Sandbox Reserved 1581

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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" />
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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.
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.

Revision as of 15:03, 26 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.

Your Heading Here (maybe something like 'Structure')

TPP Riboswitch

Drag the structure with the mouse to rotate

References

  1. ↑ 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
  2. ↑ 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
  3. ↑ 3.00 3.01 3.02 3.03 3.04 3.05 3.06 3.07 3.08 3.09 3.10 3.11 3.12 3.13 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
  4. ↑ 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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