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Literature summary for 2.7.7.7 extracted from

  • Zang, H.; Irimia, A.; Choi, J.Y.; Angel, K.C.; Loukachevitch, L.V.; Egli, M.; Guengerich, F.P.
    Efficient and high fidelity incorporation of dCTP opposite 7,8-dihydro-8-oxodeoxyguanosine by Sulfolobus solfataricus DNA polymerase Dpo4 (2006), J. Biol. Chem., 281, 2358-2372.
    View publication on PubMed

Cloned(Commentary)

Cloned (Comment) Organism
expression in Escherichia coli Saccharolobus solfataricus

Crystallization (Commentary)

Crystallization (Comment) Organism
crystal structures of Dpo4 complexes with oligonucleotides are solved with C, A, and G nucleoside triphosphates placed opposite 8-oxoG Saccharolobus solfataricus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.00044
-
dCTP pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5' Saccharolobus solfataricus
0.0077
-
dCTP pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
0.02
-
dATP pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5' Saccharolobus solfataricus
0.028
-
dGTP pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5' Saccharolobus solfataricus
0.086
-
dGTP pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
0.18
-
dATP pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus

Natural Substrates/ Products (Substrates)

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

Organism

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

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
dATP + DNAn
-
Saccharolobus solfataricus ?
-
?
dATP + DNAn
-
Saccharolobus solfataricus P2 ?
-
?
dCTP + DNAn
-
Saccharolobus solfataricus ?
-
?
dCTP + DNAn
-
Saccharolobus solfataricus P2 ?
-
?
deoxynucleoside triphosphate + DNAn
-
Saccharolobus solfataricus diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine Saccharolobus solfataricus diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays Saccharolobus solfataricus diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn
-
Saccharolobus solfataricus P2 diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine Saccharolobus solfataricus P2 diphosphate + DNAn+1
-
?
deoxynucleoside triphosphate + DNAn when insertion is opposite an unmodified G, insertion of dATP or dGTP is 1000 less efficient than dCTP. For insertion opposite 8-oxoG, the order of decreasing efficiency is dCTP, dATP, dGTP, with an order of magnitude or more difference in catalytic efficiency (kcat/Km) in each pair of comparisons. The insertion of dCTP opposite G and 8-oxoG shows similar catalytic efficiency, even with differences in the trends for kcat and Km. 90fold higher incorporation efficiency of dCTP compared to dATP opposite 8-oxoG and 4fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. The 8-oxoG:C pair shows classic Watson-Crick geometry; the 8-oxoG:A pair is in the syn:anti configuration, with the A hybridized in a Hoogsteen pair with 8-oxoG. With dGTP placed opposite 8-oxoG, pairing was not to the 8-oxoG but to the 5'C (and in classic Watson-Crick geometry), consistent with the low frequency of this frameshiftevent observed in the catalytic assays Saccharolobus solfataricus P2 diphosphate + DNAn+1
-
?
dGTP + DNAn
-
Saccharolobus solfataricus ?
-
?

Synonyms

Synonyms Comment Organism
DNA polymerase Dpo4
-
Saccharolobus solfataricus
DNA polymerase IV
-
Saccharolobus solfataricus
Dpo4
-
Saccharolobus solfataricus
SSO2448 locus name Saccharolobus solfataricus

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
37
-
assay at Saccharolobus solfataricus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
additional information
-
additional information DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine Saccharolobus solfataricus
0.000083
-
dATP pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
0.00038
-
dGTP pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5' Saccharolobus solfataricus
0.00068
-
dGTP pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
0.0025
-
dATP pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5' Saccharolobus solfataricus
0.005
-
dCTP pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8oxoG)CACT-5' Saccharolobus solfataricus
0.013
-
dCTP pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
7.8
-
assay at Saccharolobus solfataricus

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
additional information
-
additional information DNA polymerase IV (Dpo4) shows 90-fold higher incorporation efficiency of dCTP > dATP opposite 8-oxoG and 4-fold higher efficiency of extension beyond an 8-oxoG:C pair than an 8-oxoG:A pair. The catalytic efficiency for these events (with dCTP or C) is similar for G and 8-oxoG templates. Extension beyond an 8-oxoG:C pair is similar to G:C and faster than for an 8-oxoG:A pair, in contrast to other polymerases. dCTP insertion opposite 8-oxoG was lower than for opposite guanine Saccharolobus solfataricus
0.00046
-
dATP pH 7.8, 37°C, incorporation of dATP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
0.008
-
dGTP pH 7.8, 37°C, incorporation of dGTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
0.014
-
dGTP pH 7.8, 37°C, incorporation of dGTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5' Saccharolobus solfataricus
0.125
-
dATP pH 7.8, 37°C, incorporation of dATP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5' Saccharolobus solfataricus
1.7
-
dCTP pH 7.8, 37°C, incorporation of dCTP opposite (G) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(G)CACT-5' Saccharolobus solfataricus
11.36
-
dCTP pH 7.8, 37°C, incorporation of dCTP opposite (8oxoG) in the double stranded oligonucleotide: 5'-GGGGGAAGGATTC-3'/3'-CCCCCTTCCTAAG(8ocoG)CACT-5' Saccharolobus solfataricus