Sandbox reserved 1225
From Proteopedia
(Difference between revisions)
| Line 1: | Line 1: | ||
| - | == '''DNA Gyrase'' == | + | == '''DNA Gyrase''' == |
| Line 8: | Line 8: | ||
== '''Function''' == | == '''Function''' == | ||
| - | DNA Gyrase is a protein located mainly in Prokaryotes, specifically bacteria. It falls under the Topoisomerase family and can be referred to as Topoisomerase II. | + | DNA Gyrase is a protein located mainly in Prokaryotes, specifically bacteria. It falls under the Topoisomerase family and can be referred to as Topoisomerase II. This family is commonly responsible for the protein-protein interactions. DNA Gyrase is responsible for negatively induced supercoiling. This method of supercoiling is used to reduce the strain caused by the twists in DNA. It aids in compaction, as well as separation of DNA. As one can see, it plays a significant role in prokaryotes. |
| + | |||
| + | DNA gyrase is a molecular protein responsible in producing negative supercoils to reduce the tension and stress produced from the unwinding activity of helicase. DNA Gyrase uses free ATP produced from hydrolysis to effectively reduce the tension in the DNA. It does so by initiating negative supercoiling in the DNA. This negative supercoiling is the opposite of how DNA winds its self. | ||
| + | |||
<scene name='75/752515/Gyrase1/1'>TextToBeDisplayed</scene> | <scene name='75/752515/Gyrase1/1'>TextToBeDisplayed</scene> | ||
| Line 16: | Line 19: | ||
Researches specifically study this protein for multiple reasons. It could possibly help with antibacterial chemotherapy. | Researches specifically study this protein for multiple reasons. It could possibly help with antibacterial chemotherapy. | ||
| - | + | ||
== '''Structural highlights''' == | == '''Structural highlights''' == | ||
| - | The structure of DNA Gyrase consists of mainly two subunits. This First known as A contains the tyrosine which is responsible for cleavage. The second subunit B is responsible to the binding of ATPase’s active site. Both subunits work together to produce the negative supercoiling produced in DNA strands. | + | The overall structure of DNA gyrase contains more that 100 base pairs. DNA Gyrase consists of mainly two subunits. This First known as A contains the tyrosine which is responsible for cleavage. The second subunit B is responsible to the binding of ATPase’s active site. Both subunits work together to produce the negative supercoiling produced in DNA strands. The two subunits are often recognized as an A2B2 tetramer. The part of the DNA intended to be cleaved is called the G-segment. DNA gyrase also consists of WHD and TOPRIM, Winged Helix Domain, and Topoisomerase-Primase respectively. The enzyme however is still being researched because of the lack of high resolution gyrase bind to DNA. |
| + | |||
| + | |||
| + | == '''Mechanism'' == | ||
| + | |||
| + | DNA Gyrase works by introducing conformational changes to itself as well as the protein complex. The Gyrase enzyme begins by interacting with the DNA. This causes the formation of the three gates that can be opened and closed. The G-segment, introduced under the “structure” section, forms a bond and binds to the first of the 3 gates, the central DNA gate. This binding of the gate produces chiral wrapping which in then produces a T-segment with in the last of the 3 gates, the N gate. After which, the N-gate binds with ATP which then causes the gate to close. Once this process is completed, the G-segment is released from the last of the 3 gates, the C-gate. This process causes a net result of 2 negative supercoils and a linkage difference of 2 from the initial linkage. | ||
| - | This is a sample scene created with SAT to <scene name="/12/3456/Sample/1">color</scene> by Group, and another to make <scene name="/12/3456/Sample/2">a transparent representation</scene> of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes. | ||
</StructureSection> | </StructureSection> | ||
Revision as of 00:45, 5 May 2017
DNA Gyrase
| |||||||||||
== References == Schoeffler, A. J., May, A. P., & Berger, J. M. (2010). A domain insertion in Escherichia coli GyrB adopts a novel fold that plays a critical role in gyrase function. Nucleic Acids Research, 38(21), 7830-7844. doi:10.1093/nar/gkq665
Rahimi, H., Najafi, A., Eslami, H., Negahdari, B., & Moghaddam, M. M. (2016). Identification of novel bacterial DNA gyrase inhibitors: An in silico study. Journal Of Research In Pharmaceutical Sciences, 11(3), 250-258.
Travers, A., & Muskhelishvili, G. (2015). DNA structure and function. FEBS Journal, 282(12), 2279-2295. doi:10.1111/febs.13307
- ↑ Hanson, R. M., Prilusky, J., Renjian, Z., Nakane, T. and Sussman, J. L. (2013), JSmol and the Next-Generation Web-Based Representation of 3D Molecular Structure as Applied to Proteopedia. Isr. J. Chem., 53:207-216. doi:http://dx.doi.org/10.1002/ijch.201300024
- ↑ Herraez A. Biomolecules in the computer: Jmol to the rescue. Biochem Mol Biol Educ. 2006 Jul;34(4):255-61. doi: 10.1002/bmb.2006.494034042644. PMID:21638687 doi:10.1002/bmb.2006.494034042644
