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Literature summary for 3.1.26.13 extracted from

  • Su, H.P.; Yan, Y.; Prasad, G.S.; Smith, R.F.; Daniels, C.L.; Abeywickrema, P.D.; Reid, J.C.; Loughran, H.M.; Kornienko, M.; Sharma, S.; Grobler, J.A.; Xu, B.; Sardana, V.; Allison, T.J.; Williams, P.D.; Darke, P.L.; Hazuda, D.J.; Munshi, S.
    Structural basis for the inhibition of RNase H activity of HIV-1 reverse transcriptase by RNase H active site-directed inhibitors (2010), J. Virol., 84, 7625-7633.
    View publication on PubMedView publication on EuropePMC

Cloned(Commentary)

Cloned (Comment) Organism
expression of His-tagged enzyme Human immunodeficiency virus 1

Crystallization (Commentary)

Crystallization (Comment) Organism
purified recombinant detagged enzyme, mixing of 8-10 mg/ml protein in 20 mM potassium phosphate, pH 7.0, and 1 mM inhibitor nevirapine, with reservoir buffer containing 100 mM sodium cacodylate, pH 6.8, and 800 mM sodium citrate, in a 1:1 ratio, X-ray diffraction structure determination and analysis. Isolated RNase H domain is crystallized in a buffer containing 100 mM sodium citrate, pH 5.0, and 15 to 20% PEG-8000. Crystals are harvested for inhibitor soaking in the reservoir solution with the addition of 50 mM MnCl2, and 1 mM inhibitor nevirapine, at 4°C. Mn2+ is used as a surrogate for Mg2+ since soaking experiments with Mg2+ cannot reproducibly yield structures with inhibitor bound Human immunodeficiency virus 1

Inhibitors

Inhibitors Comment Organism Structure
3-cyclopentyl-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one
-
Human immunodeficiency virus 1
6-[4-(diethylamino)phenoxy]-3-[ethoxy(hydroxy)methyl]-1,4-dihydroxy-1,8-naphthyridin-2(1H)-one
-
Human immunodeficiency virus 1
ethyl 1,4-dihydroxy-2-oxo-1,2-dihydro-1,8-naphthyridine-3-carboxylate interactions between MK1 and two Mn2+ ions, which are coordinated by the RNase H active site residues D443, E478, D498, and D549, binding structure, overview. In addition, G444, S499, A538, H539, V552, and S553 contribute to the binding site Human immunodeficiency virus 1
additional information structures of naphthyridinone-containing inhibitors bound to the RNase H active site, overview. This class of compounds binds to the active site via two metal ions that are coordinated by catalytic site residues, D443, E478, D498, and D549. The directionality of the naphthyridinone pharmacophore is restricted by the ordering of D549 and H539 in the RNase H domain Human immunodeficiency virus 1
nevirapine a nonnucleoside reverse transcriptase inhibitor, NNRTI Human immunodeficiency virus 1

Metals/Ions

Metals/Ions Comment Organism Structure
Mg2+ required Human immunodeficiency virus 1
additional information metal coordination, structure, overview Human immunodeficiency virus 1

Organism

Organism UniProt Comment Textmining
Human immunodeficiency virus 1 P0C6F2 HIV-1
-
Human immunodeficiency virus 1 HXB2 P0C6F2 HIV-1
-

Purification (Commentary)

Purification (Comment) Organism
recombinant His-tagged enzyme by nickel affinity chromatography, the His6 tag is removed by proteolysis with thrombin, followed by gel filtration Human immunodeficiency virus 1

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information RNA/DNA hybrid duplex substrate Human immunodeficiency virus 1 ?
-
?
additional information RNA/DNA hybrid duplex substrate Human immunodeficiency virus 1 HXB2 ?
-
?

Synonyms

Synonyms Comment Organism
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

pH Optimum

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