Type I topoisomerase

Type I topoisomerase

Type I topoisomerases are divided into two structurally and mechanistically distinct topoisomerases: type IA and type IB.
* Type IA topoisomerases change the linking number of a circular DNA strand by units of strictly 1.
* Type IB topoisomerases change the linking number by multiples of 1 (n). Historically, type IA topoisomerases are referred to as prokayrotic topo I, while type IB topoisomerases are referred to as eukaryotic topoisomerase. This distinction, however, no longer applies as type IA and type IB topoisomerases exist in all kingdoms of life.

Functionally, these subclasses perform very specialized functions. Eukaryotic topoisomerase I (topo IB) can only relax negative supercoiled DNA, whereas prokaryotic topoisomerase I (topo IA) can introduce positive supercoils decatanate single-stranded DNA, and relax DNA.

Type IA topoisomerses

Type IA topoisomerases creates a single break in DNA, and passes a second strand or duplex through the break. This strand passage mechanism shares several features with type IIA topoisomerases. They both form a 5' phosphotyrosine intermediate, and require a divalent metal ion to perform its work. Unlike type II topoisomerases, type IA topoisomerases do not use energy to do its work (with the notable exception of reverse gyrase, see below).

Type IA topoisomerases have several domains, often number Domain 1-4. Domain I contains a Toprim domain (a Rossman fold known to coordinate Magnesium ions), domain IV and domain III each consist of a helix-turn-helix (HTH) domain; the catalytic tyrosine resides on the HTH of domain III. Domain II is a flexible bridge between domains III and IV. The structure of type IA topoisomerase resembles a lock, with Domains I, III and IV lie on the bottom of the structure [Lima, Wang, and Mondragon, Nature 1994] . The structure of topo III (see below) bound to single-stranded DNA [Changela, DiGate, and Mondragon, Nature 2001] (pdb id = 1I7D) shows how the HTH and Toprim domain are coordinated about the DNA.

"Type IA topo variants"
There are several variants of Type IA topoisomerases, differing by appendages attached to the main core (sometimes referred to as the "topo-fold"). Members of this subclass include topo I, topo III (which contain additional Zinc-binding motifs), and reverse gyrase. Reverse gyrase is particularly interesting because a ATPase domain, that resembles the helicase-like domain of the Rho transcription factor, is attached (the structure of reverse gyrase was solved by Rodriguez and Stock, EMBO J 2002). The enzyme uses the hydrolysis of ATP to introduce positive supercoils and overwinds DNA, a feature attractive in hyperthermophiles, in which reverse gyrase is known to exist. Rodriguez and Stock have done further work to identify a "latch" that is involved in communicating the hydroylsis of ATP to the introduction of positive supercoils.

The topo III variant is likewise very interesting because it has zinc-binding motifs that is thought to bind single-stranded DNA. Topo III has been identified to be associated with the BLM (for Bloom Syndrome) helicase during recombination.

Type IA topoisomerases operate through a strand-passage mechanism, using a single gate (in contrast with type II topoisomerases). First, the single-stranded DNA binds domain III and I. The catalytic tyrosine cleaves the DNA backbone, creating a transient 5' phosphotyrosine intermediate. The break is then separated, using domain II as a hinge, and a second duplex or strand of DNA is passed through. Domain III and I close and the DNA is re-annealed.

Type IB topoisomerases

In contrast to type IA topoisomerases, type 1B Topoisomerase solves the problem of overwound and underwound DNA through a controlled rotary mechanism. Crystal structures, biochemistry, and single molecule experiments have contributed to a general mechanism. The enzyme first wraps around f DNA and creates a single, 3' phosphotyrosine intermediate. The 5' end is then free to rotate, twisting it about the other strand, to relax DNA to a thermodynamic equilibrium. Once DNA is relaxed, topoisomerase reconnects broken strands.

The structure of topo IB bound to DNA has been solved (pdb id = 1A36). Topo IB is composed of a NTD, a capping lobe, a catalytic lobe, and a C-terminal domain. The capping lobe and catalytic lobe wrap around the DNA.

This is not an active process in the sense that energy in the form of ATP is not spent during the nicking or ligation steps as the reaction between the tyrosine residue at the active site of the enzyme with the phosphodiester DNA backbone simply replaces one phosphomonoester bond with another. The topoisomerase also does not use ATP during uncoiling of the DNA; rather, the torque present in the DNA drives the uncoiling. Recent single molecule experiments show that the enzyme works using a controlled rotary mechanism.

Type IB topoisomerases were originally identified in eukaryotes and in viruses. Viral topo I is unique because it binds DNA in a sequence-specific manner.

Type IC topoisomerases

Recently, a new type of topoisomerase was identified, topo V. Topo V is the founding member, and so far the only member, of the type IC topoisomerase. The crystal structure of topo V was solved.cite journal |author=Taneja B, Patel A, Slesarev A, Mondragón A |title=Structure of the N-terminal fragment of topoisomerase V reveals a new family of topoisomerases |journal=EMBO J. |volume=25 |issue=2 |pages=398–408 |year=2006 |month=January |pmid=16395333 |doi=10.1038/sj.emboj.7600922 |url=http://dx.doi.org/10.1038/sj.emboj.7600922] Type IC topoisomerases work through a controlled rotary mechanism, much like type IB topoisomerases [Bhupesh Taneja, Bernhard Schnurr,, Alexei Slesarev, John F. Marko, and Alfonso Mondragón, PNAS 2007] (pdb ID = 2CSB and 2CSD), but the fold is unique.


All topoisomerases form a phosphotyrosine intermediate between the catalytic tyrosine of the enzyme and the scissile phosphoryl of the DNA backbone.

* Type IA topoisomerases form a covalent linkage between the catalytic tyrosine and the 5'-phosphoryl.
* Type IB enzymes form a covalent 3'-phosphotyrosine intermediate.
* Type 1C topoisomerases form a covalent 3'-phosphotyrosine intermediate.

This intermediate is isoenergetic, meaning that the forward cleavage reaction and the backward religation reaction are both energetically equal. As such, no outside energy source is necessary to conduct this reaction.


As topoisomerases generate breaks in DNA, they are targets of small-molecule inhibitors that inhbit the enzyme.Type 1 topoisomerase is inhibited by irinotecan, topotecan and camptothecin.


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