PROSITE documentation PDOC52041

Topoisomerase (Topo) IIB-type catalytic domain profile

DNA topoisomerases (Topos) are enzymes that solve topological problems associated with important processes such as DNA replication, transcription, recombination and chromatin remodeling by introducing transient single or double stranded breaks in the DNA and releasing accumulated strain. They may have appeared early during the formation of the modern DNA world. Several families and subfamilies of the two types of DNA topoisomerases (I and II) have been described in the three cellular domains of life (Archaea, Bacteria and Eukarya), as well as in viruses infecting eukaryotes or bacteria. The main families of DNA topoisomerases, Topo IA, Topo IB, Topo IC (Topo V), Topo IIA and Topo IIB (Topo VI) are not homologous, indicating that they originated independently. However, some of them share homologous modules or subunits that were probably recruited independently to produce different topoisomerase activities [1,2,3,4,5].

Type II DNA topoisomerases introduce double-strand breaks in a DNA duplex and force the passage of another duplex through this break. The DNA cleavage, energy storage and religation reactions are chemically similar to those performed by Type I topoisomerases, with the formation of a phosphotyrosine link between DNA and the enzyme, except that the two strands of the DNA duplex are broken in a concerted reaction. In contrast to Topo I that can make transient links with either the 5' end (Topo IA) or the 3' end (Topo IB and IC) of the DNA breaks, all Topo II make transient links with the 5' end of the DNA breaks. All Type II enzymes can catenate (or decatenate) and knot (or unknot) circular duplex DNA, and alter DNA superhelicity by relaxing positively or negatively supercoiled DNA. In contrast to Topo I, all Type II topoisomerases are ATPdependent and multimeric enzymes with a dyad symmetry. Each "half-enzyme" is formed by the combination of one ATP binding domain and one catalytic breakage-reunion domain containing the active site tyrosine. Topo II are essential in all cells for segregation of the chromosomal DNA after DNA replication and before cell division. Although ubiquitous, Type II enzymes are organized into two families, Topo IIA and IIB [1,2,3,4,5].

Topo IIB are ubiquitous in Archaea (with the exception of Thermoplasmatales) where they have been discovered and named Topo VI. Topo IIB enzymes are composed of two subunits, TopoVIA and TopoVIB, assembling into heterotetramers. The A subunits, which cleave DNA, contain two domains also found in type IIA topoisomerases: a winged-helix DNA-binding domain (WHD) harboring the catalytic tyrosine residue used for DNA scission, and a topoisomerase/primase (TOPRIM) domain, which binds Mg(2+) ions also involved in cleavage. The topo VI B subunits are closely related to the ATPase region of type IIA topoisomerases and belong to the DNA gyrase, Hsp90, MutL (GHL) ATPase superfamily. The eukaryotic homologues of archaeal Topo VI A-subunit include the Spo11 meiotic recombination endonuclease, the A-subunit of a putative plant Topo VI, and several Spo11 paralogues from protists which role is less clear. Mechanistically, topo VI differs from type IIA DNA topoisomerase family members in two respects: first, topo VI strictly requires ATP for DNA cleavage; second, DNA cleavage by topo VI generates two-nucleotide 5'-protruding ends instead of four-nucleotide overhangs for type IIA enzymes [1,2,3,4,5].

The Topo IIB-type catalytic domain contains five α-helices and two β-strands (see <PDB:2ZBK>). The catalytic tyrosine side chain attacks the DNA phosphodiester backbone, generating a phosphodiester linkage between the protein and the 5' terminal strand and releasing a free 3' OH-terminus [1,2,3,4,5].

The profile we developed covers the entire Topo IIB-type catalytic domain.