Cloned (Comment) | Organism |
---|---|
expression of His-tagged enzyme | Human immunodeficiency virus 1 |
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 | 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 | Comment | Organism | Structure |
---|---|---|---|
Mg2+ | required | Human immunodeficiency virus 1 | |
additional information | metal coordination, structure, overview | Human immunodeficiency virus 1 |
Organism | UniProt | Comment | Textmining |
---|---|---|---|
Human immunodeficiency virus 1 | P0C6F2 | HIV-1 | - |
Human immunodeficiency virus 1 HXB2 | P0C6F2 | HIV-1 | - |
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 | 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 | Comment | Organism |
---|---|---|
RNase H | - |
Human immunodeficiency virus 1 |
Temperature Optimum [°C] | Temperature Optimum Maximum [°C] | Comment | Organism |
---|---|---|---|
37 | - |
assay at | Human immunodeficiency virus 1 |
pH Optimum Minimum | pH Optimum Maximum | Comment | Organism |
---|---|---|---|
7.8 | - |
assay at | Human immunodeficiency virus 1 |