Sandbox Reserved 1576
From Proteopedia
| (2 intermediate revisions not shown.) | |||
| Line 4: | Line 4: | ||
==Overview== | ==Overview== | ||
| - | Riboswitches are metabolite-sensing-mRNAs that interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, which create ligand-induced structural changes, that allow for controlling gene expression. They form tuning-fork structures, where the prongs go through hairpin loop interactions, and the internal bubble zips up to form an adenine binding pocket. The bound purines are held by hydrogen bonds. The encapsulated adenine is paired to cytosine through Watson-Crick base pairing. <ref name="ref1">PMID:15610857</ref> | + | Riboswitches are metabolite-sensing-mRNAs that interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, which create ligand-induced structural changes, that allow for controlling gene expression. They form tuning-fork structures, where the prongs go through hairpin loop interactions, and the internal bubble zips up to form an adenine binding pocket. The bound purines are held by hydrogen bonds. The encapsulated adenine is paired to cytosine through Watson-Crick base pairing.<ref name="ref1">PMID:15610857</ref> |
<StructureSection load='1y26' size='340' side='right' caption='A-riboswitch-adenenine complex 3D model' scene=''> | <StructureSection load='1y26' size='340' side='right' caption='A-riboswitch-adenenine complex 3D model' scene=''> | ||
| Line 13: | Line 13: | ||
The adenine bound A-riboswitch complex uses a tuning fork-like | The adenine bound A-riboswitch complex uses a tuning fork-like | ||
| - | compact fold, where a stem forms the handle of the tuning fork and the prongs are aligned parallel to each other. The central internal bubble zippers up through stacked base triple alignments between the three junction-connecting segments and two junctional base pairs, creating an adenine-sensing pocket within the RNA scaffold. <ref name="ref1" /> | + | compact fold, where a stem forms the handle of the tuning fork and the prongs are aligned parallel to each other. The central internal bubble zippers up through stacked base triple alignments between the three junction-connecting segments and two junctional base pairs, creating an adenine-sensing pocket within the RNA scaffold.<ref name="ref1" /> |
| - | The structure includes five <scene name='82/824621/Mg/1'>Mg cations</scene> (colored pink) and a bound <scene name='82/824621/Adenine/2'>adenine</scene> (colored yellow). Four of the Mg cations are located inside of the grooves and involved in the junction-connecting segments in the fold. The remaining Mg cation is on the surface and is involved in packing interactions. The four Mg cations on the inside of the complex are surrounding the bound adenine. <ref name="ref1" /> | + | The structure includes five <scene name='82/824621/Mg/1'>Mg cations</scene> (colored pink) and a bound <scene name='82/824621/Adenine/2'>adenine</scene> (colored yellow). Four of the Mg cations are located inside of the major and minor grooves and are involved in the junction-connecting segments in the fold. The remaining Mg cation is on the surface and is involved in packing interactions. The four Mg cations on the inside of the complex are surrounding the bound adenine.<ref name="ref1" /> |
</StructureSection> | </StructureSection> | ||
| Line 21: | Line 21: | ||
== Function == | == Function == | ||
| - | Riboswitches are used as a form of genetic control in some bacteria, where they modulate the expression of transport and metabolic proteins. The adenine and guanine riboswitches form nearly identical binding pockets since they are both purines. The single nucleotide in the core forms a Watson-Crick base pair with its ligand. The structure of the adenine riboswitch bound to its ligand creates RNA's ability to use A-minor motifs and base tetrads, which causes the folding required to create the binding pockets. This provides the infrastructure for targeting and discrimination between similar metabolites. <ref name="ref1" /> | + | Riboswitches are used as a form of genetic control in some bacteria, where they modulate the expression of transport and metabolic proteins. The adenine and guanine riboswitches form nearly identical binding pockets since they are both purines. The single nucleotide in the core forms a Watson-Crick base pair with its ligand. The structure of the adenine riboswitch bound to its ligand creates RNA's ability to use A-minor motifs and base tetrads, which causes the folding required to create the binding pockets. This provides the infrastructure for targeting and discrimination between similar metabolites. The adenine riboswitch is found in <I> B. subtilis, C. perfringens, </I> and <I> V. vulnificus. </I>These bacteria contain the <I>ydhL</I> gene, which allows the bacteria to sense adenine. It can also differentiate against guanine and purines.<ref name="ref1" /> |
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). |
To get started:
More help: Help:Editing. For an example of a student Proteopedia page, please see Photosystem II, Tetanospasmin, or Guanine riboswitch. |
Contents |
Adenine Riboswitch
Overview
Riboswitches are metabolite-sensing-mRNAs that interact with small ligands and direct expression of the genes involved in their metabolism. Riboswitches contain sensing "aptamer" modules, which create ligand-induced structural changes, that allow for controlling gene expression. They form tuning-fork structures, where the prongs go through hairpin loop interactions, and the internal bubble zips up to form an adenine binding pocket. The bound purines are held by hydrogen bonds. The encapsulated adenine is paired to cytosine through Watson-Crick base pairing.[1]
| |||||||||||
Function
Riboswitches are used as a form of genetic control in some bacteria, where they modulate the expression of transport and metabolic proteins. The adenine and guanine riboswitches form nearly identical binding pockets since they are both purines. The single nucleotide in the core forms a Watson-Crick base pair with its ligand. The structure of the adenine riboswitch bound to its ligand creates RNA's ability to use A-minor motifs and base tetrads, which causes the folding required to create the binding pockets. This provides the infrastructure for targeting and discrimination between similar metabolites. The adenine riboswitch is found in B. subtilis, C. perfringens, and V. vulnificus. These bacteria contain the ydhL gene, which allows the bacteria to sense adenine. It can also differentiate against guanine and purines.[1]
References
- ↑ 1.0 1.1 1.2 1.3 Serganov A, Yuan YR, Pikovskaya O, Polonskaia A, Malinina L, Phan AT, Hobartner C, Micura R, Breaker RR, Patel DJ. Structural basis for discriminative regulation of gene expression by adenine- and guanine-sensing mRNAs. Chem Biol. 2004 Dec;11(12):1729-41. PMID:15610857 doi:S1074-5521(04)00343-6
