Riboswitch
From Proteopedia
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*Adenine riboswitch | *Adenine riboswitch | ||
| - | **[[1y26]] – AR + adenine – ''Vibrio vulnificus''<br /> | + | **[[1y26]], [[4tzx]], [[4tzy]], [[4xnr]] – AR + adenine – ''Vibrio vulnificus''<br /> |
**[[3ivn]] – BsAR (mutant) – ''Bacillus subtilis''<br /> | **[[3ivn]] – BsAR (mutant) – ''Bacillus subtilis''<br /> | ||
**[[3la5]] - BsAR (mutant) + azacytosine<br /> | **[[3la5]] - BsAR (mutant) + azacytosine<br /> | ||
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**[[2hom]] – EcTPPR + TMP<br /> | **[[2hom]] – EcTPPR + TMP<br /> | ||
**[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br /> | **[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br /> | ||
| + | **[[4nya]], [[4nyb]], [[4nyc]] – EcTPPR + pyrimidine derivative<br /> | ||
| + | **[[4nyd]] – EcTPPR + hypoxanthine <br /> | ||
| + | **[[4nyg]] – EcTPPR + thyamine <br /> | ||
**[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana'' | **[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana'' | ||
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**[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic<br /> | **[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic<br /> | ||
**[[4kqy]] – BsSAMR + SAM<br /> | **[[4kqy]] – BsSAMR + SAM<br /> | ||
| + | **[[4oqu]] - SAMR + SAM - synthetic<br /> | ||
*S-adenosylhomocysteine riboswitch | *S-adenosylhomocysteine riboswitch | ||
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**[[3mum]], [[3mur]], [[3mut]] - VcGMPR (mutant) + C-di-GMP + U1 small nuclear ribonucleoprotein<br /> | **[[3mum]], [[3mur]], [[3mut]] - VcGMPR (mutant) + C-di-GMP + U1 small nuclear ribonucleoprotein<br /> | ||
**[[3muv]] - VcGMPR (mutant) + C-di-AMP + U1 small nuclear ribonucleoprotein<br /> | **[[3muv]] - VcGMPR (mutant) + C-di-AMP + U1 small nuclear ribonucleoprotein<br /> | ||
| - | **[[3q3z]] - GMPR + C-di-GMP – ''Clostridium acetobutylicum'' | + | **[[3q3z]] - GMPR + C-di-GMP – ''Clostridium acetobutylicum''<br /> |
| + | **[[4qk8]], [[4qka]] – GMPR + GTP – ''Thermoanaerobacter pseudethanolicus''<br /> | ||
| + | **[[4qk9]] – GMPR + guanosine derivative – ''Thermovirga lienii''<br /> | ||
*Glycine riboswitch | *Glycine riboswitch | ||
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**[[3suh]], [[3sux]] – EsTHFR + THF derivative – ''Eubacterium siraeum''<br /> | **[[3suh]], [[3sux]] – EsTHFR + THF derivative – ''Eubacterium siraeum''<br /> | ||
**[[3suy]] - EsTHFR + cytidine cyclic phosphate<br /> | **[[3suy]] - EsTHFR + cytidine cyclic phosphate<br /> | ||
| - | **[[3sd1]] – THFR + | + | **[[3sd1]], [[4lvv]], [[4lvx]], [[4lvw]], [[4lvy]], [[4lvz]], [[4lw0]] – THFR + purine derivative – synthetic<br /> |
**[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic<br /> | **[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic<br /> | ||
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**[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – ''Marine metagenome''<br /> | **[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – ''Marine metagenome''<br /> | ||
| + | |||
| + | *yybp-ykoy riboswitch | ||
| + | |||
| + | **[[4y1i]] – LlYYR + Mn – ''Lactobacillus lactis''<br /> | ||
| + | **[[4y1j]] – LlYYR (mutant) + Mn<br /> | ||
| + | **[[4y1m]] – EcYYR <br /> | ||
| + | |||
}} | }} | ||
[[Category: Topic Page]] | [[Category: Topic Page]] | ||
Revision as of 06:30, 4 June 2015
Normally, a variety of proteins and protein cofactors control gene expression in an organism by binding to different sites on messenger RNA (mRNA). Riboswitches are genetic regulatory elements that are built directly into the RNA. They are a type of noncoding RNA that regulate gene expression in the absence of proteins by switching from one structural conformation (shape) to another in response to ligand binding. Most contain a single binding site that recognizes a specific ligand. The ability of a riboswitch to discriminate against molecules that are similar or closely related to its ligand is essential to prevent metabolic misregulation[1].
The various classes of riboswitches discovered so far are differentiated by their respective ligands. Every class of riboswitch is characterized by an aptamer (binding site) domain, which provides the site for ligand binding, and an expression platform that undergoes conformational change. The sequences and structures of aptamer domains are highly conserved, and therefore exhibit little variation among riboswitches belonging to the same class.
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. For details on guanine riboswitch see
3D structures of riboswitch
Updated on 04-June-2015
Proteopedia Page Contributors and Editors (what is this?)
Michal Harel, Alexander Berchansky, Karsten Theis, Joel L. Sussman
