fact that the ParC CTD possesses only five blades. However, some ParC CTDs possess six blades (14,15). Thus, the GyrA-box turns out to be the only motif that is present in GyrA CTDs, but not in ParC CTDs.…”

Section: Resultsmentioning

confidence: 99%

“…Alterations of the GyrA-box-Structural studies have revealed two differences between E. coli GyrA and E. coli ParC CTDs (12)(13)(14)(15)(16). One is the presence of a GyrA-box, QRRGGKG (19), and the other is the fact that the ParC CTD possesses only five blades.…”

Section: Resultsmentioning

confidence: 99%

“…Recent structural studies, however, run counter to this view. Both GyrA (12,13) and ParC (14,15) CTDs adopt a "␤-pinwheel" fold, which is reminiscent of the predicted "␤-propeller" fold built of 6 blades (16), and not only the GyrA CTD but also the ParC CTD can bind and bend DNA (12). In addition, a single-molecule experiment has demonstrated that Escherichia coli Topo IV bends DNA upon its binding to DNA (17).…”

mentioning

confidence: 99%

“…One is the presence of a GyrA-box, QRRGGKG (19), in the first (the amino-terminal-most) blade of the GyrA CTD and the other is the fact that the ␤-pinwheel fold of the GyrA CTD consists of six blades, whereas that of the ParC CTD contains only five blades. Although all GyrA CTDs possess full six blades, ParC CTDs exhibit significant structural diversity with various numbers of blades (12,14,15). Thus, the GyrA-box is the only motif unique to the GyrA CTD.…”

mentioning

confidence: 99%

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The “GyrA-box” Is Required for the Ability of DNA Gyrase to Wrap DNA and Catalyze the Supercoiling Reaction

Kramlinger¹,

Hiasa

2006

Journal of Biological Chemistry

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DNA gyrase is the only topoisomerase that can introduce negative supercoils into DNA. It is thought that the binding of conventional type II topoisomerases, including topoisomerase IV, to DNA takes place at the catalytic domain across the DNA gate, whereas DNA gyrase binds to DNA not only at the amino-terminal catalytic domain but also at the carboxyl-terminal domain (CTD) of the GyrA subunit. The binding of the GyrA CTD to DNA allows gyrase to wrap DNA around itself and catalyze the supercoiling reaction. Recent structural studies, however, have revealed striking similarities between the GyrA CTD and the ParC CTD, as well as the ability of the ParC CTD to bind and bend DNA. Thus, the molecular basis of gyrase-mediated wrapping of DNA needs to be reexamined. Here, we have conducted a mutational analysis to determine the role of the "GyrA-box," a 7-amino acid-long motif unique to the GyrA CTD, in determining the DNA binding mode of gyrase. Either a deletion of the entire GyrA-box or substitution of the GyrA-box with 7 Ala residues abolishes the ability of gyrase to wrap DNA around itself and catalyze the supercoiling reaction. However, these mutations do not affect the relaxation and decatenation activities of gyrase. Thus, the presence of a GyrA-box allows gyrase to wrap DNA and catalyze the supercoiling reaction. The consequence of the loss of the GyrA-box during evolution of bacterial type II topoisomerases is discussed.DNA topoisomerases are ubiquitous enzymes that alter the linking number of double-stranded DNA. There are two classes of topoisomerases, type I and type II (1, 2). Type I topoisomerases alter the linking number in steps of one by breaking one strand of duplex DNA, passing the other strand through the break, and then resealing the broken strand, whereas type II topoisomerases alter the linking number in steps of two by breaking both strands, passing another segment of the helix through the break, and then resealing the broken strands. The discovery of a novel type II enzyme from Sulfolobus shibatae (3, 4) prompted the division of the type II topoisomerases into the type IIA and type IIB subtypes. All type II topoisomerases, except the S. shibatae topoisomerase VI, belong to type IIA subtype.DNA gyrase (5-7) and topoisomerase (Topo 3 ) IV (8) are type IIA topoisomerases. Gyrase and Topo IV consist of GyrA and GyrB subunits and ParC and ParE subunits, respectively. GyrA and ParC subunits catalyze strand-breakage and reunion reactions, whereas GyrB and ParE subunits hydrolyze ATP. The active forms of gyrase and Topo IV are an ␣ 2 ␤ 2 tetramer, and these topoisomerases bind double-stranded DNA. Topo IV can relax both positive and negative supercoils and catenate and decatenate covalently closed, negatively supercoiled, doublestranded circular (form I) and nicked or gapped, double-stranded circular DNA molecules. Gyrase can supercoil covalently closed, relaxed, double-stranded circular (form IЈ) DNA molecules, catenate and decatenate DNA rings, and, in the absence of ATP, relax negative supercoils (1...

