Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I

Yu, Liping; Zhu, Chang-Xi; Tse‐Dinh, Yuk‐Ching; Fesik, Stephen W.

doi:10.1021/bi00023a008

Cited by 47 publications

(41 citation statements)

References 38 publications

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“…The type I enzymes are classified as either subfamily type IA if the protein links to the 5Ј phosphate or subfamily type IB when the protein attaches to the 3Ј phosphate. There is extensive sequence similarity among members of the same subfamily (10) but almost no sequence or structural similarity between the two subfamilies (11,12). All bacterial type I topoisomerases are type IA enzymes.…”

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confidence: 99%

New Alkaloid Antibiotics That Target the DNA Topoisomerase I of Streptococcus pneumoniae

Garcı́a

Blázquez

Ferrándiz

et al. 2011

Journal of Biological Chemistry

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Streptococcus pneumoniae has two type II DNA-topoisomerases (DNA-gyrase and DNA topoisomerase IV) and a single type I enzyme (DNA-topoisomerase I, TopA), as demonstrated here. Although fluoroquinolones target type II enzymes, antibiotics efficiently targeting TopA have not yet been reported. Eighteen alkaloids (seven aporphine and 11 phenanthrenes) were semisynthesized from boldine and used to test inhibition both of TopA activity and of cell growth. Two phenanthrenes (seconeolitsine and N-methyl-seconeolitsine) effectively inhibited both TopA activity and cell growth at equivalent concentrations (ϳ17 M). Evidence for in vivo TopA targeting by seconeolitsine was provided by the protection of growth inhibition in a S. pneumoniae culture in which the enzyme was overproduced. Additionally, hypernegative supercoiling was observed in an internal plasmid after drug treatment. Furthermore, a model of pneumococcal TopA was made based on the crystal structure of Escherichia coli TopA. Docking calculations indicated strong interactions of the alkaloids with the nucleotide-binding site in the closed protein conformation, which correlated with their inhibitory effect. Finally, although seconeolitsine and N-methyl-seconeolitsine inhibited TopA and bacterial growth, they did not affect human cell viability. Therefore, these new alkaloids can be envisaged as new therapeutic candidates for the treatment of S. pneumoniae infections resistant to other antibiotics.Antibiotic resistance in bacterial pathogens is a serious clinical problem. This problem affects Streptococcus pneumoniae (the pneumococcus), which, in addition to being one of the principal human pathogens, is the main ethyological agent of community-acquired pneumonia. Annually, approximately one million children aged Ͻ5 years die of pneumococcal pneumonia, meningitis, and/or sepsis worldwide (1). Resistance to currently used antimicrobial drugs for the treatment of pneumococcal infections, including ␤-lactams and macrolides, has spread worldwide in the last two decades (2). The new fluoroquinolones, such as levofloxacin and moxifloxacin, which act on type II DNA topoisomerases, are therapeutic alternatives for treatment of adult patients with community-acquired pneumonia (3). However, although resistance to fluoroquinolones in S. pneumoniae is still lower than 3% (4), an increase in resistance is likely to occur.DNA topoisomerases participate in almost all cellular functions involving DNA transactions (5). They solve the topological problems associated with DNA replication, transcription, and recombination. In addition, these enzymes fine-tune the steady-state level of DNA supercoiling, both facilitating protein interactions with the DNA and preventing excessive supercoiling that is deleterious. In bacteria, the homeostasis of DNA supercoiling is maintained by the opposing activities of topoisomerases that relax DNA and gyrase that introduces negative supercoils. The transcriptional response to DNA relaxation involves genes coding for all the DNA topoisomerases from S...

