DNA topoisomerase II (EC 5.99.1.3) [1,2,3,4] is one of the two types of enzyme that catalyze the interconversion of topological DNA isomers. Type II topoisomerases are ATP-dependent and act by passing a DNA segment through a transient double-strand break. Topoisomerase II is found in phages, archaebacteria, prokaryotes, eukaryotes, and in African Swine Fever virus (ASF). In bacteriophage T4 topoisomerase II consists of three subunits (the product of genes 39, 52 and 60). In prokaryotes and in archaebacteria the enzyme, known as DNA gyrase, consists of two subunits (genes gyrA and gyrB [E1]). In some bacteria, a second type II topoisomerase has been identified; it is known as topoisomerase IV and is required for chromosome segregation, it also consists of two subunits (genes parC and parE). In eukaryotes, type II topoisomerase is a homodimer.

There are many regions of sequence homology between the different subtypes of topoisomerase II. The relation between the different subunits is shown in the following representation:

  <----------------About-1400-residues----------------------->

  [----------Protein 39-*-----][----Protein 52----]              Phage T4
  [----------gyrB-------*-----][--------gyrA-----------------]   Prokaryote II
                                                                 Archaea
  [----------parE-------*-----][--------parD-----------------]   Prokaryote IV
  [---------------------*------------------------------------]   Eukaryote and
                                                                 ASF

'*': Position of the pattern.

As a signature pattern for this family of proteins, we have selected a region that contains a highly conserved pentapeptide. The pattern is located in gyrB, in parE, and in protein 39 of phage T4 topoisomerase.