DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote

Slesarev, Alexei I.; Stetter, Karl O.; Lake, James A.; Gellert, Martin; Krah, Regis; Kozyavkin, Sergei A.

doi:10.1038/364735a0

Cited by 91 publications

(83 citation statements)

References 17 publications

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“…Some of the (HhH) 2 domains are involved in DNA repair, and there are at least two apurinic/apyrimidinic site-processing active sites (31,33). Topo-V displays many characteristics similar to those of type IB enzymes; it can relax positively and negatively supercoiled DNA, forms a transient covalent bond with the 3Ј end of the broken DNA, does not require magnesium for activity, and relaxes DNA by a swiveling mechanism (7,10,34). The most striking differences, which place Topo-V in an entirely different subtype, are the distinct domain organization with two different DNA processing activities, the unique structure of the topoisomerase domain, and the lack of sequence similarity with any other topoisomerase subtype (8,9).…”

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“…Until recently, only two subtypes of type I topoisomerases had been identified, type IA and IB. A third subtype, type IC, was added with the discovery and characterization of Methanopyrus kandleri topoisomerase V (Topo-V) 2 (7)(8)(9). The three type I subtypes are very different in sequence and structure, although type IB and type IC molecules share some overall mechanistic similarities (10).…”

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Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V

Rajan

Osterman

Gast

et al. 2014

Journal of Biological Chemistry

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Background: Topoisomerase V is a unique enzyme and the sole member of the IC subtype of type I topoisomerases. Results: We probed the role of several amino acids comprising the topoisomerase active site to elucidate their role in catalysis. Conclusion:The work reveals the role of several amino acids and suggests interesting parallels with type IB topoisomerases. Significance: The results expand our understanding of this new subtype of topoisomerases.

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confidence: 99%

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Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V

Rajan

Osterman

Gast

et al. 2014

Journal of Biological Chemistry

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“…In vitro formation of covalent Topo V-DNA complexes involving regular duplex DNA is, however, very inefficient. The one cleavage site mapped so far resembles the consensus site for DNA cleavage by eukaryotic topoisomerase I in the absence of camptothecin (1).…”

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“…This results in the formation of a phosphotyrosine bond between the enzyme and the 3Ј end of the broken strand. This covalent intermediate can be trapped by denaturing the enzyme during catalysis with either SDS or alkali (1,9). In vitro formation of covalent Topo V-DNA complexes involving regular duplex DNA is, however, very inefficient.…”

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The Domain Organization and Properties of Individual Domains of DNA Topoisomerase V, a Type 1B Topoisomerase with DNA Repair Activities

Belova¹,

Prasad²,

Nazimov³

et al. 2002

Journal of Biological Chemistry

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Topoisomerase V (Topo V) is a type IB (eukaryoticlike) DNA topoisomerase. It was discovered in the hyperthermophilic prokaryote Methanopyrus kandleri and is the only topoisomerase with associated apurinic/ apyrimidinic (AP) site-processing activities. The structure of Topo V in the free and DNA-bound states was probed by limited proteolysis at 37°C and 80°C. The Topo V protein is comprised of (i) a 44-kDa NH 2 -terminal core subdomain, which contains the active site tyrosine residue for topoisomerase activity, (ii) an immediately adjacent 16-kDa subdomain that contains degenerate helix-hairpin-helix (HhH) motifs, (iii) a protease-sensitive 18-kDa HhH "hinge" region, and (iv) a 34-kDa COOH-terminal HhH domain. Three truncated Topo V polypeptides comprising the NH 2 -terminal 44-kDa and 16-kDa domains (Topo61), the 44-, 16-, and 18-kDa domains (Topo78), and the COOH-terminal 34-kDa domain (Topo34) were cloned, purified, and characterized. Both Topo61 and Topo78 are active topoisomerases, but in contrast to Topo V these enzymes are inhibited by high salt concentrations. Topo34 has strong DNA-binding ability but shows no topoisomerase activity. Finally, we demonstrate that Topo78 and Topo34 possess AP lyase activities that are important in base excision DNA repair. Thus, Topo V has at least two active sites capable of processing AP DNA. The significance of multiple HhH motifs for the Topo V processivity is discussed.Methanopyrus kandleri DNA topoisomerase V (Topo V) 1 (1-5) relaxes both negatively and positively supercoiled DNA in the temperature range from 60 to 122°C by catalyzing the transient breakage of a phosphodiester bond in a single DNA strand (reviewed in Refs. 6 -8)). Topo V is active in an unsurpassable range of monovalent salt concentrations, from 0 to 0.65 M KCl or NaCl and from 0 to 3.1 M of potassium glutamate (K-Glu), and no metal cation or energy cofactor is required for Topo V activity. Cleavage of a phosphodiester bond in DNA involves a transesterification reaction in which the nucleophilic O-4 oxygen of the active site tyrosine (amino acid 226 in Topo V) (5) attacks the phosphodiester linkage (6). This results in the formation of a phosphotyrosine bond between the enzyme and the 3Ј end of the broken strand. This covalent intermediate can be trapped by denaturing the enzyme during catalysis with either SDS or alkali (1, 9). In vitro formation of covalent Topo V-DNA complexes involving regular duplex DNA is, however, very inefficient. The one cleavage site mapped so far resembles the consensus site for DNA cleavage by eukaryotic topoisomerase I in the absence of camptothecin (1).Unlike other known DNA topoisomerases, Topo V has associated apurinic/apyrimidinic (AP) site-processing activities that are important in base excision DNA repair (5). The protein incises the phosphodiester backbone at the AP site, and then at the AP endonuclease-cleaved AP site, it removes the 5Ј-2-deoxyribose-5-phosphate moiety so that a single-nucleotide gap with a 3Ј-hydroxyl and 5Ј-phosphate can be filled by a DNA poly...

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“…Our results showed that even though eukaryotic topoisomerases I can in general relax both positively and negatively supercoiled DNA, their action on DNA may result in different superhelical states. A prokaryotic enzyme DNA topoisomerase V has been purified from the hyperthermophilic methanogen Methanopyrus kandleri and found to be related to eukaryotic topoisomerase I [31]. It relaxes both positively and negatively supercoiled DNA but prefers positively over negatively supercoiled substrates [32].…”

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Vaccinia virus DNA topoisomerase I preferentially removes positive supercoils from DNA

Fernandez-Beros

Tse‐Dinh

1996

FEBS Letters

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Type I DNA topoisomerases homologous to Escherichia coli topoisomerase I normally only remove negative supercoils from DNA. Topoisomerases I from various eukaryotes share sequence homology and remove both positive and negative supercoils from DNA. Here we report that vaccinia virus topoisomerase I has significant difference in substrate preference from the other homologous type I topoisomerases. Vaccinia virus topoisomerase I shows a definite preference for removal of positive supercoiis. In contrast, topoisomerase I from human, wheat germ and Saccharomyces cerevisiae has little preference between positive and negative supercoils. The vaccinia enzyme may have evolved for functions required for optimal viral growth.

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DNA topoisomerase V is a relative of eukaryotic topoisomerase I from a hyperthermophilic prokaryote

Cited by 91 publications

References 17 publications

Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V

Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V

The Domain Organization and Properties of Individual Domains of DNA Topoisomerase V, a Type 1B Topoisomerase with DNA Repair Activities

Vaccinia virus DNA topoisomerase I preferentially removes positive supercoils from DNA

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