DNA Topoisomerase I from Mycobacterium smegmatis

Bhaduri, Tisha; Bagui, Tapan; Sikder, Devanjan; Nagaraja, Valakunja

doi:10.1074/jbc.273.22.13925

Cited by 64 publications

(81 citation statements)

References 38 publications

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“…Therefore, Sso Topo III does not appear to possess a zinc binding site. This is consistent with the notion that zinc binding may not be necessary for the activity of a type IA topoisomerase (3,29).…”

Section: Resultssupporting

confidence: 80%

supporting

confidence: 82%

“…These data suggest that zinc ribbon motifs may not be required for DNA relaxation by at least some type IA topoisomerases. This suggestion is consistent with reports that zinc binding is not necessary for the relaxation activity of topoisomerases from Mycobacterium smegmatis and Thermotoga maritima (3,29).Although type IA topoisomerases share considerable sequence and structural similarity, they display significant diversity in substrate cleavage specificity. For example, E. coli and Micrococcus luteus topoisomerases I show a limited sequence preference (5Ј-CXXX2-3Ј) (27), whereas E. coli topoisomerase III and M. smegmatis topoisomerase I are more specific in cleavage (5Ј-CT2T-3Ј and 5Ј-CG/TCT2T-3Ј, respectively) (23, 33).…”

supporting

confidence: 80%

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DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

Dai

Wang

et al. 2003

J Bacteriol

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We report the production, purification, and characterization of a type IA DNA topoisomerase, previously designated topoisomerase I, from the hyperthermophilic archaeon Sulfolobus solfataricus. Topoisomerases are ubiquitous enzymes that participate in nearly all cellular activities involving DNA transactions (5, 31). Based on their catalytic mechanisms, topoisomerases are classified into two classes: type I enzymes, which generate a transient break on one DNA strand to allow the passage of the intact strand with a linking change of one in a single reaction cycle, and type II enzymes, which introduce a transient doublestranded break to allow the passage of another duplex DNA segment with a change in linking number by steps of two (5, 30). Each class of topoisomerases is further divided into two structurally and mechanistically distinct subfamilies on the basis of the polarity of enzyme attachment to the broken strands (i.e., IA, IB, IIA, and IIB). A cellular organism possesses multiple forms of topoisomerases. For example, Escherichia coli has two type IA enzymes (topoisomerases I and III) and two type IIA enzymes (gyrase and topoisomerase IV) (30). Humans carry two enzymes of each of the subfamilies IA (topoisomerases III␣ and III␤), IB (topoisomerase I and mitochondrial topoisomerase I), and IIA (topoisomerases II␣ and II␤) (31). Sulfolobus, a group of hyperthermophilic archaea, possesses two type IA enzymes (putative topoisomerase I, identified by gene annotation, and reverse gyrase) and a type IIB enzyme (topoisomerase VI) (2,8,10). It appears that all organisms have at least one type IA topoisomerase (31).E. coli DNA topoisomerase I is the most extensively studied representative of type IA enzymes. The E. coli enzyme is composed structurally of an N-terminal transesterification domain and a C-terminal DNA binding domain (1,17). The N-terminal domain has the active site tyrosine for DNA cleavage and is capable of forming a covalent adduct with single-stranded DNA. But this domain cannot relax negatively supercoiled DNA. The C-terminal domain consists of five copies of a zinc ribbon motif and is suspected to interact with the passing strand of DNA in the relaxation of negatively supercoiled DNA (1, 12). Each of the first three zinc ribbon motifs from the N terminus in this domain contains four cysteine residues at required sites and is likely to bind zinc (28). The fourth and fifth motifs have one and no cysteine residue, respectively. Sequence analysis of type IA topoisomerase-encoding genes has revealed a significant variation with respect to the copy number of zinc ribbon motifs (0 to 5) as well as the number of tetracysteine motifs in the enzymes (12). These data suggest that zinc ribbon motifs may not be required for DNA relaxation by at least some type IA topoisomerases. This suggestion is consistent with reports that zinc binding is not necessary for the relaxation activity of topoisomerases from Mycobacterium smegmatis and Thermotoga maritima (3,29).Although type IA topoisomerases share considerable seq...

