Sandbox Reserved 1587
From Proteopedia
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== Overview == | == Overview == | ||
| - | The <scene name='82/824632/Twister_ribozyme/ | + | The <scene name='82/824632/Twister_ribozyme/8'>twister ribozyme</scene> is a catalytic RNA that is capable of self cleaving. There are two groups that ribozymes may fall into based on function: splicing ribozymes and cleaving ribozymes; the latter may be further broken down into trans-cleaving nucleases and small self-cleaving ribozymes or nucleolytic ribozymes.<ref name="structure"> PMID:27863022</ref> Twister ribozyme is a member of the nucleolytic ribozymes along with 8 other classes which include hairpin, hammerhead, hatchet, hepatitis delta virus (HDV), glucosamine-6-phosphate synthase, neurospora, pistol, and twister sister. <ref name="structure"/> |
== History == | == History == | ||
| - | Twister ribozyme was discovered in 2013 through the use of bioinformatics. They found that the twister motif occurred in many eukaryotic and bacterial species and that it likely had various biological roles.<ref name="bioinformatics"> PMID:24240507</ref> It was believed that twister RNA represented an unknown class of self-cleaving ribozymes due to the observation that twister and hammerhead ribozymes shared similar genetic contents.<ref name="bioinformatics"/> This hypothesis was tested through multiple experiments proving it to be self-cleaving. The catalytic RNA was given the name twister as the people who discovered it found it to resemble the Egyptian hieroglyph "twisted flax". | + | Twister ribozyme was discovered in 2013 through the use of bioinformatics. They found that the twister motif occurred in many eukaryotic and bacterial species and that it likely had various biological roles.<ref name="bioinformatics"> PMID:24240507</ref> It was believed that twister RNA represented an unknown class of self-cleaving ribozymes due to the observation that twister and hammerhead ribozymes shared similar genetic contents.<ref name="bioinformatics"/> This hypothesis was tested through multiple experiments proving it to be self-cleaving. The <scene name='82/824632/Twister_ribozyme_structure/6'>catalytic RNA</scene> was given the name twister as the people who discovered it found it to resemble the Egyptian hieroglyph "twisted flax". |
== Function == | == Function == | ||
| - | The twister ribozyme displays nucleolytic ribozyme activity both in vitro and in vivo and has one of the fastest catalytic rates of naturally occurring ribozymes with similar function.<ref name="article"> PMID:25038788</ref><ref name="ribozyme"> PMID:25157168</ref> The twister ribozyme appears to follow a SN2 mechanism for phosphodiester cleavage producing a 2',3'-cyclic phosphate and 5' hydroxyl product.<ref name="article"/> Twister ribozyme produces catalytic activity by orienting the P O bond that is to be cleaved for nucleophilic attack in the active site.<ref name="structure"/> The ribozyme follows general acid-base catalysis which has been supported through experimental and modeling evidence.<ref name="article"/> The reaction rate is dependent on temperature and pH as well as Mg2+ ions but they are not essential to the overall reaction.<ref name="article"/> | + | The twister ribozyme displays nucleolytic ribozyme activity both in vitro and in vivo and has one of the fastest catalytic rates of naturally occurring ribozymes with similar function.<ref name="article"> PMID:25038788</ref><ref name="ribozyme"> PMID:25157168</ref> The twister ribozyme appears to follow a SN2 mechanism for phosphodiester cleavage producing a 2',3'-cyclic phosphate and 5' hydroxyl product.<ref name="article"/> Twister ribozyme produces catalytic activity by orienting the P O bond that is to be cleaved for nucleophilic attack in the active site.<ref name="structure"/> The ribozyme follows general acid-base catalysis which has been supported through experimental and modeling evidence.<ref name="article"/> The reaction rate is dependent on temperature and pH as well as Mg2+ ions but they are not essential to the overall reaction.<ref name="article"/> |
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== Structural highlights == | == Structural highlights == | ||
| - | The structure of twister ribozyme has a highly conserved secondary structure that includes a double pseudo knot with a core comprising of a stem loop interrupted by two internal loops.<ref name="article"/> The cleavage site for the ribozyme is located within loop 1 and the <scene name='82/824632/Twister_ribozyme_active_site/ | + | The structure of twister ribozyme has a highly conserved secondary structure that includes a double pseudo knot with a core comprising of a stem loop interrupted by two internal loops.<ref name="article"/> The cleavage site for the ribozyme is located within loop 1 and the <scene name='82/824632/Twister_ribozyme_active_site/4'>active site</scene> can be found at the center of the molecule.<ref name="article"/> Active site formation of all nucleolytic ribozymes occurs through the interactions of secondary and tertiary structures.<ref name="structure"/> The double pseudo knot structure is formed by two long range tertiary interactions which are necessary for its catalytic function.<ref name="structure"/> The structure contains four magnesium ions within the ribozyme fold which are important to the stabilization of secondary structure; two have shells of water molecules and the other two have phosphate non-bridging oxygen atoms.<ref name="article"/> |
| - | 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> | ||
== References == | == References == | ||
<references/> | <references/> | ||
Current revision
| This Sandbox is Reserved from September 14, 2021, through May 31, 2022, for use in the class Introduction to Biochemistry taught by User:John Means at the University of Rio Grande, Rio Grande, OH, USA. This reservation includes 5 reserved sandboxes (Sandbox Reserved 1590 through Sandbox Reserved 1594). |
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More help: Help:Editing. For an example of a student Proteopedia page, please see Photosystem II, Tetanospasmin, or Guanine riboswitch. |
Twister Ribozyme
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References
- ↑ 1.0 1.1 1.2 1.3 1.4 Gebetsberger J, Micura R. Unwinding the twister ribozyme: from structure to mechanism. Wiley Interdiscip Rev RNA. 2017 May;8(3). doi: 10.1002/wrna.1402. Epub 2016 Nov, 14. PMID:27863022 doi:http://dx.doi.org/10.1002/wrna.1402
- ↑ 2.0 2.1 Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol. 2014 Jan;10(1):56-60. doi: 10.1038/nchembio.1386. Epub 2013 Nov, 17. PMID:24240507 doi:http://dx.doi.org/10.1038/nchembio.1386
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 Liu Y, Wilson TJ, McPhee SA, Lilley DM. Crystal structure and mechanistic investigation of the twister ribozyme. Nat Chem Biol. 2014 Sep;10(9):739-44. doi: 10.1038/nchembio.1587. Epub 2014 Jul, 20. PMID:25038788 doi:http://dx.doi.org/10.1038/nchembio.1587
- ↑ Eiler D, Wang J, Steitz TA. Structural basis for the fast self-cleavage reaction catalyzed by the twister ribozyme. Proc Natl Acad Sci U S A. 2014 Aug 25. pii: 201414571. PMID:25157168 doi:http://dx.doi.org/10.1073/pnas.1414571111
