difference between dna gyrase and topoisomerase

Type I enzymes catalyze their reactions by transiently breaking one strand of DNA and forming a covalent bond between either the 5 (IA) or 3 (IB) phosphate at the break site and the active-site tyrosine of the enzyme. The effect of exchanging positive by negative charges on the surface of the TopoIV CTD on DNA binding depends on the position of the mutation: mutations close to the N-terminus do not alter the DNA affinity, whereas binding is progressively impaired when the mutations are closer to the C-terminus (75). In this configuration, blade 1 is the last blade that is contacted by the wrapped DNA before it exits the CTD (68). WebDNA gyrase and topoisomerases are enzymes involved in the crucial processes of DNA replication, transcription, and recombination. WebWai Mun Huang, in Advances in Pharmacology, 1994. 19.2) and DNA topoisomerase (topo) IV, are type IIA enzymes. Although TopoIV protects only the central region of the DNA (103,104), deletion of the CTDs in gyrase and TopoIV leads to a decrease in DNA affinity (50,74), confirming that they contribute to DNA binding in both enzymes. 8 These two enzymes are critical bacterial enzymes that regulate the chromosomal supercoiling required for DNA synthesis. TopoIV efficiently disentangles pre-catenanes during replication elongation, and mediates chromosome decatenation at the end of the replication process to ensure chromosome segregation (19,114). DNA gyrase and topoisomerase IV: biochemical activities, physiological roles during chromosome DNA gyrase is unique among topoisomerases in its ability to introduce negative supercoils into closed-circular DNA. They also contribute to bending of the G-segment by gyrase and TopoIV (34,75,105). DNA Replication TTAGGG. Strikingly, residues in blade 1 located nearest to the ParC NTD contribute to bending of the G-segment DNA bound at the DNA-gate of the topoisomerase core (75). The different interaction with DNA thus makes the difference between intermolecular strand passage and decatenation by TopoIV, or intramolecular strand passage and supercoiling by gyrase. Acta Crystallogr., Sect. Type IIA topoisomerases include the eukaryotic topoisomerase II (TopoII) and the bacterial enzymes topoisomerase IV (TopoIV) and gyrase [reviewed in (7)]. Most bacteria have two type IIA topoisomerases, DNA gyrase and topoisomerase IV. Top: front view, bottom: top view. This enzyme was more sensitive than DNA The -strand-bearingproline is shown as a stick model in cyan. In this review, we have summarized how the type IIA topo-isomerase scaffold provides a common basis for two different biological tasks, decatenation and supercoiling. The GyrB and ParE subunits contain the same modules, namely an N-terminal ATPase domain of the GyrB-Hsp90-histidine/serine protein kinase-MutL (GHKL) phosphotransferase superfamily, connected to a C-terminal Mg2+-binding topoisomerase-primase (TOPRIM) domain by the transducer domain (27). In-line with this notion, gyrase is an essential enzyme present in all bacteria (with only one exception, see before), while TopoIV is not essential and not universally present (128). The continued emergence of bacterial resistance has created an urgent need for new and effective antibacterial agents. Negatively supercoiled DNA interacts also with blades 2, and 3, and with a strong binding site on blade 5. The complexes, called cleaved TopoIV relaxes positive supercoils much faster than negative supercoils (86,87). Magnetic tweezers experiments revealed that, similar to gyrase, the reason for the preferred action on positively supercoiled DNA is the difference in processivity: while relaxation of positive supercoils is highly processive, the relaxation of negative supercoils is entirely distributive (11,87,92). It preferentially interacts with negative crossings occurring in positively supercoiled DNA and positive catenanes (92,95). In-line with this hypothesis, the gyrase from M. tuberculosis, an organisms lacking a TopoIV, shows a different balance between supercoiling and decatenation activities, and a higher tendency to decatenate DNA (124,125). Fluoroquinolones: structure and target sites The ATP-operated clamp inhibits the rotation of the T-segment around its helical axis. makes a type IIA topoisomerase a gyrase or Despite the common principles in their core mechanism, gyrase and TopoIV display large differences in their interactions with the DNA substrate, which are intimately linked to their different activity profiles. By this arrangement, two cavities are formed, one between the N- and DNA-gate and a second between the DNA- and C-gate (Figure 2). This enzyme was more sensitive than Generally, charge removal and a concomitant weakening of DNA wrapping lead to a decrease in supercoiling activities, but enhanced decatenation, and thus generated a more TopoIV-like enzyme. By rotation of the fork, these positive supercoils can diffuse backwards, resulting in the formation of pre-catenanes behind the fork (18). Topoisomerases are the target of widely used anticancer drugs and antibiotics (15).Quinolone antibiotics, in particular, ciprofloxacin, are on the World Health Organizations List of Essential Medicines (6, 7).Collectively termed as topoisomerase poisons, these drugs bind to a