DNA Topoisomerases

Babak Nami
Seluk University
Department of Medical Genetics February, 2011
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While this structure provides a stable means of storing the genetic code, Watson and Crick noted that the two strands of DNA are intertwined, and this would require the two strands to be untwisted in order to access the information stored.

Introduction

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In

order to help overcome these problems caused by the double helix, topoisomerases bind to either singlestranded or double-stranded DNA and cut the phosphate backbone of the DNA. This intermediate break allows the DNA to be untangled or unwound, and, at the end of these processes, the DNA is reconnected again.
Topoisomerases

are isomerase enzymes that act on the topology of

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DNA supercoil and Linking number

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Why do we need DNA Topoisomerase?

DNA

supercoiling is a natural consequence of DNA double helix; DNA replication, recombination, and transcription have to separate DNA two strands permanently or temporarily, which require DNA topoisomerases to remove the topological tension.
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Discovery
The

need for this enzyme was recognized long before it was discovered. When the double-helical nature of DNA was determined by Watson and Crick, the authors noted that there must be some mechanism that would resolve the tangles that arise from this structural feature. The rst DNA topoisomerase was discovered by James Wang in 1971, the so-called protein from Escherichia coli. This enzyme, now called DNA topoisomerase I, was found to reduce the number of negative supercoils in bacteriophage DNA, SELUK UNIVERSITY as measured by DERPARTMENT OF MEDICAL GENETICS 8 changes in sedimentation coefficient.

Examples

of the type of organisms in which topoisomerases have been studied include the bacteria E. coli and Staphylococcus aureus, yeasts, Arabidopsis, Drosophila and Human. In addition, several viruses are known to encode a topoisomerase, for example, bacteriophage T4 and the animal virus.
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Classification of Topoisomerases

Type I break one strand Type IA (proc) Relax neg supercoils Passes single strand through break before resealing. Type IB (euk & proc) Relax pos or neg supercoils. Type II break two strands DNA gyrase (proc) Other euk and proc Type II Relax positively or negatively SELUK UNIVERSITY supercoiled DNA DERPARTMENT OF MEDICAL GENETICS Only gyrase induces negative

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Classification of Topoisomerases
DNA

topoisomerases cleave only one strand of the DNA are defined as type I Topoisomerase. If the intermediate of the reaction catalyzed by topoisomerases is a 5phosphodiester, we define these enzymes as type IA topoisomerases; if the intermediate is a 3- phosphodiester, these enzymes are defined as type IB enzymes; Topoisomerases that cleaves both strands to generated staggered doublestrand break are defined as type II Topoisomerase. The type IIUNIVERSITY subfamily is SELUK further divided into two subfamilies, DERPARTMENT OF MEDICAL GENETICS type IIA and IIB subfamily according to 12

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Function
All

topoisomerases proceed through covalent intermediates involving ester linkages between phosphates at the break and tyrosines in the active site. These enzymes are essential for replication as they are required to untangle the strands and so we will talk about them again when we discuss DNA replication.
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Topoisomerases l
These

enzymes remove supercoils through a mechanism that involves breaking only one of the two phosphodiester backbones. As a result, these enzymes change the linking number by 1 each time.
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Type IA Topoisomerases

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Mechanism of Topoisomerase IA
1.

Like all enzymes, Topoisoerases have active site. It refer to the Tyrosine amino acid. The hydroxyl group of a Tyrosine residue at the active site of the enzyme forms a phosphodiester bond with a 5phosphate of the DNA chain. The 3 end of the broken strand is also bound noncovalently to
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2.

After the second strand has passed through the break, the original phosphodiester bond of the first strand is reformed.

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Type IB DNA Topoisomerases

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E. Coli Topoisomerase I

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This enzyme is 864 amino-acids in length and is monomeric, it is encoded by the topA gene. The amino-terminal part of the enzyme (aas 2-590) has been crystallized:

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Different functions between E. coli DNA Topo I and III

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Human DNA Topoisomerase l

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Function of Human DNA Topoisomerase l

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Comparison E. coli and Human DNA Topo I

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Type II DNA Topoisomerases

Type

II Topoisomerase cut both strands of the DNA helix simultaneously in order to unwind it. The energy required for this is the hydrolysis of ATP, unlike type l. Topoisomerase, which is thermodynamically favored. As a result, the linking number changes by 2. The best-characterized member of this class in E.coli, Topoisomerase II better known as DNA Gyrase, is
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Type II DNA Topoisomerases

