Ribozyme

From Proteopedia

Revision as of 09:32, 19 December 2011

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

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. Hairpin RZ and hammerhead RZ are named based on their shape. The group I intron catalyzes its own selfish splicing.

Articles in Proteopedia concerning ribozymes include:

• Azoarcus group I intron
• Kink-turn motif
• Ribosome
• The Large Ribosomal Subunit

To view automatically seeded indices concerning ribozymes, see:

• Ribozyme
• Catalytic RNA
• Hammerhead
• Hairpin
• Group I intron

3D Structures of Ribozymes

Updated December 2011

Hepatitis delta virus RZ

3nkb – HDVRZ + DNA/RNA – Hepatitis delta virus
1ato – HDVRZ - NMR
2oih - HDVRZ + U1 small nuclear ribonucleoprotein A
1vc5 - HDVRZ + U1 small nuclear ribonucleoprotein A (mutant)
2oj3, 1sj3, 1sj4, 1sjf, 1vbx, 1vby, 1vbz, 1vc0 - HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A
1vc6, 1vc7, 1cx0, 1drz- HDVRZ (mutant) + U1 small nuclear ribonucleoprotein A (mutant)

glmS RZ

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 RZ

3i2q, 3i2r, 3i2s, 3i2u, 3cqs, 2d2k, 2d2l – Hairpin RZ
3gs1, 3gs5, 3gs8, 2bcy, 2bcz, 2fgp, 1x9c, 1x9k - Hairpin RZ (mutant)
3cr1 – Hairpin RZ + RNA
2k63, 2k64, 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 RZ

1nyi, 1q29, 379d, 359d, 299d, 300d, 301d, 1mme, 1hmh - 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, 2goz - Hammerhead RZ + RNA 488d – Hammerhead RZ + RNA products

Leadzyme

2ldz, 1ldz, 1nuj, 1nuv, 429d – Leadzyme – NMR

Group I intron ribozymes

1u6b, 1zzn, 3bo2, 3bo3, 3bo4, and 3iin - Azoarcus group I intron
2r8s – RZ P4-P6 domain + antibody – mouse
1y0q – RZ group I + RNA – Staphylococcus phage twort
1x8w – TtRZ – Tetrahymena thermophilia group I intron
1grz – TtRZ (mutant)
1l8v, 1gid – TtRZ P4-P6 domain
1hr2 - TtRZ P4-P6 domain (mutant)

Various RZ

1b36 – RZ loop B]] - NMR
2l5z, 1e4p – 26-mer of VS RZ – Neurospora – NMR
1yn1, 1yn2, 1tbk, 1tjz, 1hwq - VS RZ stem-loop V – NMR
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