Sandbox Reserved 1581

From Proteopedia

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Revision as of 17:33, 20 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.
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More help: Help:Editing. For an example of a student Proteopedia page, please see Photosystem II, Tetanospasmin, or Guanine riboswitch.

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You may include any references to papers as in: the use of JSmol in Proteopedia ^[1] or to the article describing Jmol ^[2] to the rescue.

1 Function
2 Disease
3 Relevance
4 Structural highlights

Function

Riboswitches regulate the synthesis of proteins and are controlled by thiamine pyrophosphate.^[3]

They are usually found within non-coding portions of messenger RNAs.^[3]

Thiamine pyrophosphate is also known as TPP. TPP is essential in all three domains of life, including: bacteria, fungi, and plants. ^[3] They use this specific riboswitch to control genes that are in charge of synthesizing thiamine and any phosphorylated derivatives.^[3] TPP and its riboswitch work together to directly regulate the synthesis of a protein related to TPP. ^[3] Thiamine pyrophosphate is the most widely distributed riboswitch of the metabolite-sensing RNA regulatory system. ^[3] The reason for this is because TPP is a form of vitamin B1, and vitamin B1 takes an essential part in many protein-catalyzed reactions; thus it is used quite often.

Magnesium Link

PAPER CITATION: ^[4]

TPP Link

Disease

Relevance

Structural highlights

TPP riboswitches were one of the first of several classes found to form successful interactions with negatively charged phosphate groups.^[3] TPP's pyrophosphate group is bound by a pair of Mg2+ ions, . ^[5] TPP's terminal phosphate group is coordinately bonded to both , but the thiazole-linked phosphate is only coordinately bonded to Mg2.^[6] Holding Mg1 in place are and they can be found within the region that previously was known for pyrophosphate recognition.^[3] Structures of proteins bound to TPP typically position Mg2+, Ca2+, or Mn2+ ions using charged amino acids, in a site equivalent .^[3] However, the TPP riboswitch is the only riboswitch that contains Mg1

This is a sample scene created with SAT to by Group, and another to make of the protein. You can make your own scenes on SAT starting from scratch or loading and editing one of these sample scenes.

References

↑ 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
↑ 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
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 ^3.7 ^3.8 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
↑ 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
↑ 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
↑ 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

Retrieved from "http://52.214.119.220/wiki/index.php/Sandbox_Reserved_1581"

@@ Line 9: / Line 9: @@
 They are usually found within non-coding portions of messenger RNAs.<ref name="ghost" />
-Thiamine pyrophosphate is also known as TPP. TPP is essential in all three domains of life, including: bacteria, fungi, and plants. <ref>PMID:16728979</ref>
+Thiamine pyrophosphate is also known as TPP. TPP is essential in all three domains of life, including: bacteria, fungi, and plants. <ref name="ghost" />
-They use this specific riboswitch to control genes that are in charge of synthesizing thiamine and any phosphorylated derivatives.<ref>PMID:16728979</ref>
+They use this specific riboswitch to control genes that are in charge of synthesizing thiamine and any phosphorylated derivatives.<ref name="ghost" />
-TPP and its riboswitch work together to directly regulate the synthesis of a protein related to TPP. <ref>PMID:16728979</ref>
+TPP and its riboswitch work together to directly regulate the synthesis of a protein related to TPP. <ref name="ghost" />
-Thiamine pyrophosphate is the most widely distributed riboswitch of the metabolite-sensing RNA regulatory system. <ref>PMID:16728979</ref>
+Thiamine pyrophosphate is the most widely distributed riboswitch of the metabolite-sensing RNA regulatory system. <ref name="ghost" />
 The reason for this is because TPP is a form of vitamin B1, and vitamin B1 takes an essential part in many protein-catalyzed reactions; thus it is used quite often.
@@ Line 28: / Line 28: @@
 == Structural highlights ==
-TPP riboswitches were one of the first of several classes found to form successful interactions with negatively charged phosphate groups.<ref>PMID:16728979</ref>
+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>PMID:16728979</ref> 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>PMID:16728979</ref>
-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>PMID:16728979</ref> Structures of proteins bound to TPP typically position Mg2+, Ca2+, or Mn2+ ions using charged amino acids, in a site equivalent .<ref>PMID:16728979</ref> However, the TPP riboswitch is the only riboswitch that contains Mg1
+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 Mg1

Sandbox Reserved 1581

From Proteopedia

Revision as of 17:33, 20 November 2019

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