Riboswitch: Difference between revisions
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== Structural highlights == | == Structural highlights == | ||
Atomic-resolution structures of riboswitch binding sites show that they make numerous hydrogen bonds with their ligands, forming contacts that stabilize RNA interactions to further increase affinity. Some binding sites form pockets that entirely engulf the ligand, and in these instances an induced-fit mechanism of binding must occur. The <scene name='47/479252/Cv/4'>riboswitch-adenine complex shows the stacking interactions of the zippered-up junctional bubble which is formed by the adenine</scene><ref>PMID:15610857</ref>. Water molecules are shown as red spheres. | Atomic-resolution structures of riboswitch binding sites show that they make numerous hydrogen bonds with their ligands, forming contacts that stabilize RNA interactions to further increase affinity. Some binding sites form pockets that entirely engulf the ligand, and in these instances an induced-fit mechanism of binding must occur. The <scene name='47/479252/Cv/4'>riboswitch-adenine complex shows the stacking interactions of the zippered-up junctional bubble which is formed by the adenine</scene><ref>PMID:15610857</ref>. Water molecules are shown as red spheres. | ||
==3D structures of riboswitch== | |||
[[Riboswitch 3D structures]] | |||
</StructureSection> | </StructureSection> | ||
==3D structures of riboswitch== | ==3D structures of riboswitch== | ||
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**[[2xnw]] – BsGR + Mn<br /> | **[[2xnw]] – BsGR + Mn<br /> | ||
**[[4fe5]], [[4fej]], [[4fel]], [[4fen]], [[4feo]], [[4fep]] – GR + hypoxanthine – synthetic<br /> | **[[4fe5]], [[4fej]], [[4fel]], [[4fen]], [[4feo]], [[4fep]] – GR + hypoxanthine – synthetic<br /> | ||
*Guanidine riboswitch | |||
**[[5nwq]] – TfGR + guanidine – ''Thermobifida fusca''<br /> | |||
**[[5nzd]] – TfGR + CDP derivative<br /> | |||
*Thiamine pyrophosphate riboswitch | *Thiamine pyrophosphate riboswitch | ||
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**[[4oqu]] - SAMR + SAM - synthetic<br /> | **[[4oqu]] - SAMR + SAM - synthetic<br /> | ||
**[[6fz0]] - SAMR + SAM - ''Candidatus pelagibacter''<br /> | **[[6fz0]] - SAMR + SAM - ''Candidatus pelagibacter''<br /> | ||
**[[6c27]] - SAMR + GTP – ''Enterococcus faecalis''<br /> | |||
*S-adenosylhomocysteine riboswitch | *S-adenosylhomocysteine riboswitch | ||
**[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''<br /> | **[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''<br /> | ||
**[[6hag]] - SAMR + SAH – proteobacteria - NMR<br /> | |||
*Lysine riboswitch | *Lysine riboswitch | ||
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**[[6ck5]] – TmPRR + PRPP – ''Thermoanaerobacter mathranii''<br /> | **[[6ck5]] – TmPRR + PRPP – ''Thermoanaerobacter mathranii''<br /> | ||
**[[6ck4]] – TmPRR + | **[[6ck4]] – TmPRR + PPGPP<br /> | ||
**[[6dnr]] – SlPRR + GTP + cytidine phosphate – ''Syntrophothermus lipocalidus''<br /> | |||
**[[6dlq]], [[6dls]], [[6dlt]] – SlPRR + GTP + cytidine phosphate + PRPP<br /> | |||
**[[6dlr]] – SlPRR + cytidine phosphate + PRPP<br /> | |||
* PPGPP riboswitch | |||
**[[6dme]], [[6dmd]], [[6dmc]] – SaPPGPPR + GTP + cytidine phosphate + guanine tetraphosphate – ''Sulfobacillus acidophilus''<br /> | |||
*PFI riboswitch | *PFI riboswitch | ||