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Literature summary 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.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

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

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
3.1.26.4 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

EC Number Protein Variants Comment Organism
3.1.26.4 D105A site-directed mutagenesis, nearly inactive mutant Thermococcus kodakarensis
3.1.26.4 D135A site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme Thermococcus kodakarensis
3.1.26.4 D7A site-directed mutagenesis, nearly inactive mutant Thermococcus kodakarensis
3.1.26.4 E8A site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme Thermococcus kodakarensis
3.1.26.4 H132A site-directed mutagenesis, reduced activity compared to the wild-type enzyme Thermococcus kodakarensis
3.1.26.4 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]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.26.4 0.00009
-
 RNA*DNA hybrid wild-type enzyme, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.00054
-
 RNA*DNA hybrid mutant D135A, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.00097
-
 RNA*DNA hybrid truncated mutant RNase HII-217, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.00118
-
 RNA*DNA hybrid mutant E8A, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.0014
-
 RNA*DNA hybrid mutant H132A, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.00155
-
 RNA*DNA hybrid truncated mutant RNase HII-207, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.0019
-
 RNA*DNA hybrid truncated mutant RNase HII-213, pH 8.0, 30°C Thermococcus kodakarensis
3.1.26.4 0.00837
-
 RNA*DNA hybrid truncated mutant RNase HII-203, pH 8.0, 30°C Thermococcus kodakarensis

Metals/Ions

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

Organism

EC Number Organism UniProt Comment Textmining
3.1.26.4 Thermococcus kodakarensis
-
 type 2 enzyme
-

Purification (Commentary)

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

Reaction

EC Number Reaction Comment Organism Reaction ID
3.1.26.4 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)

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

Synonyms

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

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
3.1.26.4 30
-
 assay at Thermococcus kodakarensis

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.1.26.4 8
-
 assay at Thermococcus kodakarensis