Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V

Rajan, Rakhi; Osterman, Amy; Gast, Alexandra T.; Mondragón, Alfonso

doi:10.1074/jbc.m114.590711

Cited by 6 publications

(20 citation statements)

References 41 publications

(88 reference statements)

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“…Finally, Lys218 is not making contacts with the DNA but is close enough to Tyr226 that it could contact the P0 phosphate. Thus, all residues that have been involved in cleavage and religation are positioned in a manner consistent with their previously assigned roles (Rajan et al, 2014).…”

Section: Active Sitesupporting

confidence: 69%

“…The residues forming the topoisomerase active site were recognized based on structural and biochemical observations (Rajan et al, 2014;Taneja et al, 2006). The complex structure confirms that Arg131, Arg143, His200, Glu215, Lys218 and Tyr226 are involved in interacting with DNA and helps understand their role in the DNA cleavage/religation reaction.…”

Section: Discussionmentioning

confidence: 90%

“…(HhH)2 domains are usually found as isolated domains, not in tandem arrangements (Shao & Grishin, 2000), which is another unusual characteristic of topoisomerase V. The topoisomerase domain has no sequence or structural similarities to other topoisomerases or any other proteins, making it a unique fold (Forterre, 2006;Taneja et al, 2006). The active site residues have been identified (Rajan, Osterman, Gast, & Mondragon, 2014), but their three dimensional arrangement suggest a different catalytic mechanism from other topoisomerases (Rajan et al, 2014). In the structures of the free protein, the topoisomerase domain active site is inaccessible as it is covered by the (HhH)2 domains (Rajan et al, 2016;Rajan et al, 2013;Rajan et al, 2010;Taneja et al, 2006).…”

Section: Introductionmentioning

confidence: 99%

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Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism

Mondragón

Osterman

2021

Preprint

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Topoisomerase V is a unique topoisomerase that combines DNA repair and topoisomerase activities. The enzyme has an unusual arrangement, with a small topoisomerase domain followed by 12 tandem (HhH)2 domains, which include three AP lyase repair domains. The unusual architecture of this enzyme bears no resemblance to any other known topoisomerase. Here we present structures of topoisomerase V in complex with DNA. The structures show that the (HhH)2 domains wrap around the DNA and in this manner appear to act as a processivity factor. There is a conformational change in the protein to expose the topoisomerase active site. The DNA bends sharply to enter the active site, which melts the DNA and probably facilitates relaxation. The structures show a DNA binding mode not observed before and provide information on the way this unusual topoisomerase relaxes DNA.

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Section: Active Sitesupporting

confidence: 69%

Section: Discussionmentioning

confidence: 90%

Section: Introductionmentioning

confidence: 99%

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Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism

Mondragón

Osterman

2021

Preprint

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“…Type IC topoisomerases comprise the most recently identified family of topoisomerases ( 6 , 7 ). Although they have many characteristics in common with type IB enzymes ( 8 – 10 ), the structure elucidation of a 61 kDa fragment of Methanopyrus kandleri Topoisomerase-V (Topo-V) ( 7 ) revealed that they form a distinct sub-type. In addition to relaxation activity, type IC enzymes show DNA repair activity ( 11 , 12 ), suggesting a close relationship between these two essential functions in hyperthermophiles.…”

Section: Introductionmentioning

confidence: 99%

“…Topo-V shows a modular structure with a 30 kDa topoisomerase domain followed by 24 helix-hairpin-helix (HhH) motifs arranged as 12 tandem (HhH) 2 domains ( 7 , 11 ). The topoisomerase domain has no sequence or structural similarity to any other topoisomerase ( 7 ), the active site is well mapped and biochemical studies have shown that the cleavage and religation reactions are similar to the ones employed by type IB enzymes ( 8 ). In addition, single molecule studies have shown that Topo-V relaxes DNA by controlled rotation or swiveling, again in a similar manner to type IB topoisomerases ( 10 ).…”

Section: Introductionmentioning

confidence: 99%

Methanopyrus kandleritopoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

2016

Self Cite

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Topoisomerase V (Topo-V) is the only topoisomerase with both topoisomerase and DNA repair activities. The topoisomerase activity is conferred by a small alpha-helical domain, whereas the AP lyase activity is found in a region formed by 12 tandem helix-hairpin-helix ((HhH)2) domains. Although it was known that Topo-V has multiple repair sites, only one had been mapped. Here, we show that Topo-V has three AP lyase sites. The atomic structure and Small Angle X-ray Scattering studies of a 97 kDa fragment spanning the topoisomerase and 10 (HhH)2 domains reveal that the (HhH)2 domains extend away from the topoisomerase domain. A combination of biochemical and structural observations allow the mapping of the second repair site to the junction of the 9th and 10th (HhH)2 domains. The second site is structurally similar to the first one and to the sites found in other AP lyases. The 3rd AP lyase site is located in the 12th (HhH)2 domain. The results show that Topo-V is an unusual protein: it is the only known protein with more than one (HhH)2 domain, the only known topoisomerase with dual activities and is also unique by having three AP lyase repair sites in the same polypeptide.

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Type IA DNA Topoisomerases: A Universal Core and Multiple Activities

Garnier

Débat

Nadal

2017

Methods in Molecular Biology

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All the type IA topoisomerases display universal characteristics relying on a core region basically responsible for the transesterification and the strand passage reaction. First limited to the bacterial domain for a long time, these enzymes were further retrieved in Archaea and Eukarya as well. This is representative of an extremely ancient origin, probably due to an inheritance from the RNA world. As remaining evidence, some current topoisomerases IA have retained a RNA topoisomerase activity. Despite the presence of this core region in all of these TopoIAs, some differences exist and are originated from variable regions, located essentially within both extremities, conferring on them their specificities. During the last 2 decades the evidence of multiple activities and dedicated roles highlighted the importance of the topoisomerases IA. It is now obvious that topoisomerases IA are key enzymes involved in the maintenance of the genome stability. The discovery of these new activities was done thanks to the use of more accurate assays, based on new sophisticated DNA substrates.

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Biochemical Characterization of the Topoisomerase Domain of Methanopyrus kandleri Topoisomerase V

Cited by 6 publications

References 41 publications

Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism

Structures of topoisomerase V in complex with DNA reveal unusual DNA binding mode and novel relaxation mechanism

Methanopyrus kandleritopoisomerase V contains three distinct AP lyase active sites in addition to the topoisomerase active site

Type IA DNA Topoisomerases: A Universal Core and Multiple Activities

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