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Function
Once

cut, the ends of the DNA are separated, and a second DNA duplex is passed through the break. his reaction allows type II topoisomerases to increase or decrease the linking number of a DNA loop by 2 units.
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Strand Passage Mechanism of type II Topoisomerases

A

strand of DNA, called the Gated, or G-segment is bound by a central DNA-binding gate (DNA-gate). A second strand of DNA, called the Transporter exchanger (sometimes called the transfer), or T-segment is captured by the oxidation of the N-terminal ATPase domain (the ATPase-gate) as two molecules of ATP are bound.
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 Hydrolysis

of ATP and release of an inorganic phosphate leads to the cleavage of the G-segment, as the catalytic tyrosines form a covalent phosphotyrosine bond with the 5' end of the DNA. Type IIA topoisomerases creates a fourbase overhang and a double-stranded break in the G-segment, while Type llB
As

forms a two-base overhang in the G-segment.

the DNA-binding gate separates, the T-segment is transferred through the Gsegment. The G-segment is sealed, leading to the C-terminal gate (or C-gate) to open, allowing for the release of the Tsegment. Release of product ADP SELUK UNIVERSITY reset leads to a DERPARTMENT OF of the system, and allows a second TMEDICAL GENETICS 45

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Classification of Topoisomerase ll
There are two subclasses of type II topoisomerases, type IIA and IIB:
Type

IIA topoisomerases include the

enzymes DNA gyrase, eukaryotic topoisomerase II (topo II), and bacterial topoisomerase lV (topo IV). These enzymes span all domains of life and are essential for function.
Type

IIB topoisomerases are structurally

and biochemically distinct, and comprise a single family member, topoisomerase VI (topo VI). Type IIB topoisomerases are found in SELUK UNIVERSITY some higher plants. DERPARTMENT OF
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Comparison Topo llA and llB

The

two classes of topoisomerases possess a similar strand passage mechanism and domain structure, however they also have several important differences. Type IIA topoisomerases form double-stranded breaks with four base pair overhangs, while type IIB topoisomerases form doublestranded breaks with two base pair overhangs (Buhler, Lebbink, Bocs,
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Type IIA Topoisomerases

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Structure of yeast topoisomerase II bound to a doublynicked 34-mer duplex DNA (PDB ID =2RGR). The Toprim fold is colored cyan; the DNA is colored orange; the HTH is colored magenta; and the C-gate is colored purple. Notice that the DNA is bent by ~160 degrees through an invariant SELUK UNIVERSITY isoleucine (Ile833 in yeast). DERPARTMENT OF
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In

cancers, the topoisomerase IIA is highly expressed in highly proliferating cells. In certain cancers, such as peripheral nerve sheath tumors, high expression of its encoded protein is also associated to poor patient survival.
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Type IIB Topoisomerases

The

organization of type IIB topoisomerases are similar to that of type IIAs, except that all type IIBs have two genes and form heterodimers. One gene, termed topo VI-B (since it resembles gyrB), contains the ATPase domain, a H2TH domain, and the transducer domain. The second gene, termed topo VI-A, contains the WHD and the Toprim
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The

ATPase domain of topo VI B was solved in multiple nucleotide states (Corbett and Berger, EMBO J 2003). It closely resembles that of the GHKL domain of topo II and MutL and shows that the nucleotide state (ADP versus ATP) effects the orientation of the transducer domain (pdb ID= 1MU5 and 1MX0). A recent structure of the topo VI A/B complex was solved, showing an open and closed conformation, two states that are predicted in the twoSELUK UNIVERSITY DERPARTMENT OF MEDICAL GENETICS

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Structure of topo VI (PDB ID =2Q2E). Monomers are colored differently. The N-terminal ATPase domain lies on the top of the molecule, forming the DNA gate, while the DNA gate lies on the bottom.
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DNA Gyrase
DNA

Gyrase is a type ll toroisomerase. It introduces negative supercoil (or relaxes positive supercoils) into DNA by looping the template so as to form a crossing, then cutting one of the double helices and passing the other through it before releasing the break, changing the linking number by two in each enzymatic step.
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This

process occurs in prokaryotes (in particular, in bacteria), whose single circular DNA is cut by DNA gyrase and the two ends are then twisted around each other to form supercoils.

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Negative Supercoiling by DNAGyrase

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Subunits of DNA gyrase form a heterotetramer with two GyrA protomers (purple) and two GyrB protomers (orange). In the supercoiling mode, the sign of the cross or node is (+) for introducing negative supercoils and (-) SELUK UNIVERSITY for removing negative supercoils. Lk, linking number. OF DERPARTMENT
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THANK YOU
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