Riboswitch: Difference between revisions
Michal Harel (talk | contribs) New page: 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 regulator... |
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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<ref name=singhetal/>. | 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<ref name=singhetal/>. | ||
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< | 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. | ||
==3D structures of riboswitch== | |||
===Adenine riboswitch=== | |||
[[1y26]] – AR + adenine – Vibrio vulnificus<br /> | |||
[[3ivn]] – BsAR (mutant) – Bacillus subtilis<br /> | |||
[[3la5]] - BsAR (mutant) + azacytosine<br /> | |||
===Guanine riboswitch=== | |||
[[1y27]] – BsGR residues 185-252 + guanine<br /> | |||
[[2g9c]], [[3fo4]], [[3fo6]], [[3ges]], [[3gog]], [[3rkf]] - BsGR (mutant) + guanine derivative<br /> | |||
[[3got]] - BsGR (mutant) + adenine derivative<br /> | |||
[[2xo1]] - BsGR aptamer domain + adenine derivative<br /> | |||
[[3g4m]], [[3ger]] - BsGR + guanine derivative<br /> | |||
[[2xnz]] - BsGR aptamer domain + guanine derivative<br /> | |||
[[2xo0]] - BsGR aptamer domain + triazine derivative<br /> | |||
[[2ees]], [[2eet]], [[2eeu]], [[2eev]], [[2eew]] - BsGR (mutant) + hypoxanthine<br /> | |||
[[3gao]] - BsGR + xanthine<br /> | |||
[[2xnw]] – BsGR + Mn | |||
Thiamine pyrophosphate riboswitch=== | |||
[[2gd]]i – TPPR + TPP – synthetic<br /> | |||
[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – Escherichia coli<br /> | |||
[[2hom]] – EcTPPR + TMP<br /> | |||
[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br /> | |||
[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – Arabidopsis thaliana | |||
===S-adenosylmethionine riboswitch=== | |||
[[2gis]] – TtSAMR + SAM – Thermoanaerobacter tengcongensis<br /> | |||
[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM<br /> | |||
[[3iqp]] - TtSAMR<br /> | |||
[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic<br /> | |||
===S-adenosylhomocysteine riboswitch=== | |||
[[3npn]], [[3npq]] – SAHR + SAH – Ralstonia solanacearum<br /> | |||
===Lysine riboswitch=== | |||
[[3d0u]] – KR ligand-binding domain + Lysine – Thermotoga maritima | |||
===FMN riboswitch=== | |||
[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN – Fusobacterium nucleatum<br /> | |||
[[2yie]] - FnFMNR aptamer domain + FMN<br /> | |||
[[3f4g]], [[3f4h – FnFMNR + flavin derivative<br /> | |||
[[2yif]] - FnFMNR + GTP | |||
===Pre-queosine riboswitch=== | |||
[[3fu2]], [[3k1v]] – BsQ1R + queosine<br /> | |||
[[3gca]] – TtQ0R + queosine<br /> | |||
[[3q50]], [[3q51]] – TtQ1R aptamer domain + queosine<br /> | |||
===C-di-GMP riboswitch=== | |||
[[3irw]], [[3mxh]] – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – Vibrio cholerae<br /> | |||
[[3iwn]] – VcGMPR + 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 /> | |||
[[3q3z]] - GMPR + C-di-GMP – Clostridium acetobutylicum | |||
===Glycine riboswitch=== | |||
[[3owi]], [[3oww]], [[3owz]] – VcGlyR + glycine<br /> | |||
[[3ox0]], [[3oxe]], [[3oxj]], [[3oxm]] – VcGlyR + GDP + cytidine cyclic phosphate<br /> | |||
[[3oxb]], [[3oxd]] – VcGlyR (mutant) + GDP + cytidine cyclic phosphate<br /> | |||
[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine<br /> | |||
===M-Box riboswitch=== | |||
[[3pdr]] – BsMBR + Mn | |||
===Tetrahydrofolate riboswitch=== | |||
[[3suh]], [[3sux]] – EsTHFR + THF derivative – Eubacterium siraeum<br /> | |||
[[3suy]] - EsTHFR + cytidine cyclic phosphate<br /> | |||
[[3sd1]] – THFR + pteridine derivative – synthetic<br /> | |||
[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic<br /> | |||