Sandbox Reserved 387
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| - | <Structure load='3RJ1' size='400' frame='true' align=' | + | |
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| + | <Structure load='3RJ1' size='400' frame='true' align='right' caption='Mediator' scene='Insert optional scene name here' /> | ||
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== Mediator == | == Mediator == | ||
| - | ''' | + | The mediator, found in the yeast ''S. cerevisiae'', connects repressors and activators bound to regulatory DNA with RNA polymerase II (Pol II). As a result, the mediator is an important regulator of eukaryotic transcription.<ref>PMID: 21725323 </ref> Also, mediator is currently being studied because of its ability and role to regulate gene expression.<ref>PMID: 20299225 </ref> Mediator is in the form of three main modules, which are the tail, arm, and head. The <scene name='Sandbox_Reserved_387/Head_module/1'>head module</scene> of the mediator is split into three domains that go through significant conformational changes, and it interacts with the Rpb7 and Rpb4 subunits of Pol II and TATA binding protein subunit of transcription factor TFIID.<ref name="nature">PMID: 21725323 </ref> |
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| - | == 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> | ||
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| + | == Structure == | ||
| + | The <scene name='Sandbox_Reserved_387/Head_module/1'>head module</scene> of mediator from ''S.cerevisiae'' is made of seven subunits which are Med22(Srb6), Med20(Srb2), Med18(Srb5), Med17(Srb4), Med11, Med6, and Med8.<ref name="nature" /> Of these subunits, Med11, Med17(Srb4), and Med22(Srb6) make the mini-head of the head module. The subunits of the core-head plus the subunits of the mini-head are what make up full head structure. The structure shows the three domains: the neck, which is shown by pink helices, the fixed jaw, which is shown by mostly pink helices and a few yellow beta sheets, and the movable jaw, which is shown by mostly yellow beta sheets and a few pink helices. | ||
| - | == 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> | ||
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. |
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Mediator
The mediator, found in the yeast S. cerevisiae, connects repressors and activators bound to regulatory DNA with RNA polymerase II (Pol II). As a result, the mediator is an important regulator of eukaryotic transcription.[1] Also, mediator is currently being studied because of its ability and role to regulate gene expression.[2] Mediator is in the form of three main modules, which are the tail, arm, and head. The of the mediator is split into three domains that go through significant conformational changes, and it interacts with the Rpb7 and Rpb4 subunits of Pol II and TATA binding protein subunit of transcription factor TFIID.[3]
Structure
The of mediator from S.cerevisiae is made of seven subunits which are Med22(Srb6), Med20(Srb2), Med18(Srb5), Med17(Srb4), Med11, Med6, and Med8.[3] Of these subunits, Med11, Med17(Srb4), and Med22(Srb6) make the mini-head of the head module. The subunits of the core-head plus the subunits of the mini-head are what make up full head structure. The structure shows the three domains: the neck, which is shown by pink helices, the fixed jaw, which is shown by mostly pink helices and a few yellow beta sheets, and the movable jaw, which is shown by mostly yellow beta sheets and a few pink helices.
References
- ↑ Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y. Architecture of the Mediator head module. Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162. PMID:21725323 doi:10.1038/nature10162
- ↑ Taatjes DJ. The human Mediator complex: a versatile, genome-wide regulator of transcription. Trends Biochem Sci. 2010 Jun;35(6):315-22. Epub 2010 Mar 17. PMID:20299225 doi:10.1016/j.tibs.2010.02.004
- ↑ 3.0 3.1 Imasaki T, Calero G, Cai G, Tsai KL, Yamada K, Cardelli F, Erdjument-Bromage H, Tempst P, Berger I, Kornberg GL, Asturias FJ, Kornberg RD, Takagi Y. Architecture of the Mediator head module. Nature. 2011 Jul 3;475(7355):240-3. doi: 10.1038/nature10162. PMID:21725323 doi:10.1038/nature10162
