Riboswitch

spinqualitylabelsall models Adenine riboswitch complex with adenine and Mg+2 ions, 1y26 Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D 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. 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. For details on guanine riboswitch see Guanine-Binding Riboswitch 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 riboswitch-adenine complex shows the stacking interactions of the zippered-up junctional bubble which is formed by the adenine. Water molecules are shown as red spheres.

3D structures of riboswitch

Updated on 29-August-2019

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• Adenine riboswitch
  • RNA, Guanine-Binding Riboswitch, Guanine riboswitch, 4xnr, 5swd, 5swe, 5uza – VvAR + adenine – Vibrio vulnificus
    
  • 5e54 – VvAR
    
  • 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
    
  • 5c7u, 5c7w - BsGR + hypoxanthine
    
  • 2ees, 2eet, 2eeu, 2eev, 2eew - BsGR (mutant) + hypoxanthine
    
  • 3gao - BsGR + xanthine
    
  • 2xnw – BsGR + Mn
    
  • 4fe5, 4fej, 4fel, 4fen, 4feo, 4fep – GR + hypoxanthine – synthetic
    
• Thiamine pyrophosphate riboswitch
  • 2gdi – TPPR + TPP – synthetic
    
  • 2hoj, 2hok, 2hol – EcTPPR + TPP + metal ion – Escherichia coli
    
  • 2hom – EcTPPR + TMP
    
  • 2hoo, 2hop – EcTPPR + TPP analog
    
  • 4nya, 4nyb, 4nyc – EcTPPR + pyrimidine derivative
    
  • 4nyd – EcTPPR + hypoxanthine
    
  • 4nyg – EcTPPR + thyamine
    
  • 3d2g, 3d2v, 3d2x - TPPR + TPP analog – Arabidopsis thaliana
• S-adenosylmethionine riboswitch
  • 2gis, 4aob, 4b5r – TtSAMR + SAM – Thermoanaerobacter tengcongensis
    
  • 3iqr, 2ydh, 2ygh - TtSAMR (mutant) + SAM
    
  • 3iqp - TtSAMR
    
  • 5fjc, 5fk1, 5fk2, 5fk3, 5fk4, 5fk5, 5fk6, 5fkd, 5fke, 5fkf, 5fkg, 5fkh - TtSAMR + SAM + GTP
    
  • 2qwy, 3e5c, 3e5e, 3e5f, 3iqn - SAMR + SAM – synthetic
    
  • 4kqy – BsSAMR + SAM
    
  • 4oqu - SAMR + SAM - synthetic
    
  • 6fz0 - SAMR + SAM - Candidatus pelagibacter
    
• S-adenosylhomocysteine riboswitch
  • 3npn, 3npq – SAHR + SAH – Ralstonia solanacearum
    
• Lysine riboswitch
  • 3dis – TmKR – Thermotoga maritima
    
  • 3d0u – TmKR ligand-binding domain + Lysine
    
  • 3dil, 3dim, 3dio, 3dix, 3diy, 3diz, 3dj2 – TmKR + Lys
    
  • 3dj0, 3dir – TmKR + Lys derivative
    
  • 3dig – TmKR + Cys derivative
    
  • 3diq – TmKR + homoArg
    
  • 4erj – TmKR + aminocaproic acid
    
  • 4erl – TmKR + Lys + Gly
    
  • 3d0x - KR - synthetic
    
• Glutamine riboswitch
  • 5ddp – QR + glutamine – human
    
  • 5ddq, 5ddr – SeQR + glutamine – Synechococcus elongatus
    
  • 5ddo – SeQR + U1 small nuclear ribonucleoprotein
    
• 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
    
  • 6dn1, 6dn2, 6dn3 - FnFMNR + RNA
    
  • 5c45, 5kx9, 6bfb - FnFMNR + inhibitor
    
• Pre-queosine riboswitch
  • 3fu2, 3k1v – BsQ1R + queosine
    
  • 3gca – TtQ0R + queosine
    
  • 3q50, 3q51 – TtQ1R aptamer domain + queosine
    
  • 4jf2, 5d5l – Q1R + GTP + deaza-aminomethyl guanine – Lactobacillus rhamnosus
    
  • 4rzd – Q1R + GTP + deaza-aminomethyl guanine – Faecalibacterium prausnitzii
    
• C-di-GMP riboswitch
  • 3irw, 3mxh – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – Vibrio cholerae
    
