Literature summary for 3.1.13.2 extracted from

Shaw-Reid, C.A.; Feuston, B.; Munshi, V.; Getty, K.; Krueger, J.; Hazuda, D.J.; Parniak, M.A.; Miller, M.D.; Lewis, D.
Dissecting the effects of DNA polymerase and ribonuclease H inhibitor combinations on HIV-1 reverse-transcriptase activities (2005), Biochemistry, 44, 1595-1606.

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Cloned(Commentary)

Cloned (Comment)	Organism
expression of wild-type and mutant enzymes in Escherichia coli strain BL21(DE3)	Human immunodeficiency virus 1

Protein Variants

Protein Variants	Comment	Organism
E89K	site-directed mutagenesis, foscarnet-resistance mutation, the mutant enzyme shows different sensitivity for inhibitors compared to the wild-type enzyme, overview	Human immunodeficiency virus 1
K103N	site-directed mutagenesis, NNRTI-resistance mutation, the mutant enzyme shows different sensitivity for inhibitors compared to the wild-type enzyme, overview	Human immunodeficiency virus 1

Inhibitors

Inhibitors	Comment	Organism	Structure
4-(1-chloro-1,1-difluoromethyl)-4-(2-phenylethynyl)-6-chloro-2H-3,1-benzoxazin-2-one	i.e. NNRTI, an efavirenz analogue, IC50 values for wild-type enzyme are 0.000002-0.000005 mM with substrates DNA-17-nucleotide-RNA hybrid or DNA-18-nucleotide-RNA hybrid, and 0.001 mm for substrate DNA-15-nucleotide-RNA hybrid or DNA-16-nucleotide-RNA hybrid, effect on mutant enzymes, overview	Human immunodeficiency virus 1
4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid	a diketo acid RNase H inhibitor, IC50 values for wild-type and mutant enzymes are 0.002-0.0035 mM with all substrates, effect on mutant enzymes, overview	Human immunodeficiency virus 1
additional information	effects of reverse transcriptase polymerase domain inhibitors on RNase H activity dependent on the substrate, overview, no inhibition of RNase H by nucleoside analogue 3'-azido-3'-deoxythymidine triphosphate	Human immunodeficiency virus 1
Phosphonoformate	the inhibitor that bind in the reverse transcriptase polymerase domain inhibits also RNase H activity, IC value for the wild-type enzyme is 0.0015 mM versus substrate DNA-18-nucleotide-RNA hybrid, with the other substrates the IC50 value is above 0.025 mM	Human immunodeficiency virus 1

KM Value [mM]

KM Value [mM]	KM Value Maximum [mM]	Substrate	Comment	Organism	Structure
additional information	-	additional information	kinetics	Human immunodeficiency virus 1
0.000007	-	DNA-17-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1
0.000011	-	DNA-18-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1
0.000052	-	DNA-16-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1
0.000053	-	DNA-15-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1

Metals/Ions

Metals/Ions	Comment	Organism	Structure
KCl	activates	Human immunodeficiency virus 1
Mg2+	activates	Human immunodeficiency virus 1

Organism

Organism	UniProt	Comment	Textmining
Human immunodeficiency virus 1	-	i.e. HIV-1	-

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg]	Specific Activity Maximum [µmol/min/mg]	Comment	Organism
additional information	-	-	Human immunodeficiency virus 1

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
DNA-15-nucleotide-RNA hybrid + H2O	-	Human immunodeficiency virus 1	?	-	?
DNA-16-nucleotide-RNA hybrid + H2O	-	Human immunodeficiency virus 1	?	-	?
DNA-17-nucleotide-RNA hybrid + H2O	-	Human immunodeficiency virus 1	?	-	?
DNA-18-nucleotide-RNA hybrid + H2O	-	Human immunodeficiency virus 1	?	-	?
DNA-RNA hybrid + H2O	fluorescent-labeled RNA-DNA duplex of 15, 16, 17, or 18 nucleotide-RNA and in each case 18 nucleotide-DNA, overview	Human immunodeficiency virus 1	?	-	?
additional information	the enzyme is part of the viral reverse transcriptase residing on distinct domains of the enzyme with the DNA polymerase activity	Human immunodeficiency virus 1	?	-	?

Synonyms

Synonyms	Comment	Organism
More	the enzyme is part of the viral reverse transcriptase	Human immunodeficiency virus 1
ribonuclease H	-	Human immunodeficiency virus 1
RNase H	-	Human immunodeficiency virus 1

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Human immunodeficiency virus 1

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	Organism	Structure
0.0018	-	DNA-17-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1
0.0032	-	DNA-18-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1
0.0135	-	DNA-15-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1
0.017	-	DNA-16-nucleotide-RNA hybrid	pH 7.8, 37°C, recombinant wild-type enzyme	Human immunodeficiency virus 1

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7.8	-	assay at	Human immunodeficiency virus 1

Ki Value [mM]

Ki Value [mM]	Ki Value maximum [mM]	Inhibitor	Comment	Organism	Structure
additional information	-	additional information	inhibition kinetics	Human immunodeficiency virus 1

IC50 Value

IC50 Value	IC50 Value Maximum	Comment	Organism	Inhibitor	Structure
0.00002	0.00005	i.e. NNRTI, an efavirenz analogue, IC50 values for wild-type enzyme are 0.00002-0.00005 mM with substrates DNA-17-nucleotide-RNA hybrid or DNA-18-nucleotide-RNA hybrid	Human immunodeficiency virus 1	4-(1-chloro-1,1-difluoromethyl)-4-(2-phenylethynyl)-6-chloro-2H-3,1-benzoxazin-2-one
0.001	-	0.001 mM for substrate DNA-15-nucleotide-RNA hybrid or DNA-16-nucleotide-RNA hyb	Human immunodeficiency virus 1	4-(1-chloro-1,1-difluoromethyl)-4-(2-phenylethynyl)-6-chloro-2H-3,1-benzoxazin-2-one
0.002	0.0035	a diketo acid RNase H inhibitor, IC50 values for wild-type and mutant enzymes are 0.002-0.0035 mM with all substrates, effect on mutant enzymes, overview	Human immunodeficiency virus 1	4-[5-(benzoylamino)thien-2-yl]-2,4-dioxobutanoic acid
0.025	-	the inhibitor that bind in the reverse transcriptase polymerase domain inhibits also RNase H activity, IC value for the wild-type enzyme is 0.0015 mM versus substrate DNA-18-nucleotide-RNA hybrid, with the other substrates the IC50 value is above 0.025 mM	Human immunodeficiency virus 1	Phosphonoformate

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Release 2023.1 (January 2023)