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Example sentences for: topoisomerases
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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.
The RDRPs of RNA viruses define one major lineage of nucleic acid polymerases, which additionally includes reverse transcriptases, archaeo-eukaryotic DNA polymerases, and nucleotide cyclases [ 8 9 10 11 12 13 ] . The DNA-dependent RNA polymerase of certain bacteriophages, such as T7, and the archaeo-eukaryotic primase (also detected in some bacteria) are divergent derivatives of the same fold [ 11 14 ] . The core catalytic domain of all these enzymes, the so-called "palm" domain, has an RNA-recognition motif (RRM)-like fold with strategically placed metal-coordinating residues, which form the active site [ 11 15 16 ] . In contrast, bacterial DnaG-type primases (also present in archaea and some eukaryotes) contain a polymerase domain of the Rossmann-like TOPRIM fold, which is shared with topoisomerases and OLD-family nucleases [ 17 18 19 ] . The recently solved structures of the DDRPs from yeast and the thermophilic bacterium Thermus thermophilus indicate that the β' subunit (according to the subunit nomenclature of Escherichia coli DDRP, which we hereinafter employ to designate all orthologs of the respective E. coli subunits) of these enzymes defines another distinct catalytic scaffold, which is unrelated to any of the above template-dependent RNA polymerases [ 20 21 22 23 24 ] . Additionally, the structural and evolutionary affinities of two other template-dependent RNA polymerases, namely RDRPs involved in PTGS [ 25 26 27 ] and primases of herpesviruses [ 28 ] , remain obscure.
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.
Finally, the in vivo catalytic activities of eukarytotic type IA topoisomerases, the topoisomerase III from various higher organisms may be related to their sequences.
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.
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