Ribozyme

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<Structure load='379d' size='400' scene='Ribozyme/Cv/3' frame='true' align='right' caption='Hammerhead ribozyme, [[379d]]'/>
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<StructureSection load='' size='350' scene='Ribozyme/Cv/3' side='right' caption='Hammerhead ribozyme, (PDB-ID [[379d]])'>
[[Ribozyme]] (RZ) is an RNA molecule which catalyzes a chemical reaction<ref>PMID:9224568</ref>.<br />
[[Ribozyme]] (RZ) is an RNA molecule which catalyzes a chemical reaction<ref>PMID:9224568</ref>.<br />
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*'''Hairpin RZ''' and '''hammerhead RZ''' are named based on their shape<ref>PMID:9849614</ref>.<br />
*'''Hairpin RZ''' and '''hammerhead RZ''' are named based on their shape<ref>PMID:9849614</ref>.<br />
*'''Group I intron''' catalyzes its own selfish splicing<ref>PMID:2197983</ref>.
*'''Group I intron''' catalyzes its own selfish splicing<ref>PMID:2197983</ref>.
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* Comparative genomic analysis revealed '''Twister''', ''Twister sister''', ''Hatchet''', and ''Pistol''' <ref>PMID:24240507</ref><ref>PMID:26167874 </ref>.
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* Comparative genomic analysis revealed '''Twister''', '''Twister sister''', '''Hatchet''', and '''Pistol''' <ref>PMID:24240507</ref><ref>PMID:26167874 </ref>.
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*[[Hairpin Ribozyme]]
*[[Hairpin Ribozyme]]
*[[Journal:JBIC:24|Human CPEB3 ribozyme's P4 domain]]
*[[Journal:JBIC:24|Human CPEB3 ribozyme's P4 domain]]
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<br />
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<br>
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To view automatically seeded indices concerning ribozymes, see:
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To view automatically PDB-IDs concerning ribozymes, see:
*[[:Category:Ribozyme|Ribozyme]]
*[[:Category:Ribozyme|Ribozyme]]
*[[:Category:Catalytic rna|Catalytic RNA]]
*[[:Category:Catalytic rna|Catalytic RNA]]
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*[[:Category:Varkud satellite|Varkud satellite]]
*[[:Category:Varkud satellite|Varkud satellite]]
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</StructureSection>
== 3D Structures of Ribozymes ==
== 3D Structures of Ribozymes ==
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[[Ribozyme 3D structures]]
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*Hepatitis delta virus ribozyme
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**[[3nkb]] – HDVRZ + DNA/RNA – Hepatitis delta virus<BR />
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**[[1ato]] – HDVRZ - NMR<BR />
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**[[2oih]], [[4pr6]] - HDVRZ + U1 small nuclear ribonucleoprotein A<BR />
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**[[1vc5]], [[4prf]] - HDVRZ + U1 small nuclear ribonucleoprotein A (mutant) <BR />
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**[[2oj3]], [[1sj3]], [[1sj4]], [[1sjf]], [[1vbx]], [[1vby]], [[1vbz]], [[1vc0]] - HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A<BR />
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**[[1vc6]], [[1vc7]], [[1cx0]], [[1drz]]- HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A (mutant)
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*glmS ribozyme
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**[[4meg]], [[4meh]] - glmS RZ – synthetic<br />
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**[[3l3c]], [[3g8s]], [[3g8t]], [[3g96]], [[3g9c]] – glmS RZ + RNA + U1 small nuclear ribonucleoprotein A<BR />
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**[[2nz4]] - glmS RZ + substrate RNA 13-mer+ U1 small nuclear ribonucleoprotein A (mutant) <BR />
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**[[3b4a]], [[3b4b]], [[3b4c]], [[2z74]], [[2z75]] – Tt-glmS RZ (mutant) + glmS RZ substrate RNA + glmS – ''Thermoanaerobacter tengcongensis''<BR />
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**[[2ho6]], [[2ho7]] - Tt-glmS RZ + glmS RZ substrate RNA<BR />
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**[[2gcs]], [[2h0s]], [[2h0x]], [[2h0z]] - Tt-glmS RZ + Tt-glmS RZ amino RNA inhibitor<BR />
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**[[2gcv]], [[2h0w]] - Tt-glmS RZ + Tt-glmS RZ product oligonucleotide
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*Hairpin ribozyme
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**[[3i2q]], [[3i2r]], [[3i2s]], [[3i2u]], [[3cqs]], [[2d2k]], [[2d2l]], [[4g6p]], [[4g6r]], [[4g6s]] – Hairpin RZ<BR />
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**[[3gs1]], [[3gs5]], [[3gs8]], [[2bcy]], [[2bcz]], [[2fgp]], [[1x9c]], [[1x9k]] - Hairpin RZ (mutant) <BR />
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**[[3cr1]] – Hairpin RZ + RNA<BR />
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**[[2k63]], [[2k64]], [[2k65]], [[2k66]] - Hairpin RZ 29-mer – NMR<BR />
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**[[3b58]], [[3b5a]], [[3b5f]], [[3b5s]], [[3b91]], [[3bbi]], [[3bbk]], [[3bbm]] - Hairpin RZ 29-mer + RNA<BR />
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**[[2npy]], [[2npz]] - Hairpin RZ + RZ domain linking strand<BR />
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**[[2p7d]], [[2p7e]], [[2p7f]], [[2oue]], [[1m5o]], [[1m5p]], [[1m5v]] - Hairpin RZ strands I, II, III +substrate strand – Tobacco ringspot virus<BR />
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**[[1m5k]] - Hairpin RZ + RNA inhibitor substrate + U1 small nuclear ribonucleoprotein A
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*Hammerhead ribozyme
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**[[1nyi]], [[1q29]], [[379d]], [[359d]], [[299d]], [[300d]], [[301d]], [[1mme]], [[1hmh]] - Hammerhead RZ<BR />
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**[[1rmn]] - Hammerhead RZ – fluorescence measurements<BR />
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**[[2ro2]], [[2rpk]] – Hammerhead RZ domain I<BR />
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**[[3czw]], [[3d0m]] - Hammerhead RZ shorter strands<BR />
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**[[2qus]], [[2quw]] - Hammerhead RZ (mutant) <BR />
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**[[2oeu]], [[2goz]] - Hammerhead RZ + RNA<br />
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**[[488d]] – Hammerhead RZ + RNA products<br />
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**[[3zd3]], [[3zd5]], [[3zp8]] - Hammerhead RZ enzyme+substrate strands<br />
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**[[3zd4]] - Hammerhead RZ enzyme strand
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*Leadzyme
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**[[2ldz]], [[1ldz]], [[1nuj]], [[1nuv]], [[429d]] – Leadzyme – NMR<BR />
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*Group I intron ribozymes
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**[[1u6b]], [[1zzn]], [[3bo2]], [[3bo3]], [[3bo4]], and [[3iin]] - ''Azoarcus'' group I intron <br/>
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**[[2r8s]] – RZ P4-P6 domain + antibody – mouse<BR />
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**[[1y0q]] – RZ group I + RNA – Staphylococcus phage twort<BR />
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**[[1x8w]] – TtRZ – ''Tetrahymena thermophilia'' group I intron<BR />
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**[[1grz]] – TtRZ (mutant) <BR />
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**[[1l8v]], [[1gid]] – TtRZ P4-P6 domain<BR />
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**[[1hr2]] - TtRZ P4-P6 domain (mutant) <BR />
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*Various ribozymes
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**[[1b36]] – RZ loop B - NMR<BR />
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**[[2l5z]], [[1e4p]], [[2mis]] – 26-mer of VS RZ – ''Neurospora'' – NMR<BR />
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**[[1yn1]], [[1yn2]], [[1tbk]], [[1tjz]], [[1hwq]] - VS RZ stem-loop V – NMR<BR />
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**[[3hhn]] – Class I ligase RZ + U1 small nuclear ribonucleoprotein A<BR />
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**[[3r1h]], [[3r1l]] - Class I ligase RZ (mutant) + U1 small nuclear ribonucleoprotein A+ RNA<br />
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**[[3fs0]], [[3ftm]] - Class II ligase RZ<br />
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**[[3cul]], [[3cun]] – Aminoacyl tRNA synthetase RZ 92-mer + U1 small nuclear ribonucleoprotein A<BR />
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**[[2cd1]], [[2cd5]], [[1xsg]], [[1f6x]], [[1f78]], [[1f7f]], [[1f7h]] – RNase P RZ P4 domain<BR />
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**[[2cd3]], [[2cd6]], [[1xsh]], [[1xst]], [[1xsu]], [[1f6z]], [[1f79]], [[1f7g]], [[1f7i]] - RNase P RZ P4 domain (mutant) <BR />
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**[[2oiu]] – L1 RZ RNA ligase<BR />
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**[[2hoj]], [[2hok]], [[2hol]], [[2hom]], [[2hoo]], [[2hop]] – THI-box riboswitch + thiamine pyrophosphate analog<BR />
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**[[2f88]] – RZ domain 5 – ''Pyaiella litorralis''<BR />
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**[[1ykq]] – Diels-Alder RZ<BR />
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**[[1ykv]], [[1yls]] - Diels-Alder RZ + reaction products<br />
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**[[4qjh]] – twister RZ – synthetic<br />
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**[[4rge]], [[4rgf]] – twister RZ env22 – synthetic<br />
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**[[5k7c]],[[5k7d]],[[5k7e]] - pistol RZ - synthetic <br/>
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}}
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== References ==
== References ==
<references/>
<references/>
[[Category: Topic Page]]
[[Category: Topic Page]]

