DNA negative supercoiling activity
Definition
Target type: molecularfunction
Catalytic introduction of negative supercoils into a DNA molecule or region thereof. In bacteria, negative supercoils are only introduced by DNA gyrase, a type II topoisomerase, but not all DNA gyrases are capable of introducing supercoils. In bacteria, the level of supercoiling varies widely between species and has been characterized properly in only a handful of organisms. The best characterized enzyme, from E.coli, is exceptionally proficient at supercoiling and this ability is not representative of all bacteria. [GOC:bhm, GOC:krc, GOC:mah, WikiPedia:DNA_gyrase]
DNA negative supercoiling is a crucial molecular function that involves the introduction of negative supercoils into a DNA molecule. This process is catalyzed by enzymes called topoisomerases, which are essential for various cellular processes, including DNA replication, transcription, and recombination.
Negative supercoiling refers to the underwinding of DNA, resulting in a more compact and twisted structure. This underwinding creates torsional stress in the DNA molecule, which is crucial for several reasons:
1. **Facilitates DNA unwinding:** Negative supercoiling makes DNA more accessible to enzymes like helicases, which are required to unwind the double helix during replication and transcription. This accessibility is essential for the proper initiation and progression of these processes.
2. **Promotes DNA bending and looping:** The torsional stress induced by negative supercoiling can promote bending and looping of the DNA molecule, which is important for regulating gene expression. DNA loops can bring distant regulatory elements closer together, facilitating protein-DNA interactions and influencing the transcription of specific genes.
3. **Compacts DNA:** Negative supercoiling helps to condense the DNA molecule, which is essential for packaging the large genome within the limited space of the nucleus. This compaction also plays a role in the organization and accessibility of genetic information.
4. **Stabilizes DNA structure:** Negative supercoiling can stabilize the DNA molecule, protecting it from damage and breakage. The underwinding introduces a degree of rigidity to the DNA structure, making it less prone to denaturation and degradation.
5. **Regulates DNA replication and repair:** Negative supercoiling is crucial for the efficient replication and repair of DNA. It provides the necessary torsional stress for the separation of DNA strands during replication and facilitates the access of repair enzymes to damaged regions of the DNA molecule.
In summary, DNA negative supercoiling activity is a critical molecular function that plays a vital role in various cellular processes, including DNA replication, transcription, gene regulation, DNA packaging, and repair. The underwinding of DNA, catalyzed by topoisomerases, creates a dynamic and functional DNA structure that is essential for the proper functioning of the cell.'
"
Proteins (2)
| Protein | Definition | Taxonomy |
|---|---|---|
| DNA gyrase subunit B | A DNA gyrase subunit B that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AES6] | Escherichia coli K-12 |
| DNA gyrase subunit A | A DNA gyrase subunit A that is encoded in the genome of Escherichia coli K-12. [PRO:DNx, UniProtKB:P0AES4] | Escherichia coli K-12 |
Compounds (18)
| Compound | Definition | Classes | Roles |
|---|---|---|---|
| ciprofloxacin | ciprofloxacin : A quinolone that is quinolin-4(1H)-one bearing cyclopropyl, carboxylic acid, fluoro and piperazin-1-yl substituents at positions 1, 3, 6 and 7, respectively. Ciprofloxacin: A broad-spectrum antimicrobial carboxyfluoroquinoline. | aminoquinoline; cyclopropanes; fluoroquinolone antibiotic; N-arylpiperazine; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic; zwitterion | antibacterial drug; antiinfective agent; antimicrobial agent; DNA synthesis inhibitor; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; environmental contaminant; topoisomerase IV inhibitor; xenobiotic |
| enoxacin | enoxacin : A 1,8-naphthyridine derivative that is 1,4-dihydro-1,8-naphthyridine with an ethyl group at the 1 position, a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a piperazin-1-yl group at the 7 position. An antibacterial, it is used in the treatment of urinary-tract infections and gonorrhoea. Enoxacin: A broad-spectrum 6-fluoronaphthyridinone antibacterial agent that is structurally related to NALIDIXIC ACID. | 1,8-naphthyridine derivative; amino acid; fluoroquinolone antibiotic; monocarboxylic acid; N-arylpiperazine; quinolone antibiotic | antibacterial drug; DNA synthesis inhibitor |
| isoniazid | Hydra: A genus of freshwater polyps in the family Hydridae, order Hydroida, class HYDROZOA. They are of special interest because of their complex organization and because their adult organization corresponds roughly to the gastrula of higher animals. hydrazide : Compounds derived from oxoacids RkE(=O)l(OH)m (l =/= 0) by replacing -OH by -NRNR2 (R groups are commonly H). (IUPAC). | carbohydrazide | antitubercular agent; drug allergen |