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Section: Resultssupporting

confidence: 80%

supporting

confidence: 82%

supporting

confidence: 80%

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DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

Dai

Wang

et al. 2003

J Bacteriol

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“…The relaxation of supercoiled pUC18 DNA was carried out as described previously (34). Briefly, 500 ng DNA was incubated with 1 unit of various type I topoisomerases for 30 min at 37°C in buffer containing 40 mM Tris-HCl (pH 8.0), 20 mM NaCl, 5 mM MgCl 2 , and 1 mM EDTA.…”

Section: Methodsmentioning

confidence: 99%

Targeting Mycobacterium tuberculosis Topoisomerase I by Small-Molecule Inhibitors

Godbole

Ahmed

Bhat

et al. 2015

Antimicrob Agents Chemother

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We describe inhibition of Mycobacterium tuberculosis topoisomerase I (MttopoI), an essential mycobacterial enzyme, by two related compounds, imipramine and norclomipramine, of which imipramine is clinically used as an antidepressant. These molecules showed growth inhibition of both Mycobacterium smegmatis and M. tuberculosis cells. The mechanism of action of these two molecules was investigated by analyzing the individual steps of the topoisomerase I (topoI) reaction cycle. The compounds stimulated cleavage, thereby perturbing the cleavage-religation equilibrium. Consequently, these molecules inhibited the growth of the cells overexpressing topoI at a low MIC. Docking of the molecules on the MttopoI model suggested that they bind near the metal binding site of the enzyme. The DNA relaxation activity of the metal binding mutants harboring mutations in the DxDxE motif was differentially affected by the molecules, suggesting that the metal coordinating residues contribute to the interaction of the enzyme with the drug. Taken together, the results highlight the potential of these small molecules, which poison the M. tuberculosis and M. smegmatis topoisomerase I, as leads for the development of improved molecules to combat mycobacterial infections. Moreover, targeting metal coordination in topoisomerases might be a general strategy to develop new lead molecules.

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“…DNA topoisomerases I (TopA) and IV (ParCE) were assayed in the absence (15) and the presence of ATP (11), respectively. One unit of both topoisomerases was defined as the amount of enzyme required to fully relax 0.5 g of supercoiled pBR322 per h.…”

Section: Methodsmentioning

confidence: 99%

Glutamate Racemase Is an Endogenous DNA Gyrase Inhibitor

Ashiuchi

Kuwana

Yamamoto

et al. 2002

Journal of Biological Chemistry

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Almost all bacteria possess glutamate racemase to synthesize D-glutamate as an essential component of peptidoglycans in the cell walls. The enforced production of glutamate racemase, however, resulted in suppression of cell proliferation. In the Escherichia coli JM109/pGR3 clone, the overproducer of glutamate racemase, the copy number (i.e. replication efficiency) of plasmid DNA declined dramatically, whereas the E. coli WM335 mutant that is defective in the gene of glutamate racemase showed little genetic competency. The comparatively low and high activities for DNA supercoiling were contained in the E. coli JM109/pGR3 and WM335 cells, respectively. Furthermore, we found that the DNA gyrase of E. coli was modulated by the glutamate racemase of E. coli in the presence of UDP-N-acetylmuramyl-L-alanine, which is a peptidoglycan precursor and functions as an absolute activator for the racemase. This is the first finding of the enzyme protein participating in both D-amino acid metabolism and DNA processing.

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DNA Topoisomerase I from Mycobacterium smegmatis

Cited by 64 publications

References 38 publications

DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

DNA Topoisomerase III from the Hyperthermophilic Archaeon Sulfolobus solfataricus with Specific DNA Cleavage Activity

Targeting Mycobacterium tuberculosis Topoisomerase I by Small-Molecule Inhibitors

Glutamate Racemase Is an Endogenous DNA Gyrase Inhibitor

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