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Literature summary for 2.7.7.7 extracted from

  • Perlow-Poehnelt, R.A.; Likhterov, I.; Wang, L.; Scicchitano, D.A.; Geacintov, N.E.; Broyde, S.
    Increased flexibility enhances misincorporation: temperature effects on nucleotide incorporation opposite a bulky carcinogen-DNA adduct by a Y-family DNA polymerase (2007), J. Biol. Chem., 282, 1397-1408.
    View publication on PubMed

Organism

Organism UniProt Comment Textmining
Saccharolobus solfataricus
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-
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Saccharolobus solfataricus Q97W02
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Saccharolobus solfataricus P2
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-
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Saccharolobus solfataricus P2 Q97W02
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-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
deoxynucleoside triphosphate + DNAn the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4 Saccharolobus solfataricus diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity Saccharolobus solfataricus diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn the molecular dynamics simulations suggest that mismatched nucleotide insertion opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG is increased at 55°C compared with 37°C because the higher temperature shifts the preference of the damaged base from the anti to the syn conformation, with the carcinogen on the more open major groove side. The mismatched dNTP structures are less distorted when the damaged base is syn than when it is anti, at the higher temperature. With the normal partner dCTP, the anti conformation with close to Watson-Crick alignment remains more favorable. The molecular dynamics simulations are consistent with the kcat values for nucleotide incorporation opposite the lesion studied, providing structural interpretation of the experimental observations. The observed temperature effect suggests that conformational flexibility plays a role in nucleotide incorporation and bypass fidelity opposite 10S-(+)-trans-anti-[benzo[a]pyrene]-N2-dG by Dpo4 Saccharolobus solfataricus P2 diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn the rate of mismatched nucleotide incorporation is greater than the rate of correct dC insertion at 55 °C, whereas at 37 °C there is little selectivity Saccharolobus solfataricus P2 diphosphate + DNAn+1
-
?

Synonyms

Synonyms Comment Organism
Dpo4
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Saccharolobus solfataricus