Literature summary for 3.1.26.4 extracted from

Muroya, A.; Tsuchiya, D.; Ishikawa, M.; Haruki, M.; Morikawa, M.; Kanaya, S.; Morikawa, K.
Catalytic center of an archaeal type 2 ribonuclease H as revealed by X-ray crystallographic and mutational analyses (2001), Protein Sci., 10, 707-714.

Search for more literature for 3.1.26.4

Cloned(Commentary)

Cloned (Comment)	Organism
overexpression of wild-type and several truncated enzymes in Escherichia coli	Thermococcus kodakarensis

Crystallization (Commentary)

Crystallization (Comment)	Organism
purified truncated enzyme RNase HII-213, comprising residues 1-213, metal-bound or metal-free, hanging drop vapour diffusion method, 15% w/v PEG 6000, 200 mM MES, pH 6.5, X-ray diffraction structure determinaion and analysis at 3.5 A resolution	Thermococcus kodakarensis

Protein Variants

Protein Variants	Comment	Organism
D105A	site-directed mutagenesis, nearly inactive mutant	Thermococcus kodakarensis
D135A	site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme	Thermococcus kodakarensis
D7A	site-directed mutagenesis, nearly inactive mutant	Thermococcus kodakarensis
E8A	site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme	Thermococcus kodakarensis
H132A	site-directed mutagenesis, reduced activity compared to the wild-type enzyme	Thermococcus kodakarensis
additional information	construction of several truncation mutants, comprising residues 1-198, 1-203, 1-207, 1-213, or 1-217 of the wild-type enzyme, the truncated mutants' activities are increased or reduced compared to the wild-type enzyme, overview	Thermococcus kodakarensis

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
0.00009	-	RNA*DNA hybrid	wild-type enzyme, pH 8.0, 30°C	Thermococcus kodakarensis
0.00054	-	RNA*DNA hybrid	mutant D135A, pH 8.0, 30°C	Thermococcus kodakarensis
0.00097	-	RNA*DNA hybrid	truncated mutant RNase HII-217, pH 8.0, 30°C	Thermococcus kodakarensis
0.00118	-	RNA*DNA hybrid	mutant E8A, pH 8.0, 30°C	Thermococcus kodakarensis
0.0014	-	RNA*DNA hybrid	mutant H132A, pH 8.0, 30°C	Thermococcus kodakarensis
0.00155	-	RNA*DNA hybrid	truncated mutant RNase HII-207, pH 8.0, 30°C	Thermococcus kodakarensis
0.0019	-	RNA*DNA hybrid	truncated mutant RNase HII-213, pH 8.0, 30°C	Thermococcus kodakarensis
0.00837	-	RNA*DNA hybrid	truncated mutant RNase HII-203, pH 8.0, 30°C	Thermococcus kodakarensis

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Co2+	-	Thermococcus kodakarensis
Mg2+	-	Thermococcus kodakarensis
Mn2+	-	Thermococcus kodakarensis
additional information	type 2 enzyme requires divalent cations	Thermococcus kodakarensis

Organism

Organism	UniProt	Comment	Textmining
Thermococcus kodakarensis	-	type 2 enzyme	-

Purification (Commentary)

Purification (Comment)	Organism
recombinant wild-type and truncated enzymes from Escherichia coli	Thermococcus kodakarensis

Reaction

Reaction	Comment	Organism	Reaction ID
Endonucleolytic cleavage to a 5'-phosphomonoester	the catalytic reaction requires 4 acidic residues, catalytic center and catalytic mechanism of type 1 and type 2 ribonucleases, type 1 enzyme requires a histidine as general base, while type 2 enzyme does not, substrate binding of type 2 enzyme	Thermococcus kodakarensis	a

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
RNA*DNA hybrid + H2O	the C-terminal domain of type 2 enzyme is involved in the interaction with the substrate	Thermococcus kodakarensis	?	-	?

Synonyms

Synonyms	Comment	Organism
KOD1	-	Thermococcus kodakarensis
ribonuclease H	-	Thermococcus kodakarensis
RNase H	-	Thermococcus kodakarensis
Tk-RNase HII	-	Thermococcus kodakarensis
type 2 ribonuclease H	-	Thermococcus kodakarensis
type 2 RNase H	-	Thermococcus kodakarensis

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
30	-	assay at	Thermococcus kodakarensis

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
8	-	assay at	Thermococcus kodakarensis

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Release 2023.1 (January 2023)