Proteopedia - User contributions [en]

Guanine riboswitch

2011-05-04T15:54:02Z

Clarence Barnes:

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-untranslated region (5'-UTR) of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
Within the bacterium, ''Bacillus subtilus'', the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/2'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>

== References ==

<references/>

Guanine riboswitch

2011-05-04T15:53:25Z

Clarence Barnes: New page: ==This is a placeholder== This is a placeholder text to help you get started in placing a Jmol applet on your page. At any time, click "Show Preview" at the bottom of this page to see how...

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{{STRUCTURE_3cin | PDB=3cin | SCENE= }}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-untranslated region (5'-UTR) of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
Within the bacterium, ''Bacillus subtilus'', the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/2'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>

== References ==

<references/>

Sandbox Reserved 402

2011-05-02T14:53:33Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-untranslated region (5'-UTR) of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
Within the bacterium, ''Bacillus subtilus'', the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/2'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>

== References ==

<references/>

Sandbox Reserved 402

2011-04-28T16:57:49Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
Within the bacterium, Bacillus subtilus, the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/2'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>

== References ==

<references/>

Sandbox Reserved 402

2011-04-24T23:28:05Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport. In bacteria, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research.
Within the bacterium, Bacillus subtilus, the guanine riboswitch is found. The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>

== References ==

<references/>

Sandbox Reserved 402

2011-04-24T23:18:35Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria which can act in the absence of protein cofactors. Riboswitches have been found to be broadly distributed among all forms of life, but all most frequently found in bacteria. In the bacterium, Bacilus subtilus, riboswitches account for the regulation of 2% of the genes, thus making them attractive for genetic research. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.
The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a guanine, hypoxanthine, or xanthine to the aptamer domain. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription. Thus, the guanine riboswitch has two distinct conformations in which it operates: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. Due to the mechanism and function of riboswitches, they are an attractive target for drug development. <ref>PMID: 15610857 </ref>

Sandbox Reserved 402

2011-04-24T17:09:58Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

[[Image:Mechanism_of_action_of_guanine riboswitch.jpg|thumb|350px|left|Mechanism of Action for Guanine Riboswitch.<ref> Mechanism of Action of Tetanospasmin (Catherine Wakeman) [image on the internet]. 2005[updated 2005 August 30; cited 2011 Apr 24]. Available from: http://en.wikipedia.org/wiki/File:Mechanism_of_action_of_tetanospasmin.gif</ref>]]

Sandbox Reserved 402

2011-04-24T17:02:46Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

[[Image:Mechanism_of_action_of_tetanospasmin.jpg|thumb|350px|left|Mechanism of Action for Tetanospasmin.<ref> Mechanism of Action of Tetanospasmin (Dr. Arnab K Rana) [image on the internet]. 2005[updated 2005 Dec 26; cited 2011 Apr 20]. Available from: http://en.wikipedia.org/wiki/File:Mechanism_of_action_of_tetanospasmin.gif</ref>]]

Sandbox Reserved 402

2011-04-24T16:53:40Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

[[Image:guanine mechanism.jpg]]

Sandbox Reserved 402

2011-04-24T03:00:38Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine-Riboswitch-Guanine complex' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down regulate the expression of genes by forming transcription terminator structures. <ref>PMID: 15610857 </ref>

Sandbox Reserved 402

2011-04-24T02:24:51Z

Clarence Barnes:

{{Template:Sandbox_Reserved_JMeans}}

<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine Riboswitch' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer (binding site) domain that results in allosteric rearrangement in the adjacent expression platform that interacts with RNA elements to regulate gene expression associated with biosythesis and transport.The <scene name='Sandbox_Reserved_402/Initial_structure_with_bases/2'>guanine riboswitch</scene> operates by the binding of a metabolite to the aptamer domain which is highly conserved. Through allosteric effects the aptamer then changes the conformation of the expression platform which results in the premature termination of transcription, inhibition of translation initiation, or mRNA self-cleavage. Thus, riboswitches have two distinct conformations in which they operate: a metabolite bound and metabolite-free folds, involving the alternative base-pairing of the regulatory RNA region.<ref>PMID: 15610857 </ref>

== Riboswitch Structure ==
The guanine riboswitch is comprised of three helices which are labeled P1, P2, and P3 which connect to form a junction. It is within this junction that ligand binding occurs. When the g-riboswitch-guanine complex is formed the kissing interactions of two hairpin loops force P2 and P3 to align in a parallel fashion and form hydrogen bonds. The <scene name='Sandbox_Reserved_402/Binding_site/1'>ligand</scene> is bound to the junction within the guanine riboswitch via several hydrogen bonds to nucleotides U22, U47, U51, C74. Due to the compactness of the binding site the ligand must utilize the induced-fit binding mechanism. <ref>PMID: 17175531 </ref>