transient pocket at the covalent enzyme-DNA interface Chapter 11 Novel bacterial topoisomerase inhibitor (NBTI) represents emerging class of non-quinolone DNA gyrase and topoisomerase IV inhibitor. The blades are numbered from the N- to the C-terminus; the box highlights blade 3. Poisons stabilize an intermediate covalent complex of topoisomerase with the DNA G-segment. Quinolone resistance in bacterial pathogens has primarily been associated with mutations in the quinolone resistance-determining regions (QRDRs) of bacterial type-II topoisomerases, which are DNA gyrase and topoisomerase IV. B. burgdorferi may reflect an evolutionary intermediate that provides support for the occurrence of such a fusion event in evolution. Mechanisms of Action and Resistance of Older and Newer Type IIA topoisomerases and reactions catalyzed. The unique hallmark reaction of gyrase, i.e. Blades 25 contain degenerate forms of this motif (58), pointing to a possible evolutionary origin of the CTD from the duplication of a single blade (see Evolution of type IIA topoisomerases). Reverse gyrase is the only topoisomerase that introduces positive supercoils into DNA in an ATP-dependent reaction. Commun. F: Struct. DNA Topoisomerases Gyrase and TopoIV perform separate, dedicated tasks during replication: gyrase removes positive supercoils in front, TopoIV removes pre-catenanes behind the replication fork. Rovinskiy N., Agbleke A.A., Chesnokova O., Pang Z., Higgins N.P. While TopoIV cleaves negatively and positively supercoiled DNA with equal efficiencies, gyrase shows less cleavage on positively supercoiled DNA. Human telomeres contain 100 to 1000 copies of which nucleotide sequence? DNA Topoisomerase (ATP Hydrolysing Gram-negative bacteria: antimicrobial activity As a result of this rotation, the ATPase domain of one protomer comes into close contact with the DNA cleavage part of the second protomer (65). The first structure of a type IIA topoisomerase reported was of a S. cerevisiaeTopoII core, missing the C-terminal region (65). DNA molecules with the same size and sequence but which differ in their linking number . By removing positive supercoils with high processivity and velocity (12), it alleviates accumulating torsional stress and ensures fork progression. In this way, both enzymes divide the labor of resolving the topological problems associated with the movement of the replication fork. In contradiction to the strand-passage mechanism, gyrase in which one of the two tyrosines is replaced by a phenyl-alanine is able to supercoil DNA in the absence of double-strand cleavage and strand passage (84). Joshi M.C., Magnan D., Montminy T.P., Lies M., Stepankiw N., Bates D. Reu D.R., Fahauer P., Mroch P.J., Ul-Haq I., Koo B.-M., Phlein A., Gross C.A., Daniel R., Brantl S., Stlke J. Manjunatha U.H., Dalal M., Chatterji M., Radha D.R., Visweswariah S.S., Nagaraja V. Aubry A., Fisher L.M., Jarlier V., Cambau E. Deckert G., Warren P.V., Gaasterland T., Young W.G., Lenox A.L., Graham D.E., Overbeek R., Snead M.A., Keller M., Aujay M. et al.. Hsieh T.-J., Farh L., Huang W.M., Chan N.-L. Tretter E.M., Lerman J.C., Berger J.M. Gyrase The global supercoiling state is determined by the delicate balance between opposing activities of the different topoisomerases present. In addition, Mycobacterium smegmatis gyrase stably binds two DNAs, similar to TopoIV (80), favoring intermolecular strand passage and decatenation. The two strands may rejoin together. Gyrase can also decatenate DNA in the presence of ATP, and relaxes negative supercoils in the absence of ATP (13). DNA gyrase consists of two copies of GyrA and two copies of GyrB and functions as an A 2 B 2 heterotetramer (Fig. a. Ligase b. DNA gyrase c. Single-stranded binding protein d. Primase In agreement with this hypothesis, mutation of the conserved proline in E.coli gyrase that enables formation of the spiral shape of the CTD leads to impaired DNA wrapping and a decrease of supercoiling activity (62). It is conceivable that topoisomerase subunits were present even during the RNA world, and then jointly took over different functions later on (128). Topoisomerase Catenated DNAs preferentially interacts with blades 3, 4, and 5. WebIn molecular biology Type I topoisomerases are enzymes that cut one of the two strands of double-stranded DNA, relax the strand, and reanneal the strand. This conformation is mediated by interactions between two motives specific for the order of Corynebacteriales, the C-loop in the ATPase domain of GyrB and the DEEE-loop in the tower domain of GyrA (69,70). Chp 24 Genes and Chromosomes Nanoparticle Brushes: Macromolecular Ligands for Materials Synthesis. FtsK also stimulates the decatenation activity of TopoIV (114). The TOPRIM domains are in a similar orientation as in gyrase, but the ParE ATPase domains are bent downwards, facing toward the C-gate, and are far apart from each other. cAccording to single-molecule FRET data (34). This balance is the result of less efficient DNA supercoiling compared to other gyrases; the decatenation activity remains lower than the one of TopoIV (124,125). Topoisomerase 1 and 2 DNA gyrase and topoisomerase IV are the targets for many antibiotics that, according to their mechanism of action, may be divided into two groups: poisons and catalytic