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| <Structure load='379d' size='400' scene='Ribozyme/Cv/3' frame='true' align='right' caption='Hammerhead ribozyme, [[379d]]'/> | | <StructureSection load='' size='350' scene='Ribozyme/Cv/3' side='right' caption='Hammerhead ribozyme, (PDB-ID [[379d]])'> |
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| | [[Ribozyme]] (RZ) is an RNA molecule which catalyzes a chemical reaction<ref>PMID:9224568</ref>.<br /> |
| | *'''Glucosamine-6-phosphate activated RZ''' (glmS RZ) is a RZ and a riboswitch which regulates genes in response to metabolites.<br /> |
| | *'''Leadzyme''' is a small, artificially-made RZ which can cleave RNA in the presence of lead. For more details on leadzyme see [[Student Projects for UMass Chemistry 423 Spring 2012-10]].<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>. |
| | * Comparative genomic analysis revealed '''Twister''', '''Twister sister''', '''Hatchet''', and '''Pistol''' <ref>PMID:24240507</ref><ref>PMID:26167874 </ref>. |
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| [[Ribozyme]] (RZ) is an RNA molecule which catalyzes a chemical reaction. The '''Glucosamine-6-phosphate activated RZ''' (glmS RZ) is a RZ and a riboswitch which regulates genes in response to metabolites. '''Leadzyme''' is a small, artificially-made RZ which can cleave RNA in the presence of lead. For more details on leadzyme see [[Student Projects for UMass Chemistry 423 Spring 2012-10]]. '''Hairpin RZ''' and '''hammerhead RZ''' are named based on their shape. The '''group I intron''' catalyzes its own selfish splicing.
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| Articles in Proteopedia concerning ribozymes include: | | Articles in Proteopedia concerning ribozymes include: |
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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]] |
| <br /> | | <br> |
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| To view automatically seeded indices concerning ribozymes, see: | | To view automatically PDB-IDs concerning ribozymes, see: |
| *[[:Category:Ribozyme|Ribozyme]] | | *[[:Category:Ribozyme|Ribozyme]] |
| *[[:Category:Catalytic rna|Catalytic RNA]] | | *[[:Category:Catalytic rna|Catalytic RNA]] |
| | *[[:Category:GlmS|GlmS]] |
| *[[:Category:Hammerhead|Hammerhead]] | | *[[:Category:Hammerhead|Hammerhead]] |
| *[[:Category:Hairpin|Hairpin]] | | *[[:Category:Hairpin|Hairpin]] |
| | *[[:Category:Hepatitis delta|Hepatitis delta virus]] |
| | *[[:Category:Twister|Twister]] |
| | *[[:Category:Twister sister|Twister sister]] |
| | *[[:Category:Hatchet|Hatchet]] |
| | *[[:Category:Pistol|Pistol]] |
| *[[:Category:Group i intron|Group I intron]] | | *[[:Category:Group i intron|Group I intron]] |
| | *[[:Category:Varkud satellite|Varkud satellite]] |
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| | </StructureSection> |
| == 3D Structures of Ribozymes == | | == 3D Structures of Ribozymes == |
| | [[Ribozyme 3D structures]] |
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| Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
| | == References == |
| {{#tree:id=OrganizedByTopic|openlevels=0|
| | <references/> |
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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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| **[[1u6b]], [[1zzn]], [[3bo2]], [[3bo3]], [[3bo4]], [[3iin]] - ''Azoarcus'' group I intron <br/>
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| }}
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| [[Category: Topic Page]] | | [[Category: Topic Page]] |
