Topoisomerase I (TOP1) dynamics: conformational transition from open to closed states

Abstract

Eukaryotic topoisomerases I (TOP1) are ubiquitous enzymes removing DNA torsional stress. However, there is little data concerning the three-dimensional structure of TOP1 in the absence of DNA, nor how the DNA molecule can enter/exit its closed conformation. Here, we solved the structure of thermostable archaeal Caldiarchaeum subterraneum CsTOP1 in an apo-form. The enzyme displays an open conformation resulting from one substantial rotation between the capping (CAP) and the catalytic (CAT) modules. The junction between these two modules is a five-residue loop, the hinge, whose flexibility permits the opening/closing of the enzyme and the entry of DNA. We identified a highly conserved tyrosine near the hinge as mediating the transition from the open to closed conformation upon DNA binding. Directed mutagenesis confirmed the importance of the hinge flexibility, and linked the enzyme dynamics with sensitivity to camptothecin, a TOP1 inhibitor targeting the TOP1 enzyme catalytic site in the closed conformation.

Evolution of TOP1 and TOP1MT Topoisomerases in Chordata

“…3). In addition, the tyrosine upstream of the Hinge (position 426) was also found conserved, in agreement with a previous work suggesting that this position interacts with the DNA duplex and guides the motion of the CAP domain upon DNA binding to enable the enzyme closing (Takahashi et al 2022). Within the CAT region, we noticed that near the Linker there are two conserved stretches of around 20 amino acids that flank a poorly conserved region (Fig.…”

“…Previous works have compared Type IB topoisomerases from different species, but often focused on a specific section of the protein or explored only a few animal species [e.g., (Champoux 1998;Takahashi et al 2022;Zhang et al 2004)].…”

“…The core domain is highly conserved and contains essential catalytic residues, being connected to the C-terminal domain by a poorly conserved Linker region formed by an extended pair of α-helices. TOP1 forms a toroidal fold with two modules entrapping the DNA molecule, a capping module matching the first half of the core domain (CAP domain or core sub-domains I and II) and a catalytic module comprising the second half of the core domain (CAT domain or core sub-domain III), the Linker and the C-terminal domain (Redinbo et al 1998 ; Stewart et al 1998 ; Takahashi et al 2022 ). The catalytic module includes several active sites relevant for the protein activity (Champoux 2001 ).…”

SUMO: A Swiss Army Knife for Eukaryotic Topoisomerases

“…SUMOylation sites in human TOP1 and TOP2α and β identified by biochemical and proteomic analyses are shown above their respective domain diagram ( Kanagasabai et al, 2009 ; Hornbeck et al, 2015 ; Matlock et al, 2015 ). TOP1 contains the N-terminal domain (NTD), the capping module (CAP), the catalytic module (CAT), the linker, and the C-terminal domain ( Takahashi et al, 2022 ), which are shown in red, darker green, lighter green, light blue, and yellow, respectively. Its catalytic tyrosine residue is shown in red.…”

Confused‐Prism[5]arene: a Conformationally Adaptive Host by Stereoselective Opening of the 1,4‐Bridged Naphthalene Flap

“…In the conformational‐selection binding model, protein conformational changes can occur before the ligand binding, and the binding of the substrate stabilizes a specific conformation of the protein. In induced‐fit binding model, [14] the conformational change is induced by the ligand and occurs upon substrate binding [17] …”