Ribozyme

Ribozyme (RZ) is an RNA molecule which catalyzes a chemical reaction. 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. Group I intron catalyzes its own selfish splicing. Comparative genomic analysis revealed Twister, Twister sister, Hatchet, and Pistol . Articles in Proteopedia concerning ribozymes include: Azoarcus group I intron Kink-turn motif Ribosome The Large Ribosomal Subunit Hairpin Ribozyme Human CPEB3 ribozyme's P4 domain To view automatically PDB-IDs concerning ribozymes, see: Ribozyme Catalytic RNA GlmS Hammerhead Hairpin Hepatitis delta virus Twister Twister sister Hatchet Pistol Group I intron Varkud satellite

spinqualitylabelsall models Hammerhead ribozyme, (PDB-ID 379d) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image

3D Structures of Ribozymes3D Structures of Ribozymes

Updated on 26-October-2020

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• Hepatitis delta virus ribozyme
  • 3nkb – HDVRZ + DNA/RNA – Hepatitis delta virus
    
  • 4prf – HDVRZ
    
  • 1ato – HDVRZ - NMR
    
  • 2oih, 4pr6 - HDVRZ + U1 small nuclear ribonucleoprotein A
    
  • 1vc5, 4prf - HDVRZ + U1 small nuclear ribonucleoprotein A (mutant)
    
  • 2oj3, 1sj3, 1sj4, 1sjf, 1vbx, 1vby, 1vbz, 1vc0 - HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A
    
  • 1vc6, 4prf, 1pr6, 1drz- HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A (mutant)
• glmS ribozyme
  • 4meg, 4meh - glmS RZ – synthetic
    
  • 3l3c, 3g8s, 3g8t, 3g96, 3g9c – glmS RZ + RNA + U1 small nuclear ribonucleoprotein A
    
  • 2nz4 - glmS RZ + substrate RNA 13-mer+ U1 small nuclear ribonucleoprotein A (mutant)
    
  • 3b4a, 3b4b, 3b4c, 2z74, 2z75 – Tt-glmS RZ (mutant) + glmS RZ substrate RNA + glmS – Thermoanaerobacter tengcongensis
    
  • 2ho6, 2ho7 - Tt-glmS RZ + glmS RZ substrate RNA
    
  • 2gcs, 2h0s, 2h0x, 2h0z - Tt-glmS RZ + Tt-glmS RZ amino RNA inhibitor
    
  • 2gcv, 2h0w - Tt-glmS RZ + Tt-glmS RZ product oligonucleotide
• Hairpin ribozyme
  • 3i2q, 3i2r, 3i2s, 3i2u, 3cqs, 2d2k, 2d2l, 4g6p, 4g6r, 4g6s – Hairpin RZ
    
  • 3gs1, 3gs5, 3gs8, 2bcy, 2bcz, 2fgp, 1x9c, 1x9k - Hairpin RZ (mutant)
    
  • 3cr1 – Hairpin RZ + RNA
    
  • 2m24, 2m23, 2k65, 2k66 - Hairpin RZ 29-mer – NMR
    
  • 3b58, 3b5a, 3b5f, 3b5s, 3b91, 3bbi, 3bbk, 3bbm - Hairpin RZ 29-mer + RNA
    
  • 2npy, 2npz - Hairpin RZ + RZ domain linking strand
    
  • 2p7d, 2p7e, 2p7f, 2oue, 1m5o, 1m5p, 1m5v - Hairpin RZ strands I, II, III +substrate strand – Tobacco ringspot virus
    
  • 1m5k - Hairpin RZ + RNA inhibitor substrate + U1 small nuclear ribonucleoprotein A
• Hammerhead ribozyme
  • 1nyi, 1q29, 379d, 359d, 299d, 300d, 301d, 1mme, 1hmh, 5di2, 5di4, 5dh6, 5dh7, 5dh8, 5eao, 5eaq - Hammerhead RZ
    
