Sandbox Reserved 1581

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== Function ==
== Function ==
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The function of this particular riboswitch does not depend on the transcription process. <ref name= "woah"> PMID:21622748 </ref> The riboswitch predominantly folds into the on state, whether TPP is present or not. <ref name= "woah"> PMID:21622748 </ref> Meanwhile, the off state aptamer structure does not appear during transcription. <ref name= "woah"> PMID:21622748 </ref>
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The function of this particular riboswitch does not depend on the transcription process. <ref name= "woah"> PMID:21622748 </ref> The riboswitch predominantly folds into the on state, whether TPP is present or not. <ref name= "woah"> PMID:21622748 </ref> Meanwhile, the off state aptamer structure does not appear during transcription. <ref name= "woah"> PMID:21622748 </ref> However, the transition from the on state to the aptamer structure is extremely slow and because of this, thiamine pyrophosphate has the chance to interact with the RNA before full formation of the aptamer structure, prompting the switch to flip. <ref name= "woah"> PMID:21622748 </ref>
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The expression of Neurospora crassa NMT1 involved in thiamine pyrophosphate (TPP) metabolism is regulated at the level of mRNA splicing by a TPP-sensing riboswitch within the precursor NMT1 mRNA. Here, using the systematic helix-based computational method, we investigated the regulation of this riboswitch. We find that the function of the riboswitch does not depend on the transcription process. Whether TPP is present or not, the riboswitch predominately folds into the ON state, while the OFF state aptamer structure does not appear during transcription. Since the transition from the ON state to the aptamer structure is extremely slow, TPP may interact with the RNA before full formation of the aptamer structure, promoting the switch flipping. The potential to fully form helix P0 of the ON state is necessary to restore ligand-dependent gene control by the riboswitch.
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TPP riboswitches were one of the first of several classes found to form successful interactions with negatively charged phosphate groups.<ref name="ghost" />
TPP riboswitches were one of the first of several classes found to form successful interactions with negatively charged phosphate groups.<ref name="ghost" />
TPP's pyrophosphate group is bound by a pair of Mg2+ ions, <scene name='82/824626/Tpp/1'>Mg1 and Mg2</scene> . <ref name="ghost" /> TPP's terminal phosphate group is coordinately bonded to both <scene name='82/824626/Tpp/1'>Mg1 and Mg2</scene>, but the thiazole-linked phosphate is only coordinately bonded to Mg2.<ref name="ghost" />
TPP's pyrophosphate group is bound by a pair of Mg2+ ions, <scene name='82/824626/Tpp/1'>Mg1 and Mg2</scene> . <ref name="ghost" /> TPP's terminal phosphate group is coordinately bonded to both <scene name='82/824626/Tpp/1'>Mg1 and Mg2</scene>, but the thiazole-linked phosphate is only coordinately bonded to Mg2.<ref name="ghost" />
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Holding Mg1 in place are <scene name='82/824626/Ahhh/2'>G60 and G78</scene> and they can be found within the region that previously was known for pyrophosphate recognition.<ref name="ghost" /> Structures of proteins bound to TPP typically position Mg2+, Ca2+, or Mn2+ ions using charged amino acids, in a site equivalent.<ref name="ghost" /> However, the TPP riboswitch is the only riboswitch that contains the Mg1 ion.<ref name="ghost" /> A bivalent cation allows TPP to reach into the pyrophosphate-binding pocket.<ref name="ghost" /> This in turn stabilizes the important tertiary interactions that are required for gene regulation, and supporting the use of Mg2+ for TPP binding in both bacterial and eukaryotic TPP riboswitches.<ref name="ghost" />
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Holding Mg1 in place are <scene name='82/824626/Ahhh/2'>G60 and G78</scene> and they can be found within the region that previously was known for pyrophosphate recognition.<ref name="ghost" /> Structures of proteins bound to TPP typically position Mg2+, Ca2+, or Mn2+ ions using charged amino acids, in a site equivalent.<ref name="ghost" /> However, the TPP riboswitch is the only riboswitch that contains the Mg1 ion.<ref name="ghost" /> A bivalent cation allows TPP to reach into the pyrophosphate-binding pocket.<ref name="ghost" /> This in turn stabilizes the important tertiary interactions that are required for gene regulation, and supporting the use of Mg2+ for TPP binding in both bacterial and eukaryotic TPP riboswitches.<ref name="ghost" />
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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.
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</StructureSection>
</StructureSection>
== References ==
== References ==
<references/>
<references/>

Revision as of 17:08, 27 November 2019

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).
To get started:
  • Click the edit this page tab at the top. Save the page after each step, then edit it again.
  • Click the 3D button (when editing, above the wikitext box) to insert Jmol.
  • show the Scene authoring tools, create a molecular scene, and save it. Copy the green link into the page.
  • Add a description of your scene. Use the buttons above the wikitext box for bold, italics, links, headlines, etc.

More help: Help:Editing. For an example of a student Proteopedia page, please see Photosystem II, Tetanospasmin, or Guanine riboswitch.

Thiamine Pyrophosphate Riboswitch

TPP Riboswitch

Drag the structure with the mouse to rotate

References

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature. 2006 Jun 29;441(7097):1167-71. Epub 2006 May 21. PMID:16728979 doi:http://dx.doi.org/nature04740
  2. ↑ 2.0 2.1 2.2 2.3 Bian J, Shen H, Tu Y, Yu A, Li C. The riboswitch regulates a thiamine pyrophosphate ABC transporter of the oral spirochete Treponema denticola. J Bacteriol. 2011 Aug;193(15):3912-22. doi: 10.1128/JB.00386-11. Epub 2011 May, 27. PMID:21622748 doi:http://dx.doi.org/10.1128/JB.00386-11
  3. ↑ Serganov A, Polonskaia A, Phan AT, Breaker RR, Patel DJ. Structural basis for gene regulation by a thiamine pyrophosphate-sensing riboswitch. Nature. 2006 Jun 29;441(7097):1167-71. Epub 2006 May 21. PMID:16728979 doi:http://dx.doi.org/nature04740
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