Sandbox Reserved 1578

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== Structural highlights ==
== Structural highlights ==
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<scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> <scene name='82/824623/Nitrogenous_base_interactions/3'>Nigrogenous Base Interaction</scene>
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The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions.
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The SAM ligand is bound within a pocket created by the <scene name='82/824623/Helix_interaction/2'>Helix Interaction</scene> (in color). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.
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The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position <scene name='82/824623/Nitrogenous_base_interactions/3'>Nucleotide Interaction</scene>(color).
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Revision as of 18:45, 29 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).
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Contents

SAM Riboswith (2GIS)

SAM Riboswitch

Drag the structure with the mouse to rotate

S-adenosylmethionine (SMA) is a riboswitch, which are structured noncoding RNA domains that selectively bind metabolites and control gene expression. Nearly all examples of the known riboswitches reside in noncoding regions of messenger RNAs where they control transcription or translation.[1]


Structural highlights

The key architecture of SAM riboswitch is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions.

The SAM ligand is bound within a pocket created by the (in color). The SAM ligand adopts a compact conformation in which the methionine stacks upon the adenine ring, stabilized in part by the π-cation interaction with the amino group pointing toward the adenine ring. Also the compact configuration of SAM creates a hydrogen bonding interaction to helix P3 and van der Waals forces interacting with the minor groove of the P1 helix.

The adenine ring of SAM is the central position between five nucleotides. The nucleotides interact by hydrogen bond attractions between themselves and the SAM ligand to stabilize position (color).


Function

Stable binding of SAM when adequate amounts are present results in it acting as a transcriptional terminator which turns off gene expression. To understand the function and specificity of SAM as a riboregulator it is important to first understand the key structures of SAM. The key architecture of SAM is composed of ligand-induced interactions between one helix and the 3' side of another helix surrounding the SAM ligand as well as hydrogen bonding interactions between the adenosine base of SAM and interactions between the main chain atoms of methionine with nucleotide interactions.

The adenine base of SAM, A45 and U57, creates a hydrogen bonding interaction to

References

  1. ↑ Montange RK, Batey RT. Structure of the S-adenosylmethionine riboswitch regulatory mRNA element. Nature. 2006 Jun 29;441(7097):1172-5. PMID:16810258 doi:10.1038/nature04819
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