Literature summary for 2.7.7.7 extracted from

Ishido, T.; Yamazaki, N.; Ishikawa, M.; Hirano, K.
Characterization of DNA polymerase beta from Danio rerio by overexpression in E. coli using the in vivo/in vitro compatible pIVEX plasmid (2011), Microb. Cell Fact., 10, 84.

Cloned(Commentary)

Cloned (Comment)	Organism
pol beta in vitro/in vivo dual expression using plasmid pIVEX, overexpression in Escherichia coli strain BL21(DE3), strain BL21(DE3)pLysS, and strain KRX, and in vitro as a C-terminal His-tagged protein. Pol beta expressed in vitro is subject to proteolysis, therefore, bacterial overexpression is used to produce the protein for kinetic analyses. KRX cells are preferred because of their reduced propensity for leaky expression of pol beta	Danio rerio

Cloned (Comment)

Organism

pol beta in vitro/in vivo dual expression using plasmid pIVEX, overexpression in Escherichia coli strain BL21(DE3), strain BL21(DE3)pLysS, and strain KRX, and in vitro as a C-terminal His-tagged protein. Pol beta expressed in vitro is subject to proteolysis, therefore, bacterial overexpression is used to produce the protein for kinetic analyses. KRX cells are preferred because of their reduced propensity for leaky expression of pol beta

Danio rerio

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.00132	-	dTTP	pH 8.8, 30°C, recombinant enzyme, in presence of Mn2+	Danio rerio
0.01469	-	dTTP	pH 8.8, 30°C, recombinant enzyme, in presence of Mg2+	Danio rerio

Metals/Ions

Metals/Ions	Comment	Organism
KCl	activates best at 10 mM	Danio rerio
Mg2+	activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+	Danio rerio
Mn2+	activates, Mn2+ shows a 8.6fold higher catalytic efficiency than Mg2+	Danio rerio
NaCl	activates best at 50 mM	Danio rerio

Natural Substrates/ Products (Substrates)

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

Organism

Organism	UniProt	Comment	Textmining
Danio rerio	Q6DRD3	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
deoxynucleoside triphosphate + DNAn	-	Danio rerio	diphosphate + DNAn+1	-	?
dTTP + DNAn	-	Danio rerio	diphosphate + DNAn+1	-	?

Synonyms

Synonyms	Comment	Organism
DNA polymerase beta	-	Danio rerio
pol beta	-	Danio rerio

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	-	Danio rerio

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.0096	-	dTTP	pH 8.8, 30°C, recombinant enzyme, in presence of Mn2+	Danio rerio
0.0123	-	dTTP	pH 8.8, 30°C, recombinant enzyme, in presence of Mg2+	Danio rerio

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
9	-	-	Danio rerio

General Information

General Information	Comment	Organism
evolution	compared to mammalian pol betas, the Danio rerio enzyme contains a P63D amino acid substitution. This substitution lies in a hairpin sequence within an 8-kDa domain, likely to be important in DNA binding	Danio rerio

kcat/KM [mM/s]

kcat/KM Value [1/mMs^-1]	kcat/KM Value Maximum [1/mMs^-1]	Substrate	Comment	Organism	Structure
0.83	-	dTTP	pH 8.8, 30°C, recombinant enzyme, in presence of Mg2+	Danio rerio
7.16	-	dTTP	pH 8.8, 30°C, recombinant enzyme, in presence of Mn2+	Danio rerio