Ribozyme

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== 3D Structures of Ribozymes ==
== 3D Structures of Ribozymes ==
[[Ribozyme 3D structures]]
[[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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**[[4prf]] – HDVRZ<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]], [[4prf]], [[1pr6]], [[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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**[[2m24]], [[2m23]], [[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]], [[5di2]], [[5di4]], [[5dh6]], [[5dh7]], [[5dh8]], [[5eao]], [[5eaq]] - 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]], [[5dqk]] - Hammerhead RZ + RNA<br />
 
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**[[488d]] – Hammerhead RZ + RNA products<br />
 
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**[[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]], [[3iin]] - RZ P9 + RNA + U1 small nuclear ribonucleoprotein <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''<BR />
 
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**[[6wls]], [[7ez0]], [[7ez2]] – TtRZ – Cryo EM<br />
 
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**[[1grz]], [[6bjx]], [[6d8l]], [[6d8m]], [[6d8n]], [[6d8o]] – 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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**[[3hhn]] – ligase RZ + U1 small nuclear ribonucleoprotein A<BR />
 
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**[[3r1h]], [[3r1l]] - ligase RZ (mutant) + U1 small nuclear ribonucleoprotein A+ RNA<br />
 
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*Group II intron ribozymes
 
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**[[6ez0]] – yRZ - NMR<BR />
 
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**[[5j01]], [[5j02]] - OiRZ - ''Oceanobacillus iheyensis'' <br/>
 
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**[[6t3k]], [[6t3n]], [[6t3r]], [[6t3s]] - OiRZ (mutant) <br/>
 
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**[[3fs0]], [[3ftm]] - ligase RZ<br />
 
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*Various ribozymes
 
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**[[1b36]] – RZ loop B - NMR<BR />
 
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**[[5v3i]] – VS RZ – ''Neurospora'' <BR />
 
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**[[2l5z]], [[1e4p]], [[2mis]] – 26-mer of VS RZ – NMR<BR />
 
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**[[1yn1]], [[1yn2]], [[1tbk]], [[1tjz]], [[1hwq]] - VS RZ stem-loop V – NMR<BR />
 
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**[[5v3i]] - VS RZ <BR />
 
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**[[4r4p]], [[4r4v]] - VS RZ (mutant)<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]], [[5dun]] – twister sRZ – synthetic<br />
 
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**[[4rge]], [[4rgf]] – twister sRZ env22 <br />
 
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**[[5t5a]], [[5y85]], [[5y87]] – twister sister RZ – Metagenome<br />
 
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**[[5k7c]],[[5k7d]],[[5k7e]], [[5ktj]], [[6ufj]], [[6ufk]] - pistol sRZ <br/>
 
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**[[6uey]], [[6uf1]] – pistol EcRZ <br />
 
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**[[6r47]] – pistol RZ – Alistipes putredinis <br />
 
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**[[6g7z]], [[6gyv]] – lariat-capping RZ – ''Didymium iridis''<BR />
 
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**[[6jq5]], [[6jq6]] – hatchet sRZ <br />
 
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**[[6xjq]], [[6xjw]], [[6xjy]], [[6xjz]] – self-alkylating RZ + antibody – ''Aeropyrum pernix'' <br />
 
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**[[7dlz]], [[7dwh]] – SAM-dependent methyltransferase sRZ + U1A <br />
 
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**[[6wll]], [[6wlm]] – Gly RZ – ''Fusobacterium nucleatum'' <br />
 
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**[[6wlt]], [[6wlu]] – Gly RZ – ''Vibrio cholerae'' <br />
 
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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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