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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The “GyrA-box” Is Required for the Ability of DNA Gyrase to Wrap DNA and Catalyze the Supercoiling Reaction

Kramlinger¹,

Hiasa

2006

Journal of Biological Chemistry

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“…The function of topo II's C-terminal region is not well understood, except that it is implicated in the regulation of topo II (25). Recent studies on two other closely related type IIA topos, DNA gyrase and topo IV, suggest that their C-terminal domains bind and bend DNA to correctly position substrate DNA for the enzymatic reaction (26,27). Although RHL1 does not have significant homology to the C terminus of DNA gyrase or topo IV, it is possible that RHL1 performs a similar function.…”

Section: Hyp7 Is Essential For Successive Endocycles Beyond 8cmentioning

confidence: 99%

RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth

Sugimoto‐Shirasu

Roberts

Stacey

et al. 2005

Proc. Natl. Acad. Sci. U.S.A.

107

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How cells achieve their final sizes is a pervasive biological question. One strategy to increase cell size is for the cell to amplify its chromosomal DNA content through endoreduplication cycles. Although endoreduplication is widespread in eukaryotes, we know very little about its molecular mechanisms. Successful progression of the endoreduplication cycle in Arabidopsis requires a plant homologue of archaeal DNA topoisomerase (topo) VI. To further understand how DNA is endoreduplicated and how this process is regulated, we isolated a dwarf Arabidopsis mutant, hyp7 (hypocotyl 7), in which various large cell types that in the wild type normally endoreduplicate multiple times complete only the first two rounds of endoreduplication and stall at 8C. HYP7 encodes the RHL1 (ROOT HAIRLESS 1) protein, and sequence analysis reveals that RHL1 has similarity to the C-terminal domain of mammalian DNA topo II␣, another type II topo that shares little sequence homology with topo VI. RHL1 shows DNA binding activity in vitro, and we present both genetic and in vivo evidence that RHL1 forms a multiprotein complex with plant topo VI. We propose that RHL1 plays an essential role in the topo VI complex to modulate its function and that the two distantly related topos, topo II and topo VI, have evolved a common domain that extends their function. Our data suggest that plant topo II and topo VI play distinct but overlapping roles during the mitotic cell cycle and endoreduplication cycle.endoreduplication ͉ hypocotyl ͉ root hairless T he control of cell size is a highly regulated process with inputs from genetic, hormonal, and environmental cues. Yeast and mammalian cells usually only double their size during their development; therefore, a key question in their size control is how proliferating cells coordinate cell growth and cell division to maintain size homeostasis. Yeast and many mammalian cells have a cell size checkpoint mechanism in which cells divide only when they reach a critical size (1), whereas some mammalian cells may control their size through extracellular signals (2). Although plant cells also double their cell size during proliferation, they commonly undergo an additional, massive (sometimes Ͼ1,000-fold), postmitotic cell enlargement. Such a large increase in volume is driven by a combination of production of new cytoplasmic mass and cell expansion (driven by water uptake and vacuolar growth), but little is known about the underlying mechanisms involved. Recent genetic evidence strongly supports the classical ''karyoplasmic ratio'' theory that one mechanism to increase cell size is by increasing the ploidy level within a cell, for example through endoreduplication, defined as the amplification of chromosomal DNA without corresponding cell division (3). Several mutants and transgenic plants that have aberrant levels of endoreduplication have been isolated and have led to the identification of key regulators of the endoreduplication cycle or endocycle (3-7). How these regulators control downstream events, however, rem...

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Introduction and Historical Perspective

Forterre

2011

Cancer Drug Discovery and Development

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Structure of the Topoisomerase IV C-terminal Domain

Cited by 46 publications

References 54 publications

The “GyrA-box” Is Required for the Ability of DNA Gyrase to Wrap DNA and Catalyze the Supercoiling Reaction

The “GyrA-box” Is Required for the Ability of DNA Gyrase to Wrap DNA and Catalyze the Supercoiling Reaction

RHL1 is an essential component of the plant DNA topoisomerase VI complex and is required for ploidy-dependent cell growth

Introduction and Historical Perspective

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