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Example sentences for: topoisomerases
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Previous studies have shown that E. coli DNA topoisomerase I cleavage of single-stranded DNA occurs with selectivity for sites with the C nucleotide base at the - 4 position [ 9 10 ] and that the enzyme preferentially cleaves at junctions of double-stranded and single-stranded DNA [ 8 ] . Several different 5'-end labeled substrates were prepared and used in cleavage assays to compare the cleavage sites selected by Top67 versus topoisomerase I. The results showed that with single-stranded substrates, Top67 also preferred cleavage sites with a C nucleotide base at the -4 position as reported for most of the type IA topoisomerases [ 12 ] . There were some differences from topoisomerase I in the relative distribution of cleavage products among the potential cleavage sites (Figure 4a,4b).
The hyperthermophilic topoisomerase I from Thermotoga maritima has been shown to coordinate one Zn(II) with a unique tetracysteine motif Cys-X-Cys-X 16 -Cys-X-Cys but Zn(II) binding is not required for relaxation activity [ 33 ] . The sequence of this unique tetracysteine motifs is somewhat different from those present in other type IA topoisomerases in that the other tetracysteine motifs always had at least two amino acids separating the pairs of cysteines (Cys-X 2-11 -Cys), instead of just one amino acid (Cys-X-Cys) in T. maritima topoisomerase I [ 33 ] . Therefore the structure and function of the single Zn(II) binding motif in T. maritima may differ from the multiple Zn(II) binding motifs in E. coli topoisomerase I. Direct interaction between DNA and the T. maritima Zn(II) binding motif has not been demonstrated.
The relaxation and decatenation activities of T. maritima topoisomerase I appear to be significantly more efficient than those of the E. coli topoisomerase I [ 33 ] . Based on their primary sequences, a number of bacterial topoisomerase I enzymes do not appear to coordinate any Zn(II) with tetracysteines motifs while other type IA topoisomerase has up to 4 tetracysteine motifs [ 7 ] . The topoisomerase I from Mycobacterium smegmatis has been demonstrated biochemically not to bind Zn(II) [ 34 ] . In contrast, mutation disrupting the fourth Zn(II) motif of Helicobacter pylori topoisomerase I abolished enzyme function in vivo [ 35 ] . Therefore there may be significant differences in the mechanisms of type IA topoisomerases from different organisms with respect to requirement of Zn(II) binding for relaxation activity.
There is also another possible explanation for the varied number of tetracysteine motifs and requirement of Zn(II) for relaxation activity found in different type IA topoisomerases.
There are two homologous type IA topoisomerases present in E. coli . Topoisomerase III has potent DNA decatenating activity for resolution of plasmid DNA replication intermediates, but much weaker relaxation activity than topoisomerase I [ 17 ] . To exhibit maximal relaxation activity, topoisomerase III requires high temperature (52°C) along with low magnesium and monovalent ion [ 17 18 ] . In contrast, E. coli topoisomerase I was not active in the in vitro assay for resolution of plasmid DNA replication intermediates [ 19 ] . Removal of the C-terminal 49 amino acids from the 653 amino acid topoisomerase III protein resulted in drastic reduction of catalytic activity [ 20 ] . Fusion of the carboxyl-terminal 312 amino acid residues of E. coli topoisomerase I, which includes the entire ZD domain, onto the 605 N-terminal amino acids of topoisomerase III generated a hybrid topoisomerase that has relaxation activity resembling topoisomerase III along with weak decatenating activity [ 21 ] . Although preferring single-stranded DNA as binding substrate, topoisomerase I had been shown to also bind double-stranded DNA [ 22 ] , but there is no data available to indicate which domain in the enzyme is responsible for this interaction.
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