C-terminal domains of Escherichia coli topoisomerase I belong to the zinc-ribbon superfamily

J Mol Biol. 2000 Jun 23;299(5):1165-77. doi: 10.1006/jmbi.2000.3841.


Detection of remote evolutionary connections is increasingly difficult with sequence and structural divergence. A combination of sequence and structural analysis, in which statistically supported sequence similarity had a crucial impact, revealed that Escherichia coli topoisomerase I C-terminal fragment is evolutionarily related to the three tetracysteine zinc-binding domains of the enzyme. Spatial structure analysis of this C-terminal fragment indicates that it consists of two structurally similar domains and suggests homology between them. Sequence similarity between the zinc-binding domains of type Ia topoisomerases and transcription regulators of known spatial structure helps to conclude that E. coli topo I contains five copies of a zinc ribbon domain at the C terminus. Two of these domains, corresponding to the C-terminal fragment, lost their cysteine residues and are probably not able to bind zinc. Present analyses lead to the classification of the C-terminal fragment of E. coli topoisomerase I as a member of zinc ribbon superfamily, despite the absence of zinc-binding sites.

MeSH terms

  • Amino Acid Sequence
  • Binding Sites
  • Cysteine / metabolism
  • DNA Topoisomerases, Type I / chemistry*
  • DNA Topoisomerases, Type I / classification*
  • DNA Topoisomerases, Type I / metabolism
  • Escherichia coli / enzymology*
  • Evolution, Molecular
  • Models, Molecular
  • Molecular Sequence Data
  • Peptide Fragments / chemistry
  • Peptide Fragments / classification
  • Peptide Fragments / metabolism
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Transcription Factors / chemistry
  • Transcription Factors / metabolism
  • Zinc / metabolism*


  • Peptide Fragments
  • Transcription Factors
  • DNA Topoisomerases, Type I
  • Zinc
  • Cysteine