inhibitors. This structure captured gyrase with all three gates in the closed state. The novel bacterial topoisomerase inhibitors (NBTIs) represent one of Nevertheless, the mechanisms for topology sensing are different for the two enzymes. In the context of TopoIV, positively supercoiled DNA is bound mostly through blades 2, 3and 4. (A) Crystal structure of the gyrase CTD from E.coli [PDB-ID: 1zi0 (61)]. Topoisomerases such as DNA gyrase (Type II Topoisomerase) play a role in relieving some of the stress during DNA/RNA As a result, the enzyme is also a gyrase with respect to its preference for positively supercoiled DNA substrates (91). Without the GyrA-box, the tight connection between the first and last blade is missing, and the ParC CTD adopts an open, C-shaped structure with a gap between these blades (Figure 3D) (50,56). In Escherichia coli two type II topoisomerases are involved in enabling both DNA replication and timely DNA segregation, namely Gyrase and Topoisomerase IV (TopoIV). Escherichia coli has two topoisomerases type I: topoisomerase I and topoisomerase III and two topoisomerases type II: topoisomerase II or gyrase and topoisomerase IV. We show here that single strand binding protein stimulates DNA topoisomerase I activity without direct protein-protein interactions. Gyrase activity is critical during transcription, and in the beginning of and during replication, whereas TopoIV activity is essential for chromosome segregation at the end of the replication process (16,86). In fact, in B. burgdorferi, the CTD is present as a separate DNA binding protein, independent of gyrase (132). WebRationale 2: Fluoroquinolones bind to enzymes gyrase and topoisomerase, blocking the relaxation and migration processes of bacterial DNA replication. The preferential relaxation of positive supercoils by TopoIV and the conversion of positive into negative supercoils by gyrase jointly remove excess positive supercoils in bacteria without relaxation of negative supercoiling required for DNA compaction and metabolism. DNA gyrase and topoisomerase IV: biochemical activities, Here, a double-stranded DNA segment, the G-segment, is bound, bent or distorted, and finally cleaved by the catalytic tyrosines (39,40). According to phylogenetic analyses, this enzyme is a hybrid enzyme with a gyrase-like topoisomerase core and a TopoIV-like CTD (126). Its IC50s for the decatenating activity of the mutant topoisomerase IV harboring an amino acid change in ParC were 15.1 for Gly-81 Cys and 7.92 g/ml for Asp-87 Tyr. The subjects of this chapter, DNA gyrase (Fig. DNA Topoisomerases - PubMed According to the twin-domain model, negative supercoils accumulate behind the translocating machinery, whereas positive supercoils are formed in the unwound DNA ahead (3,4). The DNA-stimulated ATPase activity of the gyrase variants correlated with the wrapping propensity. When helicase and topoisomerase meet WebNXL101 is one of a new class of quinoline antibacterial DNA gyrase and topoisomerase IV inhibitors showing potent activity against gram-positive bacteria, including methicillin- and fluoroquinolone-resistant strains. The current state of the art of gyrase and TopoIV inhibition has been reviewed elsewhere (2426). showed that mutations of positive charges in different blades of TopoIV have differential effects on the interaction of TopoIV with different DNA substrate, and on different activities of TopoIV. According to the cryo-EM structure of E.coli gyrase, the GyrA-box faces away from the NTD and from the G-segment binding site (68). WebEnter the email address you signed up with and we'll email you a reset link. In the first part, we will compare their structural features. 9 Over time, quinolone resistance Positive DNA supercoiling becomes possible Possible evolutionary pathway for the appearance of gyrase and TopoIV. Alternatively, the -pinwheel may be based on the prevalent Greek key motif as a repeating unit, which follows the DABC topology (30) (see Evolution of type IIA topoisomerases). WebHelicasetopoisomerase coupling in RG2 supercoiling. To alter supercoiling, DNA gyrase has two sets of jaws that allow it to grab onto two regions of DNA. Type IIA topoisomerases catalyze a variety of different reactions: eukaryotic topoisomerase II relaxes DNA in an ATP-dependent reaction, whereas the bacterial representatives gyrase and topoisomerase IV (TopoIV) preferentially introduce negative supercoils into DNA (gyrase) or decatenate DNA (TopoIV). According to the current model, type IIA topoisomerases change the topological state of DNA by a strand-passage mechanism (Figure 5) (reviewed in (76)). DNA gyrase is a type II topoisomerase that can introduce negative supercoils into DNA at the expense of ATP hydrolysis. Type II Topoisomerase - an overview | ScienceDirect Topics of and resistance to quinolones 21,22,25,26 Gyrase is the only type II topoisomerase that can actively introduce negative supercoils into DNA. 1.1 DNA Gyrase. The antibacterial potency of a quinolone is defined in part by its potency against the two enzyme targets; the more sensitive of the two enzymes within a cell is the primary target. Gyrase is a tetramer of the form A 2 B 2.The tetramer has two chambers that can accommodate two strands of DNA.
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