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Literature summary for 1.17.4.1 extracted from
- Nucleoside analogue triphosphates allosterically regulate human ribonucleotide reductase and identify chemical determinants that drive substrate specificity (2016), Biochemistry, 55, 5884-5896 .
Activating Compound
| Activating Compound | Comment | Organism | Structure |
|---|---|---|---|
| ATP | binding of deoxynucleoside triphosphate effectors (ATP/dATP, dGTP, and dTTP) modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. The unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP | Homo sapiens |  |
| ATP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop. The unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Saccharomyces cerevisiae | |
| ATP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop. The unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Homo sapiens | |
| dATP | binding of deoxynucleoside triphosphate effectors (ATP/dATP, dGTP, and dTTP) modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. The unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP | Homo sapiens | |
| dATP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop.. The unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Saccharomyces cerevisiae | |
| dATP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop.. The unprotonated N1 of adenosine is the primary determinant of ATP/dATP-directed specificity for CDP. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Homo sapiens | |
| dGTP | binding of deoxynucleoside triphosphate effectors (ATP/dATP, dGTP, and dTTP) modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. The O6 and protonated N1 of dGTP direct specificity for ADP | Homo sapiens | |
| dGTP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop. The O6 and protonated N1 of dGTP direct specificity for ADP. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Saccharomyces cerevisiae | |
| dGTP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop. The O6 and protonated N1 of dGTP direct specificity for ADP. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Homo sapiens | |
| dTTP | binding of deoxynucleoside triphosphate effectors (ATP/dATP, dGTP, and dTTP) modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. The 5-methyl, O4, and N3 groups of dTTP contributes to specificity for GDP | Homo sapiens | |
| dTTP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Saccharomyces cerevisiae | |
| dTTP | binding of deoxynucleoside triphosphate effectors ATP/dATP, dGTP, and dTTP modulates the specificity of class I ribonucleotide reductase for CDP, UDP, ADP, and GDP substrates. dNTP effectors and NDP substrates bind on either side of a flexible nine-amino acid loop. Interactions with the effector nucleobase alter loop 2 geometry, resulting in changes in specificity among the four NDP substrates of ribonucleotide reductase | Homo sapiens | |
Cloned(Commentary)
| Cloned (Comment) | Organism |
|---|---|
| expression in Escherichia coli BL-21 (DE3) | Saccharomyces cerevisiae |
| expression in Escherichia coli BL-21 (DE3) | Homo sapiens |
Protein Variants
| Protein Variants | Comment | Organism |
|---|---|---|
| D287A | the mutant enzyme (mutation in the ribonucleoside-diphosphate reductase large subunit RRM1) is deficient in allosteric regulation by dGTP and dTTP, but not ATP/dATP | Homo sapiens |
| D287A | the mutant enzyme is deficient in allosteric regulation by dGTP and dTTP, but not ATP/dATP | Homo sapiens |
Organism
| Organism | UniProt | Comment | Textmining |
|---|---|---|---|
| Homo sapiens | P23921 | ribonucleoside-diphosphate reductase large subunit | - |
| Homo sapiens | P23921 and P31350 | P23921: ribonucleoside-diphosphate reductase large subunit RRM1, P31350: ribonucleoside-diphosphate reductase subunit RRM2 | - |
| Saccharomyces cerevisiae | - |
- |
- |
Purification (Commentary)
| Purification (Comment) | Organism |
|---|---|
- |
Saccharomyces cerevisiae |
- |
Homo sapiens |
Substrates and Products (Substrate)
| Substrates | Comment Substrates | Organism | Products | Comment (Products) | Rev. | Reac. |
|---|---|---|---|---|---|---|
| ADP + thioredoxin | - |
Saccharomyces cerevisiae | 2'-dADP + thioredoxin disulfide + H2O | - |
? | |
| ADP + thioredoxin | - |
Homo sapiens | 2'-dADP + thioredoxin disulfide + H2O | - |
? | |
| CDP + thioredoxin | - |
Homo sapiens | 2'-dCDP + thioredoxin disulfide + H2O | - |
? | |
| CDP + thioredoxin | CDP is the favored substrate. However, the kcat/Km values for ADP, GDP, and UDP are within 100-fold of the value for CDP | Saccharomyces cerevisiae | 2'-dCDP + thioredoxin disulfide + H2O | - |
? | |
| CDP + thioredoxin | for ATP-bound enzyme CDP is the favored substrate | Homo sapiens | 2'-dCDP + thioredoxin disulfide + H2O | - |
? | |
| GDP + thioredoxin | - |
Saccharomyces cerevisiae | 2'-dGDP + thioredoxin disulfide + H2O | - |
? | |
| GDP + thioredoxin | - |
Homo sapiens | 2'-dGDP + thioredoxin disulfide + H2O | - |
? | |
| UDP + thioredoxin | - |
Saccharomyces cerevisiae | 2'-dUDP + thioredoxin disulfide + H2O | - |
? | |
| UDP + thioredoxin | - |
Homo sapiens | 2'-dUDP + thioredoxin disulfide + H2O | - |
? | |
Synonyms
| Synonyms | Comment | Organism |
|---|---|---|
| class I ribonucleotide reductase | - |
Saccharomyces cerevisiae |
| class I ribonucleotide reductase | - |
Homo sapiens |
General Information
| General Information | Comment | Organism |
|---|---|---|
| metabolism | the enzyme maintains balanced pools of deoxyribonucleotide substrates for DNA replication by converting ribonucleoside diphosphates to 2'-deoxyribonucleoside diphosphates | Saccharomyces cerevisiae |
| metabolism | the enzyme maintains balanced pools of deoxyribonucleotide substrates for DNA replication by converting ribonucleoside diphosphates to 2'-deoxyribonucleoside diphosphates | Homo sapiens |
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