Model of DNA strand cleavage by topoisomerase I.

Formation of the covalent bond involving

tyrosine 723 is shown, as are other active site amino acids believed to function in the
cleavage process.

A model for topoisomerase II action. As indicated, ATP binding to the two ATPase
domains causes them to dimerize and drives the reactions shown. Because a single
cycle of this reaction can occur in the presence of a non-hydrolyzable ATP analog,
ATP hydrolysis is thought to be needed only to reset the enzyme for each new
reaction cycle. This model is based on structural and mechanistic studies of the
enzyme

Action of topoisomerases during DNA replication (A) As the two strands of template DNA unwind, the
DNA ahead of the replication fork is forced to rotate in the opposite direction, causing circular molecules
to become twisted around themselves. (B) This problem is solved by topoisomerases, which catalyze the
reversible breakage and joining of DNA strands. The transient breaks introduced by these enzymes serve
as swivels that allow the two strands of DNA to rotate freely around each other.

Structure of a Topoisomerase.
The structure of a complex between a fragment
of human topoisomerase I and DNA.

Structure of Topoisomerase II.

A composite structure of topoisomerase II formed
from the amino-terminal ATP-binding domain of E. coli topoisomerase II (green) and the
carboxyl-terminal fragment from yeast topoisomerase II (yellow). Both units form dimeric
structures as shown.

The mode of action of Type I and Type II DNA topoisomerases. (A) A Type I
topoisomerase makes a nick in one strand of a DNA molecule, passes the intact strand
through the nick, and reseals the gap. (B) A Type II topoisomerase makes a doublestranded break in the double helix, creating a gate through which a second segment of
the helix is passed.

Topoisomerase I Mechanism. On binding to DNA, topoisomerase I cleaves one

strand of the DNA through a tyrosine (Y) residue attacking a phosphate. When the
strand has been cleaved, it rotates in a controlled manner around the other strand.
The reaction is completed by religation of the cleaved strand. This process results
in partial or complete relaxation of a supercoiled plasmid.

The reversible nicking reaction catalyzed by a eucaryotic DNA topoisomerase I

enzyme. As indicated, these enzymes transiently form a single covalent bond with DNA;
this allows free rotation of the DNA around the covalent backbone bonds linked to the
blue phosphate.

The DNA-helix-passing reaction catalyzed by DNA topoisomerase II. Identical

reactions are used to untangle DNA inside the cell. Unlike type I topoisomerases, type II
enzymes use ATP hydrolysis and some of the bacterial versions can introduce
superhelical tension into DNA. Type II topoisomerases are largely confined to
proliferating cells in eucaryotes; partly for that reason, they have been popular targets for
anticancer drugs.

Topoisomerase II Mechanism. Topoisomerase II first binds one DNA duplex termed the G (for gate) segment.
The binding of ATP to the two N-terminal domains brings these two domains together. This conformational
change leads to the cleavage of both strands of the G segment and the binding of an additional DNA duplex, the
T segment. This T segment then moves through the break in the G segment and out the bottom of the enzyme.
The hydrolysis of ATP resets the enzyme with the G segment still bound.

Model of topoisomerase 2 catalysis. The DNA duplex that undergoes cleavage is referred to as the G-segment (for gate)
and the other DNA duplex is referred to as the T-segment (for transported). Binding of the G-segment (step 1) results in a
conformational change (step 2) in which the active site tyrosines (shown as purple circles) are brought into position for
cleavage of the G-segment. After binding of the T-segment and ATP, a clamp is formed around the T-segment (step 3),
which is then transported though the gap in the G-segment (step 4). Subsequently, the G-strand is religated and the
Tsegment is released (step 5). After ATP hydrolysis, the clamp is opened and the cycle can repeat

Linking Number.
The relations
between the linking
number (Lk),
twisting number
(Tw), and writhing
number (Wr) of a
circular DNA
molecule revealed
schematically