Riboswitch

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==3D structures of riboswitch==
==3D structures of riboswitch==
 +
 +
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
===Adenine riboswitch===
===Adenine riboswitch===
-
[[1y26]] – AR + adenine – Vibrio vulnificus<br />
+
[[1y26]] – 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 />
===Guanine riboswitch===
===Guanine riboswitch===
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[[2ees]], [[2eet]], [[2eeu]], [[2eev]], [[2eew]] - BsGR (mutant) + hypoxanthine<br />
[[2ees]], [[2eet]], [[2eeu]], [[2eev]], [[2eew]] - BsGR (mutant) + hypoxanthine<br />
[[3gao]] - BsGR + xanthine<br />
[[3gao]] - BsGR + xanthine<br />
-
[[2xnw]] – BsGR + Mn
+
[[2xnw]] – BsGR + Mn<br />
 +
[[4fe5]], [[4fej]], [[4fel]], [[4fen]], [[4feo]], [[4fep]] – GR + hypoxanthine – synthetic<br />
===Thiamine pyrophosphate riboswitch===
===Thiamine pyrophosphate riboswitch===
[[2gdi]] – TPPR + TPP – synthetic<br />
[[2gdi]] – TPPR + TPP – synthetic<br />
-
[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – Escherichia coli<br />
+
[[2hoj]], [[2hok]], [[2hol]] – EcTPPR + TPP + metal ion – ''Escherichia coli''<br />
[[2hom]] – EcTPPR + TMP<br />
[[2hom]] – EcTPPR + TMP<br />
[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br />
[[2hoo]], [[2hop]] – EcTPPR + TPP analog<br />
-
[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – Arabidopsis thaliana
+
[[3d2g]], [[3d2v]], [[3d2x]] - TPPR + TPP analog – ''Arabidopsis thaliana''
===S-adenosylmethionine riboswitch===
===S-adenosylmethionine riboswitch===
-
[[2gis]] – TtSAMR + SAM – Thermoanaerobacter tengcongensis<br />
+
[[2gis]], [[4aob]], [[4b5r]] – TtSAMR + SAM – ''Thermoanaerobacter tengcongensis''<br />
[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM<br />
[[3iqr]], [[2ydh]], [[2ygh]] - TtSAMR (mutant) + SAM<br />
[[3iqp]] - TtSAMR<br />
[[3iqp]] - TtSAMR<br />
[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic<br />
[[2qwy]], [[3e5c]], [[3e5e]], [[3e5f]], [[3iqn]] - SAMR + SAM – synthetic<br />
 +
[[4kqy]] – BsSAMR + SAM<br />
===S-adenosylhomocysteine riboswitch===
===S-adenosylhomocysteine riboswitch===
-
[[3npn]], [[3npq]] – SAHR + SAH – Ralstonia solanacearum<br />
+
[[3npn]], [[3npq]] – SAHR + SAH – ''Ralstonia solanacearum''<br />
===Lysine riboswitch===
===Lysine riboswitch===
-
[[3d0u]] – KR ligand-binding domain + Lysine – Thermotoga maritima
+
[[3d0u]] – TmKR ligand-binding domain + Lysine – ''Thermotoga maritima''<br />
 +
[[4erj]] – TmKR + aminocaproic acid<br />
 +
[[4erl]] – TmKR + Lys + Gly<br />
===FMN riboswitch===
===FMN riboswitch===
-
[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN – Fusobacterium nucleatum<br />
+
[[3f2q]], [[3f2t]], [[3f2w]], [[3f2x]], [[3f2y]], [[3f30]], [[3f4e]] – FnFMNR + FMN – ''Fusobacterium nucleatum''<br />
[[2yie]] - FnFMNR aptamer domain + FMN<br />
[[2yie]] - FnFMNR aptamer domain + FMN<br />
[[3f4g]], [[3f4h]] – FnFMNR + flavin derivative<br />
[[3f4g]], [[3f4h]] – FnFMNR + flavin derivative<br />
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[[3gca]] – TtQ0R + queosine<br />
[[3gca]] – TtQ0R + queosine<br />
[[3q50]], [[3q51]] – TtQ1R aptamer domain + queosine<br />
[[3q50]], [[3q51]] – TtQ1R aptamer domain + queosine<br />
 +
[[4jf2]] – Q1R + GTP + deaza-aminomethyl guanine – ''Lactobacillus rhamnosus''<br />
===C-di-GMP riboswitch===
===C-di-GMP riboswitch===
-
[[3irw]], [[3mxh]] – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – Vibrio cholerae<br />
+
[[3irw]], [[3mxh]] – VcGMPR + C-di-GMP + GTP + U1 small nuclear ribonucleoprotein – ''Vibrio cholerae''<br />
[[3iwn]] – VcGMPR + C-di-GMP + U1 small nuclear ribonucleoprotein<br />
[[3iwn]] – VcGMPR + C-di-GMP + U1 small nuclear ribonucleoprotein<br />
[[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 />
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[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine<br />
[[3p49]] – FnGlyR + U1 small nuclear ribonucleoprotein + glycine<br />
===M-Box riboswitch===
===M-Box riboswitch===
-
[[3pdr]] – BsMBR + Mn
+
[[3pdr]] – BsMBR + Mn<br />
 +
===T-Box riboswitch===
 +
[[4lck]] – sTBR + tRNA-Gly + ribosomal protein YBXF – synthetic<br />
 +
[[4mgn]] – sTBR + tRNA-Gly <br />
 +
 
===Tetrahydrofolate riboswitch===
===Tetrahydrofolate riboswitch===
-
[[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 + pteridine derivative – synthetic<br />
[[3sd1]] – THFR + pteridine derivative – synthetic<br />
[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic<br />
[[3sd3]] – THFR (mutant) + pteridine derivative – synthetic<br />
 +
===Fluoride riboswitch===
 +
[[3vrs]] – TpR + Mn + K + F – ''Thermotoga petrophila''<br />
 +
[[4en5]] – TpR + Mg + Tl + F <br />
 +
[[4enc]] – TpR + Mg + K + F <br />
 +
[[4ena]] – TpR + Mg + Cs + GTP + F <br />
 +
[[4enb]] – TpR + Mg + Ir + K + GTP + F <br />
 +
 +
===Cobalamine riboswitch===
 +
[[4frg]], [[4frn]], [[4gma]], [[4gxy]] – CoR + aptamer domain – ''Marine metagenome''<br />
 +
 +
[[Category: Topic Page]]

Revision as of 09:20, 28 April 2014

Template:STRUCTURE 1y26

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

Contents

3D structures of riboswitch

Updated on 28-April-2014

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
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
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
2qwy, 3e5c, 3e5e, 3e5f, 3iqn - SAMR + SAM – synthetic
4kqy – BsSAMR + SAM

S-adenosylhomocysteine riboswitch

3npn, 3npq – SAHR + SAH – Ralstonia solanacearum

Lysine riboswitch

3d0u – TmKR ligand-binding domain + Lysine – Thermotoga maritima
4erj – TmKR + aminocaproic acid
4erl – TmKR + Lys + Gly

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
4jf2 – Q1R + GTP + deaza-aminomethyl guanine – Lactobacillus rhamnosus

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

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
3sd1 – THFR + pteridine 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

Cobalamine riboswitch

4frg, 4frn, 4gma, 4gxy – CoR + aptamer domain – Marine metagenome

Proteopedia Page Contributors and Editors (what is this?)

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

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