| nalidixic acid | 1,8-naphthyridine derivative; monocarboxylic acid; quinolone antibiotic | antibacterial drug; antimicrobial agent; DNA synthesis inhibitor | |
| norfloxacin | norfloxacin : A quinolinemonocarboxylic acid with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin is bactericidal and its mode of action depends on blocking of bacterial DNA replication by binding itself to an enzyme called DNA gyrase. Norfloxacin: A synthetic fluoroquinolone (FLUOROQUINOLONES) with broad-spectrum antibacterial activity against most gram-negative and gram-positive bacteria. Norfloxacin inhibits bacterial DNA GYRASE. | fluoroquinolone antibiotic; N-arylpiperazine; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic | antibacterial drug; DNA synthesis inhibitor; environmental contaminant; xenobiotic |
| ofloxacin | 9-fluoro-3-methyl-10-(4-methylpiperazin-1-yl)-7-oxo-2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinoline-6-carboxylic acid : An oxazinoquinoline that is 2,3-dihydro-7H-[1,4]oxazino[2,3,4-ij]quinolin-7-one substituted by methyl, carboxy, fluoro, and 4-methylpiperazin-1-yl groups at positions 3, 6, 9, and 10, respectively. ofloxacin : A racemate comprising equimolar amounts of levofloxacin and dextrofloxacin. It is a synthetic fluoroquinolone antibacterial agent which inhibits the supercoiling activity of bacterial DNA gyrase, halting DNA replication. Ofloxacin: A synthetic fluoroquinolone antibacterial agent that inhibits the supercoiling activity of bacterial DNA GYRASE, halting DNA REPLICATION. | 3-oxo monocarboxylic acid; N-arylpiperazine; N-methylpiperazine; organofluorine compound; oxazinoquinoline | |
| gatifloxacin | gatifloxacin : A monocarboxylic acid that is 4-oxo-1,4-dihydroquinoline-3-carboxylic acid which is substituted on the nitrogen by a cyclopropyl group and at positions 6, 7, and 8 by fluoro, 3-methylpiperazin-1-yl, and methoxy groups, respectively. Gatifloxacin is an antibiotic of the fourth-generation fluoroquinolone family, that like other members of that family, inhibits the bacterial topoisomerase type-II enzymes. Gatifloxacin: A fluoroquinolone antibacterial agent and DNA TOPOISOMERASE II inhibitor that is used as an ophthalmic solution for the treatment of BACTERIAL CONJUNCTIVITIS. | N-arylpiperazine; organofluorine compound; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic | antiinfective agent; antimicrobial agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor |
| triclosan | aromatic ether; dichlorobenzene; monochlorobenzenes; phenols | antibacterial agent; antimalarial; drug allergen; EC 1.3.1.9 [enoyl-[acyl-carrier-protein] reductase (NADH)] inhibitor; EC 1.5.1.3 (dihydrofolate reductase) inhibitor; fungicide; persistent organic pollutant; xenobiotic | |
| 4-cumylphenol | diarylmethane | ||
| 4-phenoxyphenol | phenoxyphenol | ||
| bis(4-oxyphenyl)sulfide | 4,4'-thiodiphenol: structure in first source | phenols | |
| moxifloxacin | moxifloxacin : A quinolone that consists of 4-oxo-1,4-dihydroquinoline-3-carboxylic acid bearing a cyclopropyl substituent at position 1, a fluoro substitiuent at position 6, a (4aS,7aS)-octahydro-6H-pyrrolo[3,4-b]pyridin-6-yl group at position 7 and a methoxy substituent at position 8. A member of the fluoroquinolone class of antibacterial agents. Moxifloxacin: A fluoroquinolone that acts as an inhibitor of DNA TOPOISOMERASE II and is used as a broad-spectrum antibacterial agent. | aromatic ether; cyclopropanes; fluoroquinolone antibiotic; pyrrolidinopiperidine; quinolinemonocarboxylic acid; quinolone; quinolone antibiotic | antibacterial drug |
| linezolid | acetamides; morpholines; organofluorine compound; oxazolidinone | antibacterial drug; protein synthesis inhibitor | |
| gemifloxacin | gemifloxacin : A 1,4-dihydro-1,8-naphthyridine with a carboxy group at the 3-position, an oxo sustituent at the 4-position, a fluoro substituent at the 5-position and a substituted pyrrolin-1-yl group at the 7-position. Gemifloxacin: A naphthyridine and fluoroquinolone derivative antibacterial agent and DNA TOPOISOMERASE II inhibitor that is used for the treatment of community-acquired pneumonia and acute bacterial infections associated with chronic bronchitis. | 1,8-naphthyridine derivative; fluoroquinolone antibiotic; monocarboxylic acid; quinolone antibiotic | antibacterial drug; antimicrobial agent; topoisomerase IV inhibitor |
| pd 0305970 | |||
| gsk299423 | GSK299423: structure in first source | ||
| novobiocin | novobiocin : A coumarin-derived antibiotic obtained from Streptomyces niveus. Novobiocin: An antibiotic compound derived from Streptomyces niveus. It has a chemical structure similar to coumarin. Novobiocin binds to DNA gyrase, and blocks adenosine triphosphatase (ATPase) activity. (From Reynolds, Martindale The Extra Pharmacopoeia, 30th ed, p189) | carbamate ester; ether; hexoside; hydroxycoumarin; monocarboxylic acid amide; monosaccharide derivative; phenols | antibacterial agent; antimicrobial agent; EC 5.99.1.3 [DNA topoisomerase (ATP-hydrolysing)] inhibitor; Escherichia coli metabolite; hepatoprotective agent |
| clorobiocin | clorobiocin: chlorine-containing antibiotic related to novobiocin |