Riboswitch: Difference between revisions

← Older edit

Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman, Karsten Theis

@@ Line 1: / Line 1: @@
-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<ref name=scimag>Breaker, Ronald R. (28 March, 2008). Complex Riboswitches. ''Science'', 319(5871), 1795-1797. doi:[http://dx.doi.org/10.1126/science.1152621 10.1126/science.1152621]</ref>.
+<StructureSection load='' size='350' side='right' scene='47/479252/Cv/1' caption='Adenine riboswitch complex with adenine and Mg+2 ions, [[1y26]]'>
+__TOC__
+== Function ==
+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<ref name=scimag>Breaker, Ronald R. (28 March, 2008). Complex Riboswitches. ''Science'', 319(5871), 1795-1797. doi:[http://dx.doi.org/10.1126/science.1152621 10.1126/science.1152621]</ref>.
-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.
+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.
+*'''M-box riboswitch''' recognizes Mg+2<ref>PMID:21315082</ref>.
+*'''YdaO riboswitch''' recognizes ATP<ref>PMID:23086297</ref>.
+*'''yybp-ykoy riboswitch''' recognizes Mn+2<ref>PMID:25794618</ref>.
+*'''PRPP riboswitch''' recognizes phosphoribosyl pyrophosphate<ref>PMID:29504937</ref>.
+*'''ZMP riboswitch''' recognizes aminoimidazole-4-carboxamide riboside 5'-monophosphate<ref>PMID:32795418</ref>.
+*'''ZTP riboswitch''' recognizes aminoimidazole-4-carboxamide riboside 5'-triphosphate<ref>PMID:32795418</ref>.
+*'''ThiM riboswitch''' recognizes thiamine pyrophosphate<ref>PMID:34644399</ref>.
+For details on guanine riboswitch see<br />
+* [[Guanine-Binding Riboswitch]]<br />
+* [[Guanine riboswitch]].
+== 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.
 ==3D structures of riboswitch==
+[[Riboswitch 3D structures]]
+</StructureSection>
-===Adenine riboswitch===
+== References ==
-[[1y26]] – AR + adenine – Vibrio vulnificus<br />
+<references/>
-[[3ivn]] – BsAR (mutant) – Bacillus subtilis<br />
+[[Category: Topic Page]]
-[[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===
-[[2gdi]] – 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 />