Literature summary for 2.7.7.7 extracted from

Cahova, H.; Panattoni, A.; Kielkowski, P.; Fanfrlik, J.; Hocek, M.
5-Substituted pyrimidine and 7-substituted 7-deazapurine dNTPs as substrates for DNA polymerases in competitive primer extension in the presence of natural dNTPs (2016), ACS Chem. Biol., 11, 3165-3171 .

Application

Application	Comment	Organism
synthesis	the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved	Geobacillus stearothermophilus
synthesis	the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved	Thermococcus kodakarensis
synthesis	the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved	Pyrococcus woesei
synthesis	the very good competition of 7-substituted 7-deazapurine dNTPs, and still reasonably good activity of 5-substituted pyrimidine dNTPs, in the presence of their natural counterparts is very encouraging for further development of methods of polymerase synthesis of modified DNA and for possible in cellulo and even in vivo applications if satisfactory delivery of modified dNTPs will be solved	Thermococcus litoralis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism
0.0032	-	TTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0041	-	7-phenyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0053	-	dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0056	-	7-phenyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.006	-	5-phenyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0061	-	7-methyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0063	-	5-ethynyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0067	-	dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0073	-	7-ethynyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0075	-	7-ethynyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0079	-	5-phenyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0087	-	dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0095	-	7-vinyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0109	-	7-vinyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0111	-	7-methyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0125	-	7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0131	-	5-vinyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0141	-	5-vinyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
0.0151	-	5-ethynyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	Geobacillus stearothermophilus	-	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	Thermococcus kodakarensis	-	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	Pyrococcus woesei	-	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	Thermococcus litoralis	-	diphosphate + DNAn+1	-	?

Organism

Organism	UniProt	Comment	Textmining
Geobacillus stearothermophilus	-	-	-
Pyrococcus woesei	P61876	-	-
Thermococcus kodakarensis	-	-	-
Thermococcus litoralis	P30317	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.
5-ethynyl-dCTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
5-ethynyl-dUTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
5-phenyl-dCTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
5-phenyl-dUTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
5-vinyl-dCTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
5-vinyl-dUTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-deaza-dGTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-ethynyl-7-deaza-dATP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-ethynyl-7-deaza-dGTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-methyl-7-deaza-dATP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-methyl-7-deaza-dGTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-phenyl-7-deaza-dATP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-phenyl-7-deaza-dGTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-vinyl-7-deaza-dATP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
7-vinyl-7-deaza-dGTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	-	Thermococcus kodakarensis	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	-	Pyrococcus woesei	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	-	Thermococcus litoralis	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTP's (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts	Thermococcus kodakarensis	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts	Pyrococcus woesei	diphosphate + DNAn+1	-	?
a 2'-deoxyribonucleoside 5'-triphosphate + DNAn	systematic study of competition PEX experiments with a series of 7-substituted 7-deazapurine and 5-substituted pyrimidine dNTPs bearing substituents of varying bulkiness in the presence of their natural counterparts (unmodified dNTPs). Most of these modified dNRTP's are good to excellent substrates for Bst and KOD XL polymerases and still moderate to good substrates for Pwo and Vent(exo-) polymerases. 7-Deazapurine dNTPs bearing p-electron-containing substituents (ethynyl and phenyl, as well as 7-vinyl-7-deazaadenine) are generally better substrates of Bst polymerase than natural dATP or dGTP, respectively. The corresponding 5-substituted cytosine dNTPs (dCRTP) are comparable to dCTP, whereas the 5-substituted uracil dURTPs are generally worse substrates than TTP. The measured kinetic parameters follow the same trend and confirm that 7-phenyl-7-deazapurine dNTPs have higher affinity to the active site of the polymerase than their natural counterparts	Thermococcus litoralis	diphosphate + DNAn+1	-	?
dATP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
dCTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
dGTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?
TTP + DNAn	-	Geobacillus stearothermophilus	diphosphate + DNAn+1	-	?

Synonyms

Synonyms	Comment	Organism
KDO XL DNA polymerase	-	Thermococcus kodakarensis
Vent polymerase	-	Thermococcus litoralis

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism
4.6	-	5-ethynyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
5.5	-	7-methyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
6.1	-	dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
6.3	-	7-ethynyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
6.6	-	TTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
7.1	-	7-vinyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
7.5	-	5-phenyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
8	-	dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
9.3	-	5-phenyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
10.4	-	5-ethynyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
12.1	-	7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
12.7	-	7-methyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
13.1	-	dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
13.5	-	7-phenyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
13.7	-	7-phenyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
13.8	-	7-vinyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
15.4	-	5-vinyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
17.5	-	7-ethynyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
17.7	-	5-vinyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism
650	-	7-vinyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
690	-	5-ethynyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
730	-	5-ethynyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
880	-	7-ethynyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
900	-	7-methyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
910	-	dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
970	-	7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
990	-	dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
1100	-	5-vinyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
1140	-	7-methyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
1180	-	5-phenyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
1250	-	5-phenyl-dCTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
1350	-	5-vinyl-dUTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
1450	-	7-vinyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
2060	-	TTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
2330	-	7-ethynyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
2410	-	7-phenyl-7-deaza-dATP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
2470	-	dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus
3340	-	7-phenyl-7-deaza-dGTP	pH and temperature not specified in the publication	Geobacillus stearothermophilus