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Literature summary for 2.7.7.6 extracted from
- Macromolecular micromovements: how RNA polymerase translocates (2009), Curr. Opin. Struct. Biol., 19, 701-707.
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| crystal structure of the core enzyme at 3.3 A resolution | Thermus aquaticus |
| crystal structure of the core enzyme at about 3.3 A resolution | Saccharomyces cerevisiae |
| crystal structure of the core enzyme at about 3.3 A resolution | Saccharolobus solfataricus |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | Thermus aquaticus | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | ? | - |
? |  |
| additional information | Thermus thermophilus | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | ? | - |
? | |
| additional information | Escherichia coli | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | ? | - |
? | |
| additional information | Saccharomyces cerevisiae | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | ? | - |
? | |
| additional information | Saccharolobus solfataricus | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | ? | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | - |
- |
- |
| Saccharolobus solfataricus | - |
- |
- |
| Saccharomyces cerevisiae | - |
- |
- |
| Thermus aquaticus | - |
- |
- |
| Thermus thermophilus | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | Thermus aquaticus | ? | - |
? | |
| additional information | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | Thermus thermophilus | ? | - |
? | |
| additional information | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | Escherichia coli | ? | - |
? | |
| additional information | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | Saccharomyces cerevisiae | ? | - |
? | |
| additional information | multi-subunit DNA-dependent RNA polymerases synthesize RNA molecules thousands of nucleotides long. The reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the DNA template, or threading of the DNA and the nascent RNA molecule through the enzyme. Reiteration of the nucleotide addition/translocation cycle without dissociation from the DNA and RNA requires both isomorphic and metamorphic conformational flexibility of a magnitude substantial enough to accommodate the requisite molecular motions | Saccharolobus solfataricus | ? | - |
? | |
| additional information | RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview | Thermus aquaticus | ? | - |
? | |
| additional information | RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview | Thermus thermophilus | ? | - |
? | |
| additional information | RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview | Escherichia coli | ? | - |
? | |
| additional information | RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview | Saccharomyces cerevisiae | ? | - |
? | |
| additional information | RNAP adds nucleotides to the 3'-end of the growing RNA and translocates reiteratively, in single nucleotide steps. Translocation mechanism models, concerning conformational changes, allosteric effects and isomerization, and model evaluation, overview | Saccharolobus solfataricus | ? | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| More | conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview | Thermus aquaticus |
| More | conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview | Thermus thermophilus |
| More | conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview | Escherichia coli |
| More | conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview | Saccharomyces cerevisiae |
| More | conformational plasticity of the active center and importance of the bridge helix structure for enzyme activity, overview | Saccharolobus solfataricus |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| DNA-dependent RNA polymerase | - |
Thermus aquaticus |
| DNA-dependent RNA polymerase | - |
Thermus thermophilus |
| DNA-dependent RNA polymerase | - |
Escherichia coli |
| DNA-dependent RNA polymerase | - |
Saccharomyces cerevisiae |
| DNA-dependent RNA polymerase | - |
Saccharolobus solfataricus |
| RNA polymerase | - |
Thermus aquaticus |
| RNA polymerase | - |
Thermus thermophilus |
| RNA polymerase | - |
Escherichia coli |
| RNA polymerase | - |
Saccharomyces cerevisiae |
| RNA polymerase | - |
Saccharolobus solfataricus |
| RNAP | - |
Thermus aquaticus |
| RNAP | - |
Thermus thermophilus |
| RNAP | - |
Escherichia coli |
| RNAP | - |
Saccharomyces cerevisiae |
| RNAP | - |
Saccharolobus solfataricus |
General Information
| General Information | Comment | Organism |
|---|---|---|
| malfunction | reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation | Thermus aquaticus |
| malfunction | reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation | Thermus thermophilus |
| malfunction | reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation | Escherichia coli |
| malfunction | reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation | Saccharomyces cerevisiae |
| malfunction | reverse translocation, i.e. backtracking, by a distance of one or more nucleotides disrupts the configuration of the catalytic center, leading to a temporary, spontaneously resolved, halt of the RNAP, called pausing, or to a transition into an irreversible arrested state. The latter can be restored to functionality by the endonucleolytic cleavage of the RNA or by pushing the backtracked complex from behind. Non-backtracked paused complexes are also described for bacterial RNAPs, where addition of the incoming NTP is hindered owing to isomerization of the active site into an inactive conformation | Saccharolobus solfataricus |
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