Riboswitch
From Proteopedia
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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. | 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 [[Guanine-Binding Riboswitch]] | + | 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<br /> |
| + | * [[Guanine-Binding Riboswitch]]<br /> | ||
| + | * [[Guanine riboswitch]]. | ||
==3D structures of riboswitch== | ==3D structures of riboswitch== | ||
Revision as of 08:20, 2 January 2014
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
Adenine riboswitch
1y26 – AR + adenine – Vibrio vulnificus
3ivn – BsAR (mutant) – Bacillus subtilis
3la5 - BsAR (mutant) + azacytosine
Guanine riboswitch
1y27 – BsGR residues 185-252 + guanine
2g9c, 3fo4, 3fo6, 3ges, 3gog, 3rkf - BsGR (mutant) + guanine derivative
3got - BsGR (mutant) + adenine derivative
2xo1 - BsGR aptamer domain + adenine derivative
3g4m, 3ger - BsGR + guanine derivative
2xnz - BsGR aptamer domain + guanine derivative
2xo0 - BsGR aptamer domain + triazine derivative
2ees, 2eet, 2eeu, 2eev, 2eew - BsGR (mutant) + hypoxanthine
3gao - BsGR + xanthine
2xnw – BsGR + Mn
Thiamine pyrophosphate riboswitch
2gdi – TPPR + TPP – synthetic
2hoj, 2hok, 2hol – EcTPPR + TPP + metal ion – Escherichia coli
2hom – EcTPPR + TMP
2hoo, 2hop – EcTPPR + TPP analog
3d2g, 3d2v, 3d2x - TPPR + TPP analog – Arabidopsis thaliana
S-adenosylmethionine riboswitch
2gis – TtSAMR + SAM – Thermoanaerobacter tengcongensis
3iqr, 2ydh, 2ygh - TtSAMR (mutant) + SAM
3iqp - TtSAMR
2qwy, 3e5c, 3e5e, 3e5f, 3iqn - SAMR + SAM – synthetic
S-adenosylhomocysteine riboswitch
3npn, 3npq – SAHR + SAH – Ralstonia solanacearum
Lysine riboswitch
3d0u – KR ligand-binding domain + Lysine – Thermotoga maritima
FMN riboswitch
3f2q, 3f2t, 3f2w, 3f2x, 3f2y, 3f30, 3f4e – FnFMNR + FMN – Fusobacterium nucleatum
2yie - FnFMNR aptamer domain + FMN
3f4g, 3f4h – FnFMNR + flavin derivative
2yif - FnFMNR + GTP
Pre-queosine riboswitch
3fu2, 3k1v – BsQ1R + queosine
3gca – TtQ0R + queosine
3q50, 3q51 – TtQ1R aptamer domain + queosine
C-di-GMP riboswitch
3irw, 3mxh – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – Vibrio cholerae
3iwn – VcGMPR + C-di-GMP + U1 small nuclear ribonucleoprotein
3mum, 3mur, 3mut - VcGMPR (mutant) + C-di-GMP + U1 small nuclear ribonucleoprotein
3muv - VcGMPR (mutant) + C-di-AMP + U1 small nuclear ribonucleoprotein
3q3z - GMPR + C-di-GMP – Clostridium acetobutylicum
Glycine riboswitch
3owi, 3oww, 3owz – VcGlyR + glycine
3ox0, 3oxe, 3oxj, 3oxm – VcGlyR + GDP + cytidine cyclic phosphate
3oxb, 3oxd – VcGlyR (mutant) + GDP + cytidine cyclic phosphate
3p49 – FnGlyR + U1 small nuclear ribonucleoprotein + glycine
M-Box riboswitch
3pdr – BsMBR + Mn
Tetrahydrofolate riboswitch
3suh, 3sux – EsTHFR + THF derivative – Eubacterium siraeum
3suy - EsTHFR + cytidine cyclic phosphate
3sd1 – THFR + pteridine derivative – synthetic
3sd3 – THFR (mutant) + pteridine derivative – synthetic
Proteopedia Page Contributors and Editors (what is this?)
Michal Harel, Alexander Berchansky, Karsten Theis, Joel L. Sussman
