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Literature summary for 2.7.7.7 extracted from

  • Zhang, H.; Eoff, R.L.; Kozekov, I.D.; Rizzo, C.J.; Egli, M.; Guengerich, F.P.
    Structure-function relationships in miscoding by Sulfolobus solfataricus DNA polymerase Dpo4: guanine N2,N2-dimethyl substitution produces inactive and miscoding polymerase complexes (2009), J. Biol. Chem., 284, 17687-17699.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
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Saccharolobus solfataricus

Crystallization (Commentary)

Crystallization (Comment) Organism
Dpo4 in complex with DNA duplex containing N2,N2-dimethyl-substituted guanine-modified template, sitting drop vapor diffusion method, using 10-15% polyethylene glycol 3350 (w/v), 30 mM NaCl, 100 mM MgCl2, and 3% glycerol (v/v) Saccharolobus solfataricus
sitting drop, vapor-diffusion method with the reservoir solution containing 10–15% polyethylene glycol 3350 (w/v), 30 mm NaCl, 100 mm MgCl2, and 3% glycerol (v/v). One crystal structure of Dpo4 with a primer having a 3'-terminal dideoxycytosine opposite template N2,N2-dimethylguanine in a post-insertion position shows dideoxycytosine folded back into the minor groove, as a catalytically incompetent complex. A second crystal has two unique orientations for the primer terminal dideoxycytosine as follows: (I) flipped into the minor groove and (II) a long pairing with N2,N2-dimethylguanine in which one hydrogen bond exists between the O-2 atom of dideoxycytosine and the N-1 atom of N2,N2-dimethylguanine, with a second water-mediated hydrogen bond between the N-3 atom of dideoxycytosine and the O-6 atom of N2,N2-dimethylguanine. A crystal structure of Dpo4 with dTTP opposite template N2,N2-dimethylguanine reveals a wobble orientation Saccharolobus solfataricus

Inhibitors

Inhibitors Comment Organism Structure
N2,N2-dimethyl guanine the presence of N2,N2-dimethyl guanine lowers the catalytic efficiency for incorporation of dCTP of DNA polymerase Dpo4 16000fold Saccharolobus solfataricus
N2,N2-dimethylguanine the presence of N2,N2-dimethylguanine lowers the catalytic efficiency of the DNA polymerase Dpo4 16000fold. Dpo4 inserts dNTPs almost at random during bypass of N2,N2-dimethylguanine, and much of the enzyme is kinetically trapped by an inactive ternary complex when N2,N2-dimethylguanine is present Saccharolobus solfataricus

Organism

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

Purification (Commentary)

Purification (Comment) Organism
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Saccharolobus solfataricus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
deoxynucleoside triphosphate + DNAn
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Saccharolobus solfataricus diphosphate + DNAn+1
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?
deoxynucleoside triphosphate + DNAn
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Saccharolobus solfataricus P2 diphosphate + DNAn+1
-
?

Synonyms

Synonyms Comment Organism
DNA polymerase Dpo4
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Saccharolobus solfataricus