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Literature summary for 2.7.7.7 extracted from

  • Johnson, K.A.
    The kinetic and chemical mechanism of high-fidelity DNA polymerases (2010), Biochim. Biophys. Acta, 1804, 1041-1048.
    View publication on PubMedView publication on EuropePMC

Inhibitors

Inhibitors Comment Organism Structure
EDTA complete inhibition Escherichia phage T7
EDTA complete inhibition Homo sapiens

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
additional information
-
additional information kinetics of nucleotide binding and incorporation, detailed overview. Weak binding is followed by a fast conformational change leading to much tighter binding, which is then followed by the chemical reaction, fast release of diphosphate, structure-function modeling Homo sapiens
additional information
-
additional information kinetics of nucleotide binding and incorporation, detailed overview. Weak binding is followed by a fast conformational change leading to much tighter binding, which is then followed by the chemical reaction, following the chemistry step, the enzyme shows fast release of diphosphate and then translocates to allow the binding of the next nucleotide, structure-function modeling. single turnover analysis shows that that the rate of the chemical reaction and the rate of diphosphate release are coincident Escherichia phage T7

Localization

Localization Comment Organism GeneOntology No. Textmining
mitochondrion
-
Homo sapiens 5739
-

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Homo sapiens
Mg2+ required, two metal ion mechanism, nucleotide binds to the enzyme as an Mg–dNTP-2 complex, overview. Mg2+ enforces tetrahedral geometry Escherichia phage T7
Mn2+ supports chemistry, but leads to markedly decreased fidelity by accelerating the rate of incorporation of mismatches, routinely used to generate random mutations during PCR. Mn2+ accommodates square planar, tetrahedral, and octahedral coordination Escherichia phage T7
additional information Ca2+ supports nucleotide binding but not catalysis Escherichia phage T7

Natural Substrates/ Products (Substrates)

Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
deoxynucleoside triphosphate + DNAn Homo sapiens
-
diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn Escherichia phage T7 gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction diphosphate + DNAn+1
-
?

Organism

Organism UniProt Comment Textmining
Escherichia phage T7
-
-
-
Homo sapiens
-
-
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
deoxynucleoside triphosphate + DNAn
-
Homo sapiens diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn
-
Escherichia phage T7 diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn gamma-phosphates of the incoming dNTP, contributing to charge neutralization and alignment of the alpha-phosphate for reaction Escherichia phage T7 diphosphate + DNAn+1
-
?

Synonyms

Synonyms Comment Organism
mitochondrial DNA polymerase
-
Homo sapiens
T7 DNA polymerase
-
Escherichia phage T7

General Information

General Information Comment Organism
additional information structural, kinetic and thermodynamic basis for the extraordinary accuracy of high-fidelity DNA polymerases, overview. The changes in enzyme structure following nucleotide binding govern the fate of the bound nucleotide, and the conformational change plays an essential role in establishing enzyme selectivity, conformational coupling between enzyme structure and fidelity, modeling of the universal mechanism: while the correct substrate induces a structure to facilitate catalysis, the wrong substrate induces a structure to slow catalysis and promote substrate release. Two-step sequence for nucleotide binding, two metal ion mechanism, nucleotide binds to the enzyme as an Mg-dNTP-2 complex, overview Escherichia phage T7
additional information the incorporation of 8-oxo-dGTP and 3'-azido-3'-deoxythymidine 5'-triphosphate by the human mitochondrial DNA polymerase provides an exception to the general rule that diphosphate release is fast. Analysis of the burst kinetics during incorporation of 8-oxo-dGTP shows that the amplitude of the burst is dependent upon the nucleotide concentration, diphosphate release is extremely slow following the incorporation of 3'-azido-3'-deoxythymidine 5'-triphosphate. The reversible chemistry and slow release of diphosphate decreases the specificity constant for the incorporation of 3'-azido-3'-deoxythymidine 5'-triphosphate and 8-oxo-dGTP. Brownian ratchet model, overview Homo sapiens