Mechanistic study of<i>E. coli</i>DNA topoisomerase I: cleavage of oligonucleotides

Tse‐Dinh, Yuk‐Ching; McCarron, B.G.H.; Arentzen, René; Chowdhry, Vinay

doi:10.1093/nar/11.24.8691

Cited by 35 publications

(19 citation statements)

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“…DNA cleavage by Topo IA could occur in the presence of EDTA (Tse-Dinh et al, 1983; Domanico and Tse-Dinh, 1991) and metal ions were absent in crystal structures of Topo IA and Topo IA-DNA complexes (Lima et al, 1994; Mondragon and Digate, 1999; Changela et al, 2001). The hallmark of TOPRIM is the conserved carboxylates, however, and their role normally is to coordinate metal ions (Aravind et al, 1998; Keck et al, 2000; Kato et al, 2003; Rezacova et al, 2008).…”

Section: Metal Dependence Of Toprim Enzymes and Srsmentioning

confidence: 99%

“…The Lys conserved among type IA topoisomerases (K8 in Fig. 5) may alleviate the metal dependence in the cleavage step, but Topo IA requires metal ions for the ligation step (the second chemical reaction) (Tse-Dinh et al, 1983; Domanico and Tse-Dinh, 1991). According to its location observed in the Topo II structures (Dong and Berger, 2007; Schmidt et al, 2010), the metal ion would be in position to coordinate and activate the nucleophile 3´-OH in the ligation step.…”

Section: Metal Dependence Of Toprim Enzymes and Srsmentioning

confidence: 99%

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Topoisomerases and site-specific recombinases: similarities in structure and mechanism

Yang

2010

Critical Reviews in Biochemistry and Molecular Biology

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The processes of DNA topoisomerization and site-specific recombination are fundamentally similar: DNA cleavage by forming a phospho-protein covalent linkage, DNA topological rearrangement, and DNA ligation coupled with protein regeneration. Type IB DNA topoisomerases are structurally and mechanistically homologous to tyrosine recombinases. Both enzymes nick DNA double helices independent of metal ions, form 3´-phosphotyrosine intermediates, and rearrange the free 5´ ends relative to the uncut strands by swiveling. In contrast, serine recombinases generate 5´-phospho-serine intermediates. A 180° relative rotation of the two halves of a 100kDa terameric serine recombinase and DNA complex has been proposed as the mechanism of strand exchange. Here I propose an alternative mechanism. Interestingly, the catalytic domain of serine recombinases has structural similarity to the TOPRIM domain, conserved among all Type IA and Type II topoisomerases and responsible for metal binding and DNA cleavage. TOPRIM topoisomerases also cleave DNA to generate 5´-phosphate and 3´-OH groups. Based on the existing biochemical data and crystal structures of Topoisomerase II and serine recombinases bound to pre- and post-cleavage DNA, I suggest a strand passage mechanism for DNA recombination by serine recombinases. This mechanism is reminiscent of DNA topoisomerization and does not require subunit rotation.

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Section: Metal Dependence Of Toprim Enzymes and Srsmentioning

confidence: 99%

Section: Metal Dependence Of Toprim Enzymes and Srsmentioning

confidence: 99%

Topoisomerases and site-specific recombinases: similarities in structure and mechanism

Yang

2010

Critical Reviews in Biochemistry and Molecular Biology

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“…One concern when measuring binding affinity is the rate of oligonucleotide cleavage; it depends on the length and sequence of the substrate (28,29), so while an incubation period of 3 min allows for binding, minimal amounts of product would be expected to be formed even when the reaction is saturated with enzyme. It is also possible that whereas cleavage may occur, the FIG.…”

Section: Effect Of Mutations On Bindingmentioning

confidence: 99%

Biochemical Characterization of an Invariant Histidine Involved in Escherichia coli DNA Topoisomerase I Catalysis

Perry

Mondragón

2002

Journal of Biological Chemistry

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An invariant histidine residue, His-365 in Escherichia coli DNA topoisomerase I, is located at the active site of type IA DNA topoisomerases and near the active site tyrosine. Its ability to participate in the multistep catalytic process of DNA relaxation was investigated. His-365 was mutated to alanine, arginine, asparagine, aspartate, glutamate, and glutamine to study its ability to participate in general acid/base catalysis and bind DNA. The mutants were examined for pH-dependent DNA relaxation and cleavage, salt-dependent DNA relaxation, and salt-dependent DNA binding affinity. The mutants relax DNA in a pH-dependent manner and at low salt concentrations. The pH dependence of all mutants is different from the wild type, suggesting that His-365 is responsible for the pH dependence of the enzyme. Additionally, whereas the wild type enzyme shows pH-dependent oligonucleotide cleavage, cleavage by both H365Q and H365A is pH-independent. H365Q cleaves DNA with rates similar to the wild type enzyme, whereas H365A has a slower rate of DNA cleavage than the wild type but can cleave more substrate overall. H365A also has a lower DNA binding affinity than the wild type enzyme. The binding affinity was determined at different salt concentrations, showing that the alanine mutant displaces half a charge less upon binding DNA than an inactive form of topoisomerase I. These observations indicate that His-365 participates in DNA binding and is responsible for optimal catalysis at physiological pH.Type I DNA topoisomerases transiently cleave the phosphodiester backbone of one DNA strand to allow single-or double-stranded DNA to pass through the break before resealing it. This allows for the interconversion of topological isomers, which is necessary for nearly all cellular transactions of DNA such as replication, transcription, and recombination (1). Type I enzymes are further divided into two subfamilies, type IA and type IB. Type IA DNA topoisomerases form a covalent linkage to the 5Ј-phosphoryl end of the cleaved DNA, whereas type IB DNA topoisomerases undergo a transesterification reaction to the 3Ј-phosphoryl end. All topoisomerases cleave the phosphodiester bond via a phosphotyrosine intermediate. Creation of the transient break, strand passage, and religation of DNA by type IA topoisomerases is a multistep process. A proposed mechanism (3) has the following steps. 1) The enzyme recognizes and binds a single-stranded DNA region, positioning the DNA in the active site. 2) Cleavage of the single-stranded DNA occurs at the active site, via formation of a covalent bond between the 5Ј-phosphoryl and the hydroxyl of the active site tyrosine, whereas the 3Ј end of the DNA remains non-covalently bound to the enzyme.3) The enzyme opens to allow passage of the other strand through the gap or gate created by separating the broken ends of the cleaved DNA. 4) Following strand passage, the enzyme closes, trapping the passing DNA inside. 5) Once the gate is closed, the enzyme re-ligates the cleaved strand. 6) The enzyme opens to releas...

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“…The site of cleavage is in both cases four bases from the 3' end. Oligo(dG) or oligo(dC) are very poorly or not cleaved at all (TSE-DINH et al 1983). …”

Section: Prokaryotic Type I Topoisomerasesmentioning

confidence: 99%