Topoisomerases and site-specific recombinases: similarities in structure and mechanism

Abstract

The processes of DNA topoisomerization and site-specific recombination are fundamentally similar: DNA cleavage by forming a phospho-protein covalent linkage, DNA topological rearrangement, and DNA ligation coupled with protein regeneration. Type IB DNA topoisomerases are structurally and mechanistically homologous to tyrosine recombinases. Both enzymes nick DNA double helices independent of metal ions, form 3´-phosphotyrosine intermediates, and rearrange the free 5´ ends relative to the uncut strands by swiveling. In contrast, serine recombinases generate 5´-phospho-serine intermediates. A 180° relative rotation of the two halves of a 100kDa terameric serine recombinase and DNA complex has been proposed as the mechanism of strand exchange. Here I propose an alternative mechanism. Interestingly, the catalytic domain of serine recombinases has structural similarity to the TOPRIM domain, conserved among all Type IA and Type II topoisomerases and responsible for metal binding and DNA cleavage. TOPRIM topoisomerases also cleave DNA to generate 5´-phosphate and 3´-OH groups. Based on the existing biochemical data and crystal structures of Topoisomerase II and serine recombinases bound to pre- and post-cleavage DNA, I suggest a strand passage mechanism for DNA recombination by serine recombinases. This mechanism is reminiscent of DNA topoisomerization and does not require subunit rotation.

Tyrosyl-DNA Phosphodiesterase I Catalytic Mutants Reveal an Alternative Nucleophile That Can Catalyze Substrate Cleavage

“…DNA topoisomerases, on the other hand, catalyze changes in the linkage of DNA strands or helices, whereas site-specific recombinases catalyze the reciprocal exchanges of double-stranded DNA molecules (reviewed in Ref. 37). Yet, despite the biological diversity of these activities, these enzymes share a reaction mechanism that involves the formation of a covalent enzyme-DNA intermediate.…”

Serine Resolvases

“…Although the overall fold has been noted to show similarities to that of 5′ → 3′ exonucleases and topoisomerases of the TOPRIM fold, the active site is unrelated to either of those (29, 30). In the solution dimer, the E helices of two subunits dock against each other and into a shallow groove on the partner’s surface.…”

Manual classification strategies in the ECOD database

“…For example, Toprim (topoisomerase‐primase) domain is present in various proteins that function in DNA/RNA metabolism . Toprim adopts a Rossmann‐like fold consisting of repeating beta‐alpha units with conserved acidic residues clustered at the C‐terminal end of the parallel four‐stranded beta‐sheet . Toprim domains typically occur in DNA/RNA‐manipulating enzymes (topoisomerases type IA and type II, DnaG‐type primases, and OLD family nucleases) and likely use the conserved acidic residues to coordinate catalytically active metal ions; however, RecR Toprim has lost some of the conserved acidic residues and functions instead as a protein‐protein interaction module .…”