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Literature summary for 3.6.4.13 extracted from
- Structural insights into the mechanism of the DEAH-box RNA helicase Prp43 (2017), eLife, 6, e21510 .
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| purified recombinant Prp43 with bound RNA in an active state, i.e. ctPrp43DELTAN-U7-ADP-BeF3-, ctPrp43DELTAN-ADP-BeF3-(HR), and ctPrp43DELTAN-ADP-BeF3-(LR), X-ray diffraction structure determination and analysis at 1.78-3.24 A resolution | Thermochaetoides thermophila |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| additional information | design of a mutant of Prp43 which allows us to trap the closed conformation by the introduction of an internal disulfide bond (ctPrp43-IDSB). For this purpose, one cysteine is introduced into the RecA1 domain and another one into the ratchet-like domain at exposed positions to maximize the number of formed disulfide bonds. The wild-type protein contains nine cysteines, the ctPrp43-IDSB mutant two additional ones, the majority of ctPrp43-IDSB exhibits the internal disulfide bridge. Prp43 trapped in the closed conformation is impaired in its helicase activity. The intrinsic ATPase activity of ctPrp43-IDSB is similar to the one determined for wild-type ctPrp43. ctPrp43-IDSB is also stimulated by ctPfa1-GP and by U16-RNA in the presence of the ctPfa1-GP, but in the contrast to wild-type Prp43 also just by U16-RNA. Prp43 in the trapped closed conformation appears to be more prone for the stimulation of the ATPase. Conformational rearrangements at the helicase core, structure analysis, overview | Thermochaetoides thermophila |
Metals/Ions
| Metals/Ions | Comment | Organism | Structure |
|---|---|---|---|
| Mg2+ | required | Thermochaetoides thermophila |  |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | Thermochaetoides thermophila | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Thermochaetoides thermophila IMI 039719 | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Thermochaetoides thermophila DSM 1495 | - |
ADP + phosphate | - |
? | |
| ATP + H2O | Thermochaetoides thermophila CBS 144.50 | - |
ADP + phosphate | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Thermochaetoides thermophila | G0RY84 | - |
- |
| Thermochaetoides thermophila CBS 144.50 | G0RY84 | - |
- |
| Thermochaetoides thermophila DSM 1495 | G0RY84 | - |
- |
| Thermochaetoides thermophila IMI 039719 | G0RY84 | - |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ATP + H2O | - |
Thermochaetoides thermophila | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Thermochaetoides thermophila IMI 039719 | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Thermochaetoides thermophila DSM 1495 | ADP + phosphate | - |
? | |
| ATP + H2O | - |
Thermochaetoides thermophila CBS 144.50 | ADP + phosphate | - |
? | |
| additional information | RNA loading mechanism of Prp43, and catalytic mechanism, detailed overview. Prp43 binds RNA in a sequence-independent fashion. Analysis of interactions between Prp43 and the U7-RNA and of the ATP-bound enzyme structure. Prp43 adopts an open conformation after ATP binding and switches into the closed conformation after binding to RNA. Prp43 translocates RNA via its Hook-Turn | Thermochaetoides thermophila | ? | - |
- |
|
| additional information | RNA loading mechanism of Prp43, and catalytic mechanism, detailed overview. Prp43 binds RNA in a sequence-independent fashion. Analysis of interactions between Prp43 and the U7-RNA and of the ATP-bound enzyme structure. Prp43 adopts an open conformation after ATP binding and switches into the closed conformation after binding to RNA. Prp43 translocates RNA via its Hook-Turn | Thermochaetoides thermophila IMI 039719 | ? | - |
- |
|
| additional information | RNA loading mechanism of Prp43, and catalytic mechanism, detailed overview. Prp43 binds RNA in a sequence-independent fashion. Analysis of interactions between Prp43 and the U7-RNA and of the ATP-bound enzyme structure. Prp43 adopts an open conformation after ATP binding and switches into the closed conformation after binding to RNA. Prp43 translocates RNA via its Hook-Turn | Thermochaetoides thermophila DSM 1495 | ? | - |
- |
|
| additional information | RNA loading mechanism of Prp43, and catalytic mechanism, detailed overview. Prp43 binds RNA in a sequence-independent fashion. Analysis of interactions between Prp43 and the U7-RNA and of the ATP-bound enzyme structure. Prp43 adopts an open conformation after ATP binding and switches into the closed conformation after binding to RNA. Prp43 translocates RNA via its Hook-Turn | Thermochaetoides thermophila CBS 144.50 | ? | - |
- |
|
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| CTHT_0005780 | - |
Thermochaetoides thermophila |
| DEAH-box RNA helicase | - |
Thermochaetoides thermophila |
| Prp43 | - |
Thermochaetoides thermophila |
| spliceosomal DEAH-box RNA helicase | - |
Thermochaetoides thermophila |
Turnover Number [1/s]
| Turnover Number Minimum [1/s] | Turnover Number Maximum [1/s] | Substrate | Comment | Organism | Structure |
|---|---|---|---|---|---|
| 0.084 | - |
ATP | recombinant enzyme mutant ctPrp43-IDSB, pH and temperature not specified in the publication | Thermochaetoides thermophila | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| evolution | helicase Prp43 is an outstanding member of the DEAH-box subfamily since it has implications in different substantive cellular processes | Thermochaetoides thermophila |
| additional information | RNA loading mechanism of Prp43, overview. Prp43 binds RNA in a sequence-independent fashion. Analysis of crystal structures of Prp43 complexes in different functional states and the analysis of structure-based mutants providing insights into the unwinding and loading mechanism of RNAs. The Prp43-ATP-analogue-RNA complex shows the localization of the RNA inside a tunnel formed by the two RecA-like and C-terminal domains. In the ATP-bound state this tunnel can be transformed into a groove prone for RNA binding by large rearrangements of the C-terminal domains. Several conformational changes between the ATP- and ADP-bound states explain the coupling of ATP hydrolysis to RNA translocation, mainly mediated by a beta-turn of the RecA1 domain containing the identified RF motif. This mechanism is clearly different to those of other RNA helicases. Prp43 adopts an open conformation after ATP binding and switches into the closed conformation after binding to RNA. Active site structures, localization of the Hook-Turn in the RecA1 domain and of the Hook-Loop in the RecA2 domain in the ctPrp43DELTAN-U7-ADP-BeF3- complex structure | Thermochaetoides thermophila |
| physiological function | the DEAH-box helicase Prp43 is a key player in pre-mRNA splicing as well as the maturation of rRNAs, RNA loading mechanism of Prp43, detailed overview. Prp43 acts at the latest stage of the splicing cycle and it is required to dismantle the intron-lariat spliceosome into the excised lariat and the U2-U5-U6 snRNPs. The target substrate of Prp43 during this process is the RNA network between the U2 snRNP and the branch site of the intron. In the spliceosome, Prp43 is crosslinked exclusively to the pre-mRNA and not to any snRNAs. The opening of the tunnel by the displacement of the C-terminal domains is crucial for the helicase function of Prp43 | Thermochaetoides thermophila |
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