I am studying DNA replication.
Topoisomerases = cuts and rejoins the helix
after reading the definition above, I don't know how to distinguish it from helicase.
whats the difference between unwinding the helix and cutting the helix?
TOPOISOMERASE
Topoisomerases (type I: EC 5.99.1.2, type II: EC 5.99.1.3) are enzymes that act on the topology of DNA. The double-helical configuration that DNA strands naturally reside in makes them difficult to separate, and yet they must be separated by helicase proteins if other enzymes are to transcribe the sequences that encode proteins, or if chromosomes are to be replicated. In so-called circular DNA, in which double helical DNA is bent around and joined in a circle, the two strands are topologically linked, or knotted. Otherwise identical loops of DNA having different numbers of twists are topoisomers, and cannot be interconverted by any process that does not involve the breaking of DNA strands. Topoisomerases catalyze and guide the unknotting of DNA.
The insertion of viral DNA into chromosomes and other forms of recombination can also require the action of topoisomerases.
Many drugs operate through interference with the topoisomerases. The broad-spectrum fluoroquinolone antibiotics act by disrupting the function of bacterial type II topoisomerases. Some chemotherapy drugs work by interfering with topoisomerases in cancer cells: type 1 is inhibited by irinotecan and topotecan, while type 2 is inhibited by etoposide and teniposide.
Type I topoisomerases
Both type I and type II topoisomerases change the supercoiling of DNA. Type I topoisomerases function by nicking one of the strands of the DNA double helix, twisting it around the other strand, and re-ligating the nicked strand. This is not an active process in the sense that energy in the form of ATP is not spent by the topoisomerase during uncoiling of the DNA; rather, the torque present in the DNA drives the uncoiling. Type I enzymes can be further subdivided into type IA and type IB, based on their chemistry of action. Type IA topoisomerases change the linking number of a circular DNA strand by units of strictly 1, wherease Type IB topoisomerases change the linking number by multiples of 1. 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 while type IB enzymes form a covalent 3'-phosphotyrosine intermediate. Apart from these similarities, they have very different mechanisms of action, have different crystal structures and appear not to have similar evolutionary ancestors.
Type II topoisomerases
Type II topoisomerases cut both strands of the DNA helix simultaneously. Once cut, the ends of the DNA are separated, and a second DNA duplex is passed through the break. Following passage, the cut DNA is resealed. This reaction allows type II topoisomerases to increase or decrease the linking number of a DNA loop by 2 units, and promotes chromosome disentanglement. For example, DNA gyrase, a type II topoisomerase observed in E. coli and most other prokaryotes, introduces negative supercoils and decreases the linking number by 2. Gyrase also is able to remove knots from the bacterial chromosome. There are two subclasses of type II topoisomerases, type IIA and IIB. Type IIA topoisomerases include the enzymes DNA gyrase, eukaryotic topoisomerase II, and bacterial topoisomerase IV. Type IIB topoisomerases are structurally and biochemically distinct, and comprise a single family member, topoisomerase VI. Type IIB topoisomerases are found in archaea and some higher plants. In cancers, the topoisomerase IIalpha 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.
HELICASE:
Helicases are a class of enzymes vital to all living organisms. They are motor proteins that translocate unidirectionally along single-stranded nucleic acids using energy derived from nucleotide hydrolysis, often separating the two strands of a nucleic acid double helix in the process. (i.e. DNA, RNA, or RNA-DNA hybrid)
Function
Many cellular processes (DNA replication, RNA transcription, DNA recombination, DNA repair) involve separation of the nucleic acid strands. There are many helicases (14 identified so far in E. coli, 24 in human cells) resulting from the great variety of processes in which strand separation must be catalyzed. All helicases separate the strands of a double helix using the energy derived from ATP hydrolysis. They move along one strand with a directionality specific to each enzyme (3'-5' or 5'-3') while separating the strands.
Structural Features
The common features shared by helicases account for the fact that they display amino acid sequence homology to a certain degree: they all possess common sequence motifs located in the central part of their sequence. These are thought to be specifically involved in ATP binding, ATP hydrolysis and translocation on the nucleic acid template. The variable part of the amino acid sequence is related to the specific features of each helicase. Based on the presence of the so-called helicase motifs, it is possible to attribute a putative helicase activity to a given protein. However, the presence of these motifs does not necessarily imply that the protein indeed possesses helicase activity. Based on the presence and the form of the helicase motifs, helicases have been separated in 4 superfamilies and 2 smaller families. Some members of these families are indicated, with the organism from which they are extracted, and their function.
Helicases adopt different structures and oligomerization states. Whereas DnaB-like helicases unwind DNA as donut shaped hexamers, other enzymes have been shown to be active as monomers or dimers. Their precise mechanisms of action are still unclear.
Helicase Superfamilies
Superfamily I: UvrD (E. coli, DNA repair), Rep (E. coli, DNA replication), PcrA (Bacillus stearothermophilus, role not precisely known), Dda (bacteriophage T4, replication initiation).
Superfamily II: RecQ (E. coli, DNA repair), BLM (human, DNA repair), WRN (human, DNA repair), NS3[1] (Hepatitis C virus, replication). TRCF (Mfd) (E.coli, transcription-repair coupling factor).
Superfamily III: LTag (Simian Virus 40, replication), E1 (human papillomavirus, replication).
DnaB-like family: DnaB (E. coli, replication), gp41 (bacteriophage T4, DNA replication), T7gp4 (bacteriophage T7, DNA replication).
Rho-like family: Rho (E. coli, Transcription termination factor ).