Current revision

Hammerhead ribozyme, (PDB-ID 379d)

Drag the structure with the mouse to rotate

3D Structures of Ribozymes

Ribozyme 3D structures

References

  1. ↑ Tang J, Breaker RR. Rational design of allosteric ribozymes. Chem Biol. 1997 Jun;4(6):453-9. PMID:9224568
  2. ↑ Amarzguioui M, Prydz H. Hammerhead ribozyme design and application. Cell Mol Life Sci. 1998 Nov;54(11):1175-202. PMID:9849614 doi:http://dx.doi.org/10.1007/s000180050247
  3. ↑ Cech TR. Self-splicing of group I introns. Annu Rev Biochem. 1990;59:543-68. PMID:2197983 doi:http://dx.doi.org/10.1146/annurev.bi.59.070190.002551
  4. ↑ Roth A, Weinberg Z, Chen AG, Kim PB, Ames TD, Breaker RR. A widespread self-cleaving ribozyme class is revealed by bioinformatics. Nat Chem Biol. 2014 Jan;10(1):56-60. doi: 10.1038/nchembio.1386. Epub 2013 Nov, 17. PMID:24240507 doi:http://dx.doi.org/10.1038/nchembio.1386
  5. ↑ Weinberg Z, Kim PB, Chen TH, Li S, Harris KA, Lunse CE, Breaker RR. New classes of self-cleaving ribozymes revealed by comparative genomics analysis. Nat Chem Biol. 2015 Aug;11(8):606-10. doi: 10.1038/nchembio.1846. Epub 2015 Jul, 13. PMID:26167874 doi:http://dx.doi.org/10.1038/nchembio.1846

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Michal Harel, Wayne Decatur, Joel L. Sussman, Alexander Berchansky

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