Topoisomerase II

Topoisomerase II
Name	Topoisomerase II
Ec number	5.99.1.3
Other names	DNA topoisomerase II, ATP-dependent DNA topoisomerase

Topoisomerase II is a ubiquitous ATP-dependent enzyme that alters DNA topology by creating transient double-stranded breaks to manage supercoiling, decatenate chromosomes, and resolve knots during replication and segregation. It plays essential roles in Mitosis, Meiosis, DNA replication, and Chromosome segregation across Bacteria, Archaea, and Eukaryota, and is a target for diverse chemotherapeutics and antibacterial agents. Comparative studies feature models from Escherichia coli, Saccharomyces cerevisiae, Homo sapiens, and Arabidopsis thaliana to define conserved motifs and divergent regulatory interactions.

Structure and Mechanism

Topoisomerase II is a homodimeric enzyme with multi-domain architecture including ATPase, DNA-cleavage, and C-terminal domains; structural snapshots derive from cryo‑EM and X-ray crystallography studies of complexes with ATP, ADP, and DNA. Crystal structures informed by work at institutions like the Max Planck Institute and Cold Spring Harbor Laboratory reveal an N-terminal Bergerat fold related to the GHKL ATPase family studied in Mycobacterium tuberculosis Hsp90 analogs, and a central breakage-reunion domain homologous to type II topoisomerases characterized in Escherichia coli gyrase. The catalytic cycle involves ATP-dependent dimerization, strand passage, phosphotyrosyl bond formation, and religation; mechanistic models compare data from single-molecule studies at Harvard University, University of Oxford, and Caltech. Metal ion coordination (often Mg2+) in the active site is consistent with observations in complexes solved by teams at Stanford University and the Wadsworth Center.

Function and Biological Roles

Topoisomerase II resolves positive and negative supercoils ahead of replisomes studied in contexts such as the Replisome at forks characterized by researchers at Cold Spring Harbor Laboratory and Rockefeller University. It decatenates sister chromatids during anaphase, a process examined in model organisms like Saccharomyces cerevisiae and Drosophila melanogaster, and facilitates transcriptional elongation at loci analyzed in Homo sapiens cell lines by groups at MIT and University of Cambridge. Roles in chromatin remodeling intersect with factors such as Cohesin, Condensin, and the SWI/SNF complex identified in studies from European Molecular Biology Laboratory and National Institutes of Health. In prokaryotes, related type II enzymes like DNA gyrase—investigated in Bacillus subtilis and Mycobacterium tuberculosis—perform negative supercoiling essential for transcriptional regulation described in work at Johns Hopkins University.

Isoforms and Evolution

Eukaryotic genomes typically encode two major isoforms, often termed alpha and beta in mammals, with distinct expression patterns during cell cycle phases noted in studies from University of California, San Francisco and Columbia University. Phylogenetic analyses using sequences from databases curated at the European Bioinformatics Institute and National Center for Biotechnology Information trace divergence across Vertebrata, Arthropoda, and Plantae, with prokaryotic type II topoisomerases such as gyrase forming a separate clade identified in comparative genomics at Wellcome Sanger Institute. Evolutionary pressures from antimicrobial and anticancer therapeutics have driven adaptive mutations documented in surveillance studies at Centers for Disease Control and Prevention and World Health Organization datasets.

Regulation and Cellular Control

Expression and activity are regulated transcriptionally and post-translationally, involving cell cycle regulators like Cyclin-dependent kinase 1 and ubiquitin ligases characterized at European Molecular Biology Laboratory and Max Planck Institute for Biochemistry. Post-translational modifications include phosphorylation by kinases such as Protein kinase A and SUMOylation pathways elucidated in work at University of Toronto and Institut Pasteur. Interaction networks incorporate chromatin factors such as TopBP1, BRCA1, and histone modifiers studied at Dana-Farber Cancer Institute and Memorial Sloan Kettering Cancer Center, linking topoisomerase II function to DNA damage response pathways mapped by researchers at Sanger Institute and National Cancer Institute.

Clinical Significance and Inhibitors

Topoisomerase II is a principal target for anticancer drugs including anthracyclines (e.g., Doxorubicin), epipodophyllotoxins (e.g., Etoposide), and newer catalytic inhibitors developed in collaborations between Pfizer, Novartis, and academic groups at University of Pennsylvania. Resistance mechanisms involve mutations and altered expression first reported in clinical research at Mayo Clinic and Memorial Sloan Kettering Cancer Center. Bacterial type II enzymes (gyrase and Topo IV) are targets of antibiotics like Fluoroquinolones discovered and developed by companies including Bayer and Merck; resistance trends are monitored by European Medicines Agency and Food and Drug Administration surveillance. Clinical toxicities such as therapy-related acute myeloid leukemia correlate with topoisomerase II–linked chromosomal translocations studied at St. Jude Children's Research Hospital and Fred Hutchinson Cancer Research Center.

Experimental Methods and Assays

Biochemical assays include relaxation, decatenation, and cleavage assays developed in core labs at Cold Spring Harbor Laboratory and Lawrence Berkeley National Laboratory using substrates from New England Biolabs. Single-molecule techniques like magnetic tweezers and optical trapping pioneered at University of Chicago and EPFL probe enzyme dynamics; cryo‑EM workflows at Max Planck Institute and MRC Laboratory of Molecular Biology provide high-resolution structures. Genetic approaches employ knockouts and RNAi in Mus musculus, Drosophila melanogaster, and Saccharomyces cerevisiae performed at facilities such as Broad Institute and Whitehead Institute, while high-throughput screening for inhibitors is carried out in industry-academic partnerships exemplified by collaborations between GlaxoSmithKline and University of Cambridge.

Category:Enzymes