Literature summary for 3.1.26.4 extracted from

Rychlik, M.P.; Chon, H.; Cerritelli, S.M.; Klimek, P.; Crouch, R.J.; Nowotny, M.
Crystal structures of RNase H2 in complex with nucleic acid reveal the mechanism of RNA-DNA junction recognition and cleavage (2010), Mol. Cell, 40, 658-670.

Search for more literature for 3.1.26.4

Cloned(Commentary)

Cloned (Comment)	Organism
expression of wild-type and truncated D107N mutant enzymes in Escherichia coli	Thermotoga maritima

Crystallization (Commentary)

Crystallization (Comment)	Organism
RNase H2 in complex with nucleic acid containing a 5'RNA-DNA3' junction, X-ray diffraction structure determination and analysis at 2.0 A resolution	Thermotoga maritima

Protein Variants

Protein Variants	Comment	Organism
D107N	site-directed mutagenesis, inactive mutant	Thermotoga maritima
G21S	site-directed mutagenesis, the mutation is located in the conserved GRG 2'-OH-sensing motif, the mutant has much lower activity on RNA/DNA and DNA-RNA/DNA in the presence of Mn2+. In the presence of Mg2+ it also shows reduced activity on substrates with (5')RNA-DNA(3') junction	Thermotoga maritima
additional information	construction of a truncated mutant with 15 residues removed from the C-terminus	Thermotoga maritima
R22A	site-directed mutagenesis, the R22A mutation does not alter Tm-RNase H2 activity on most substrates compared to the wild-type enzyme	Thermotoga maritima
Y163F	site-directed mutagenesis, Y163 is a key residue involved in 2'-OH binding, and its mutation to phenylalanine seriously reduces activity against all tested substrates	Thermotoga maritima

Metals/Ions

Metals/Ions	Comment	Organism	Structure
Mg2+	the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview	Thermotoga maritima
Mn2+	the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+, binding structure and activation mechanism, overview	Thermotoga maritima

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
additional information	Thermotoga maritima	RNase H2 hydrolyzes RNA of RNA/DNA hybrids and can nick duplex DNAs containing a single ribonucleotide. It shows a unique mechanism of recognition and substrate-assisted cleavage with preference for junction substrates. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion	?	-	?

Organism

Organism	UniProt	Comment	Textmining
Thermotoga maritima	Q9X017	-	-

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
DNA-RNA-DNA/DNA hybrid + H2O	a duplex containing a (5')RNA-DNA(3') junction with one, three, or six ribonucleotides, i.e. DNA5-RNA1-DNA6/DNA12, DNA3-RNA3-DNA6/DNA12, and RNA6-DNA6/DNA12, and a substrate with a (5')DNA-RNA(3') junction, DNA5-RNA7/DNA12	Thermotoga maritima	?	-	?
additional information	RNase H2 hydrolyzes RNA of RNA/DNA hybrids and can nick duplex DNAs containing a single ribonucleotide. It shows a unique mechanism of recognition and substrate-assisted cleavage with preference for junction substrates. A conserved tyrosine residue distorts the nucleic acid at the junction, allowing the substrate to function in catalysis by participating in coordination of the active site metal ion	Thermotoga maritima	?	-	?
poly(rA)/poly(dT) + H2O	-	Thermotoga maritima	?	-	?
RNA/DNA hybrid + H2O	an RNA/DNA hybrid (RNA12/DNA12)	Thermotoga maritima	?	-	?

Synonyms

Synonyms	Comment	Organism
RNase H2	-	Thermotoga maritima
type 2 RNase H	-	Thermotoga maritima

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.5	10	Mg-dependent hydrolysis activity by Tm-RNase H2 gradually increases from pH 7.5 to 10 without reaching a maximum	Thermotoga maritima
8.5	-	Mn-dependent activity of Tm-RNase H2 is the highest at around pH 8.5	Thermotoga maritima

pH Range

pH Minimum	pH Maximum	Comment	Organism
7.5	10	activity range dependent on cation added	Thermotoga maritima

General Information

General Information	Comment	Organism
additional information	the full-length and C-terminally truncated enzymes have similar activity, and both are around 600fold more active in the presence of Mn2+ compared to Mg2+. Residue Y163 is important for binding of both (5')RNA-DNA(3') junctions and RNA/DNA substrates	Thermotoga maritima
physiological function	RNase H2 junction recognition is important for the removal of RNA embedded in DNA and may play an important role in DNA replication and repair	Thermotoga maritima

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Release 2023.1 (January 2023)