== Regulation Mechanism ==

Metabolite-binding riboswitches are triggered if a high concentration of the metabolite is present within the cell. Under these conditions, the metabolite will interact with the aptamer domain, with high affinity and selectivity, which will then stabilize the metabolite bound fold in the nascent RNA, and in so doing prevents the formation of the metabolite-free fold. This typically results in the stabilization or disruption of a regulatory hairpin, which prematurely terminates transcription or sequesters the ribosome-binding site, thereby regulating gene expression. In the absence of the metabolite when the 5’-UTR is transcribed the riboswitch folds into the metabolite-free fold which does not interfere with the expression of the adjacent open reading frame.
In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine with high precision to down-regulate the expression of genes by forming transcription terminator structures.

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<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine Riboswitch' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer domain that results in allosteric rearrangement in the adjacent expression platform to regulate gene expression associated with biosythesis and transport. In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine (1) with high precision to down-regulate the expression of genes by forming transcription terminator structures.

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{{Template:Sandbox_Reserved_JMeans}}
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<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine Riboswitch' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer domain that results in allosteric rearrangement in the adjacent expression platform to regulate gene expression associated with biosythesis and transport. In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine (1) with high precision to down-regulate the expression of genes by forming transcription terminator structures.

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<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine Riboswitch' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Riboswitches are highly conserved metabolite binding domains that are present in the 5'-UTR of certain mRNAs in bacteria. These structural elements bind specific metabolites in the aptamer domain that results in allosteric rearrangement in the adjacent expression platform to regulate gene expression associated with biosythesis and transport. In Bacillus subtilis, the 5'-UTR of xpt-pbuX mRNA binds guanine (1) with high precision to down-regulate the expression of genes by forming transcription terminator structures.
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[[Image:Function_of_riboswitch.png]]

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Clarence Barnes: /* Guanine Riboswitch */

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<Structure load='1Y27' size='400' frame='true' align='right' caption='Hexokinase' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Hexokinase is the first enzyme that changes Glucose during the energy investment stage of glycolysis. This enzyme functions to phosphorylate glucose,and in doing so reduce ATP into ADP.
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<Structure load='1BDG' size='400' frame='true' align='right' caption='Hexokinase' scene='Insert optional scene name here' />
'''
== Guanine Riboswitch ==
'''
Hexokinase is the first enzyme that changes Glucose during the energy investment stage of glycolysis. This enzyme functions to phosphorylate glucose,and in doing so reduce ATP into ADP.
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<Structure load='1BDG' size='400' frame='true' align='right' caption='Hexokinase' scene='Insert optional scene name here' />
'''
== Hexokinase ==
'''
Hexokinase is the first enzyme that changes Glucose during the energy investment stage of glycolysis. This enzyme functions to phosphorylate glucose,and in doing so reduce ATP into ADP.
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<Structure load='1Y27' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
==Guanine Riboswitch (maybe something like 'Structure')==<StructureSection load='1dq8' size='500' side='right' caption='Structure of HMG-CoA reductase (PDB entry [[1dq8]])' scene=''>Anything in this section will appear adjacent to the 3D structure and will be scrollable.</StructureSection>

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<Structure load='1Y27' size='400' frame='true' align='right' caption='Guanine Riboswitch' scene='Insert optional scene name here' />
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== Guanine Riboswitch ==

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<Structure load='1Y27' size='500' frame='true' align='right' caption='Insert caption here' scene='Insert optional scene name here' />
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== Guanine Riboswitch ==

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<Structure load='1a6m' size='500' frame='true' align='right' caption='My molecule' scene='Insert optional scene name here' />
[[My molecule

== My molecule ==

This is a really cool molecule that is very important for cell function.
'''Cool enzyme'''
<scene name='Sandbox_Reserved_402/My_molecule/1'>First molecule</scene>
<scene name='Sandbox_Reserved_402/My_molecule/2'>My molecule</scene>

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[[My molecule

== My molecule ==

This is a really cool molecule that is very important for cell function.
'''Cool enzyme'''
<scene name='Sandbox_Reserved_402/My_molecule/1'>TextToBeDisplayed</scene>
<scene name='Sandbox_Reserved_402/My_molecule/2'>My molecule</scene>

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<Structure load='1a6m' size='500' frame='true' align='right' caption='My molecule' scene='Insert optional scene name here' />
[[My molecule

== My molecule ==

This is a really cool molecule that is very important for cell function.

<scene name='Sandbox_Reserved_402/My_molecule/1'>TextToBeDisplayed</scene>

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