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Literature summary for 1.17.4.1 extracted from
- Closing the circle on ribonucleotide reductases (2011), Nat. Struct. Mol. Biol., 18, 251-253.
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| ATP | activation by ATP has a regulatory function | Salmonella enterica subsp. enterica serovar Typhimurium |  |
| ATP | activation by ATP has a regulatory function | Escherichia coli | |
| ATP | activation by ATP has a regulatory function | Pseudomonas aeruginosa | |
Crystallization (Commentary)
| Crystallization (Comment) | Organism |
|---|---|
| low-resolution crystal structure of an alpha2beta2 complex | Salmonella enterica subsp. enterica serovar Typhimurium |
Inhibitors
| Inhibitors | Comment | Organism | Structure |
|---|---|---|---|
| dATP | inhibition by dATP has a regulatory function | Escherichia coli | |
| dATP | inhibition by dATP has a regulatory function | Pseudomonas aeruginosa | |
| dATP | inhibition by dATP has a regulatory function | Salmonella enterica subsp. enterica serovar Typhimurium | |
Natural Substrates/ Products (Substrates)
| Natural Substrates | Organism | Comment (Nat. Sub.) | Natural Products | Comment (Nat. Pro.) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| nucleoside 5'-diphosphate + thioredoxin | Salmonella enterica subsp. enterica serovar Typhimurium | class I and class II RNRs | 2'-deoxynucleoside 5'-diphosphate + thioredoxin disulfide + H2O | - |
? | |
| nucleoside 5'-diphosphate + thioredoxin | Escherichia coli | class I and class II RNRs | 2'-deoxynucleoside 5'-diphosphate + thioredoxin disulfide + H2O | - |
? | |
| nucleoside 5'-diphosphate + thioredoxin | Pseudomonas aeruginosa | class I and class II RNRs | 2'-deoxynucleoside 5'-diphosphate + thioredoxin disulfide + H2O | - |
? | |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Escherichia coli | - |
- |
- |
| Pseudomonas aeruginosa | - |
- |
- |
| Salmonella enterica subsp. enterica serovar Typhimurium | - |
- |
- |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| additional information | in the class I RNRs, a tyrosine radical is generated in the beta2 subunit, a di-ironoxo enzyme. In class II a tyrosine radical is generated directly on alpha or alpha2 by cleavage of adenosylcobalamin. In both cases, the radical is channeled to a cysteine in the active site of the alpha subunit to initiate catalysis | Salmonella enterica subsp. enterica serovar Typhimurium | ? | - |
? | |
| additional information | in the class I RNRs, a tyrosine radical is generated in the beta2 subunit, a di-ironoxo enzyme. In class II a tyrosine radical is generated directly on alpha or alpha2 by cleavage of adenosylcobalamin. In both cases, the radical is channeled to a cysteine in the active site of the alpha subunit to initiate catalysis | Escherichia coli | ? | - |
? | |
| additional information | in the class I RNRs, a tyrosine radical is generated in the beta2 subunit, a di-ironoxo enzyme. In class II a tyrosine radical is generated directly on alpha or alpha2 by cleavage of adenosylcobalamin. In both cases, the radical is channeled to a cysteine in the active site of the alpha subunit to initiate catalysis | Pseudomonas aeruginosa | ? | - |
? | |
| nucleoside 5'-diphosphate + thioredoxin | class I and class II RNRs | Salmonella enterica subsp. enterica serovar Typhimurium | 2'-deoxynucleoside 5'-diphosphate + thioredoxin disulfide + H2O | - |
? | |
| nucleoside 5'-diphosphate + thioredoxin | class I and class II RNRs | Escherichia coli | 2'-deoxynucleoside 5'-diphosphate + thioredoxin disulfide + H2O | - |
? | |
| nucleoside 5'-diphosphate + thioredoxin | class I and class II RNRs | Pseudomonas aeruginosa | 2'-deoxynucleoside 5'-diphosphate + thioredoxin disulfide + H2O | - |
? | |
Subunits
| Subunits | Comment | Organism |
|---|---|---|
| monomer or dimer | class II enzymes show a monomeric or dimeric structure | Salmonella enterica subsp. enterica serovar Typhimurium |
| monomer or dimer | class II enzymes show a monomeric or dimeric structure | Escherichia coli |
| monomer or dimer | class II enzymes show a monomeric or dimeric structure | Pseudomonas aeruginosa |
| More | structures of the active holoenzymes of class I-III RNRs, structure comparisons, overview | Salmonella enterica subsp. enterica serovar Typhimurium |
| More | structures of the active holoenzymes of class I-III RNRs, structure comparisons, overview | Escherichia coli |
| More | structures of the active holoenzymes of class I-III RNRs, structure comparisons, overview | Pseudomonas aeruginosa |
| oligomer | class I enzyme show a alpha2beta2 complex structure, modeling | Salmonella enterica subsp. enterica serovar Typhimurium |
| oligomer | class I enzyme show a alpha2beta2 complex structure, modeling | Pseudomonas aeruginosa |
| oligomer | class I enzymes show a alpha2beta2 complex structure, modeling | Escherichia coli |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| class I RNR | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
| class I RNR | - |
Escherichia coli |
| class I RNR | - |
Pseudomonas aeruginosa |
| class II RNR | - |
Salmonella enterica subsp. enterica serovar Typhimurium |
Cofactor
| Cofactor | Comment | Organism | Structure |
|---|---|---|---|
| thioredoxin | - |
Salmonella enterica subsp. enterica serovar Typhimurium | |
| thioredoxin | - |
Escherichia coli | |
General Information
| General Information | Comment | Organism |
|---|---|---|
| additional information | RNRs are allosterically regulated on two levels, overall activity and substrate specificity. The substrate specificity is regulated by the binding of dNTPs to the specificity site, ATP and dATP upregulate the reduction of CDP and UDP, whereas dTTP upregulates GDP reduction and dGTP increases the rate of ADP reduction. This regulation is essential to maintain balanced dNTP pools for DNA synthesis and repair | Salmonella enterica subsp. enterica serovar Typhimurium |
| additional information | RNRs are allosterically regulated on two levels, overall activity and substrate specificity. The substrate specificity is regulated by the binding of dNTPs to the specificity site, ATP and dATP upregulate the reduction of CDP and UDP, whereas dTTP upregulates GDP reduction and dGTP increases the rate of ADP reduction. This regulation is essential to maintain balanced dNTP pools for DNA synthesis and repair | Pseudomonas aeruginosa |
| additional information | RNRs are allosterically regulated on two levels, overall activity and substrate specificity. The substrate specificity is regulated by the binding of dNTPs to the specificity site, ATP and dATP upregulate the reduction of CDP and UDP, whereas dTTP upregulates GDP reduction and dGTP increases the rate of ADP reduction. This regulation is essential to maintain balanced dNTP pools for DNA synthesis and repair. The overall activity is regulated by the binding of dATP (inhibition) or ATP (stimulation) to the socalled activity site in the ATP cone domain of the alpha2 subunit of RNRs from class Ia | Escherichia coli |
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