  • 1rmn - Hammerhead RZ – fluorescence measurements
    
  • 2ro2, 2rpk – Hammerhead RZ domain I
    
  • 3czw, 3d0m - Hammerhead RZ shorter strands
    
  • 2qus, 2quw - Hammerhead RZ (mutant)
    
  • 2oeu, 5dqk - Hammerhead RZ + RNA
    
  • 488d – Hammerhead RZ + RNA products
    
  • 3zd5, 3zp8 - Hammerhead RZ enzyme+substrate strands
    
  • 3zd4 - Hammerhead RZ enzyme strand
• Leadzyme
  • 2ldz, 1ldz, 1nuj, 1nuv, 429d – Leadzyme – NMR
    
• Group I intron ribozymes
  • 1u6b, 1zzn, 3bo2, 3bo3, 3bo4, 3iin - RZ P9 + RNA + U1 small nuclear ribonucleoprotein
    
  • 2r8s – RZ P4-P6 domain + antibody – mouse
    
  • 1y0q – RZ group I + RNA – Staphylococcus phage twort
    
  • 1x8w – TtRZ – Tetrahymena thermophilia
    
  • 1grz, 6bjx, 6d8l, 6d8m, 6d8n, 6d8o – TtRZ (mutant)
    
  • 1l8v, 1gid – TtRZ P4-P6 domain
    
  • 1hr2 - TtRZ P4-P6 domain (mutant)
    
  • 3hhn – ligase RZ + U1 small nuclear ribonucleoprotein A
    
  • 3r1h, 3r1l - ligase RZ (mutant) + U1 small nuclear ribonucleoprotein A+ RNA
    
• Group II intron ribozymes
  • 6ez0 – yRZ - NMR
    
  • 5j01, 5j02 - OiRZ - Oceanobacillus iheyensis
    
  • 6t3k, 6t3n, 6t3r, 6t3s - OiRZ (mutant)
    
  • 3fs0, 3ftm - ligase RZ
    
• Various ribozymes
  • 1b36 – RZ loop B - NMR
    
  • 5v3i – VS RZ – Neurospora
    
  • 2l5z, 1e4p, 2mis – 26-mer of VS RZ – NMR
    
  • 1yn1, 1yn2, 1tbk, 1tjz, 1hwq - VS RZ stem-loop V – NMR
    
  • 5v3i - VS RZ
    
  • 4r4p, 4r4v - VS RZ (mutant)
    
  • 3hhn – Class I ligase RZ + U1 small nuclear ribonucleoprotein A
    
  • 3r1h, 3r1l - Class I ligase RZ (mutant) + U1 small nuclear ribonucleoprotein A+ RNA
    
  • 3fs0, 3ftm - Class II ligase RZ
    
  • 3cul, 3cun – Aminoacyl tRNA synthetase RZ 92-mer + U1 small nuclear ribonucleoprotein A
    
  • 2cd1, 2cd5, 1xsg, 1f6x, 1f78, 1f7f, 1f7h – RNase P RZ P4 domain
    
  • 2cd3, 2cd6, 1xsh, 1xst, 1xsu, 1f6z, 1f79, 1f7g, 1f7i - RNase P RZ P4 domain (mutant)
    
  • 2oiu – L1 RZ RNA ligase
    
  • 2hoj, 2hok, 2hol, 2hom, 2hoo, 2hop – THI-box riboswitch + thiamine pyrophosphate analog
    
  • 2f88 – RZ domain 5 – Pyaiella litorralis
    
  • 1ykq – Diels-Alder RZ
    
  • 1ykv, 1yls - Diels-Alder RZ + reaction products
    
  • 4qjh, 5dun – twister RZ – synthetic
    
  • 4rge, 4rgf – twister RZ env22 – synthetic
    
  • 5t5a, 5y85, 5y87 – twister sister RZ – Metagenome
    
  • 5k7c,5k7d,5k7e, 5ktj - pistol RZ - synthetic
    
  • 6gyv – lariat-capping RZ – Didymium iridis