  • 3iwn, 4yb1 – 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
    
  • 4qk8, 4qka – GMPR + GTP – Thermoanaerobacter pseudethanolicus
    
  • 4qk9 – GMPR + guanosine derivative – Thermovirga lienii
    
  • 4yaz, 4yb0 – GMPR + C-di-GMP - Geobacter
    
• C-di-AMP riboswitch
  • 4w90, 4w92 – VBsAMPR + C-di-AMP + U1 small nuclear ribonucleoprotein
    
  • 3muv – AMPR + C-di-AMP + U1 small nuclear ribonucleoprotein - synthetic
    
  • 4qk8 – AMPR + C-di-AMP + GTP - Thermoanaerobacter pseudethanolicus
    
  • 4qk8, 4qka – AMPR + C-di-AMP + GTP - Thermoanaerobacter pseudethanolicus
    
  • 4qlm, 4qln – AMPR + C-di-AMP - Thermoanaerobacter tengcongensis
    
  • 4qk9 – AMPR + C-di-AMP + GTP derivative - Thermovirga lienii
    
• 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
    
  • 2qbz – BsMBR + Mg
    
• T-Box riboswitch
  • 4lck – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic
    
  • 4mgn – sTBR + tRNA-Gly
    
• Tetrahydrofolate riboswitch
  • 3suh, 3sux – EsTHFR + THF derivative – Eubacterium siraeum
    
  • 3suy - EsTHFR + cytidine cyclic phosphate
    
  • 4lvv, 4lvx, 4lvw, 4lvy, 4lvz, 4lw0 – THFR + purine derivative – synthetic
    
  • 3sd3 – THFR (mutant) + pteridine derivative – synthetic
    
• Fluoride riboswitch
  • 3vrs – TpR + Mn + K + F – Thermotoga petrophila
    
  • 4en5 – TpR + Mg + Tl + F
    
  • 4enc – TpR + Mg + K + F
    
  • 4ena – TpR + Mg + Cs + GTP + F
    
  • 4enb – TpR + Mg + Ir + K + GTP + F
    
  • 5kh8 – R - synthetic - NMR
    
• Cobalamine riboswitch
  • 4frg, 4frn, 4gma, 4gxy – CoR + aptamer domain – Marine metagenome
    
• yybp-ykoy riboswitch
  • 4y1i – LlYYR + Mn – Lactobacillus lactis
    
  • 4y1j – LlYYR (mutant) + Mn
    
  • 4y1m – EcYYR
    
• ykkc riboswitch
  • 5u3g – TpR + gusanidine – Dikeya dadantii
    
• PRPP riboswitch
  • 6ck5 – TmPRR + PRPP – Thermoanaerobacter mathranii
    
  • 6ck4 – TmPRR + ppGpp
    
• PFI riboswitch
  • 4znp – TpR + AICAR – synthetic
    
• NICO riboswitch
  • 4rum – TpR + Co – synthetic
    
• ZMP riboswitch
  • 4xw7, 4xwf – TpR + AICAR – Actinomyces odontolyticus
    
• ZTP riboswitch
  • 5btp – TpR + AICAR – Fusobacterium ulcerans
    
• Guanidine riboswitch
  • 5t83 – TpR + guanidine – Sulfobacillus acidophilus
    
  • 5ndh, 5ndi, 5nef, 5neo, 5nep, 5neq, 5nex, 5nom – TpR + guanidine derivative – Gloeobacter violaceus
    
  • 5vj9, 5vjb – TpR + guanidine – Pseudomonas aeruginosa
    

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