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confidence: 99%

New Alkaloid Antibiotics That Target the DNA Topoisomerase I of Streptococcus pneumoniae

Garcı́a

Blázquez

Ferrándiz

et al. 2011

Journal of Biological Chemistry

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“…DNA gyrase of Escherichia coli comprises subunits encoded by the gyrA and gyrB genes and is a heterotetramer of A2+B2 configuration, while the eukaryotic topoisomerase enzymes, which can be viewed as single chain chimeras of the two DNA gyrase subunits, are consequently homodimeric in structure 17 . [33][34][35] .…”

Section: Prokaryotic Topoisomerasesmentioning

confidence: 99%

Topoisomerase as target for antibacterial and anticancer drug discovery

Kathiravan

Khilare

Nikoomanesh

et al. 2012

Journal of Enzyme Inhibition and Medicinal Chemistry

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“…Although both the ␣ and the ␤ carboxyl terminal regions contain several potential zinc finger motifs, there is very little homology between the two. The carboxyl terminus of E. coli topo I shows some similarity to the ␣ isozymes and has been shown to possess five zinc ribbon domains with the first three binding zinc (22)(23)(24). This region in E. coli topo I binds ssDNA (25,26) as well as interacting with RNA polymerase II (27), suggesting that these regions in the ␣ and ␤ isozymes may be multifunctional as well.…”

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confidence: 99%

Drosophila melanogaster Topoisomerase IIIα Preferentially Relaxes a Positively or Negatively Supercoiled Bubble Substrate and Is Essential during Development

Plank¹,

Chu

Pohlhaus

et al. 2005

Journal of Biological Chemistry

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Eukaryotic type IA topoisomerases are important for the normal function of the cell, and in some cases essential for the organism, although their role in DNA metabolism remains to be elucidated. In this study, we cloned Drosophila melanogaster topoisomerase (topo) III␣ from an embryonic cDNA library and expressed and purified the protein to >95% homogeneity. This enzyme partially relaxes a hypernegatively supercoiled plasmid substrate consistent with other purified topo IIIs. A novel, covalently closed bubble substrate was prepared for this study, which topo III␣ fully relaxed, regardless of the handedness of the supercoils. Experiments with the bubble substrate demonstrate that topo III␣ has much different reaction preferences from those obtained by plasmid substrate-based assays. This is presumably due to the fact that solution conditions can affect the structure of plasmid based substrates and therefore their suitability as a substrate. A mutant allele of the Top3␣ gene, Top3␣ 191, was isolated through imprecise excision mutagenesis of an existing P-element inserted in the first intron of the gene. Top3␣ 191 is recessive lethal, with most of the homozygous individuals surviving to pupation but never emerging to adulthood. Whereas this mutation can be rescued by a Top3␣ transgene, ubiquitous overexpression of D. melanogaster topo III␤ cannot rescue this allele.DNA topoisomerases are ubiquitous enzymes found in all cells and some viruses that regulate the topology of DNA in such cellular processes as replication, transcription, and recombination (1, 2). These enzymes work by making a transient covalent bond to the phosphodiester backbone of the DNA, creating a protein mediated DNA gate, which allows another strand (or strands) of DNA to pass through this reversible break. Type II topoisomerases create double-stranded breaks, and double strand passage, whereas type I topoisomerases break a single strand of DNA. The type I topoisomerases are further divided into the IA and IB subfamilies, based on structural and mechanistic differences (3, 4). Topoisomerase III (topo III) 1 is a member of the type IA subfamily that is conserved from bacteria to humans.Topo III was originally purified by following superhelical relaxation activity from extracts of Escherichia coli containing a deletion for topo I (5). This enzyme was also independently purified based on its decatenating abilities in an assay utilizing plasmid DNA replication intermediates (6). Despite the strong sequence homology that this protein shares with E. coli topo I (7), purified topo III shows a weak ability to relax negatively supercoiled DNA (5). The relaxation activity of Topo III is strongly inhibited by single-stranded DNA (ssDNA) (5), and the enzyme was subsequently shown to preferentially bind ssDNA. The decatenase activity of topo III also depends on the presence of single-stranded regions in the catenated DNA (6). Recently, Nurse et al. showed that topo III serves as a decatenase in vivo by removing precatenanes that arise during replication of ci...

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Solution structure of the C-terminal single-stranded DNA-binding domain of Escherichia coli topoisomerase I

Cited by 47 publications

References 38 publications

New Alkaloid Antibiotics That Target the DNA Topoisomerase I of Streptococcus pneumoniae

New Alkaloid Antibiotics That Target the DNA Topoisomerase I of Streptococcus pneumoniae

Topoisomerase as target for antibacterial and anticancer drug discovery

Drosophila melanogaster Topoisomerase IIIα Preferentially Relaxes a Positively or Negatively Supercoiled Bubble Substrate and Is Essential during Development

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