Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.7 (DNA polymerase)
17,007 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

We have studied a mutant Moloney murine leukemia virus with a deletion in reverse transcriptase (RT) which is predicted to make its RNase H domain resemble structurally that of human immunodeficiency virus RT. This deletion was based on improved RNase H homology alignments made possible by the recently solved three-dimensional structure for Escherichia coli RNase H. This mutant Moloney murine leukemia virus RT was fully active in the oligo(dT)-poly(rA) DNA polymerase assay and retained nearly all of wild-type RT's RNase H activity in an in situ RNase H gel assay. However, proviruses reconstructed to include this deletion were noninfectious. Minus-strand strong-stop DNA was made by the deletion mutant, but the amount of minus-strand translocation was intermediate to the very low level measured with RNase H-null virions and the high level seen with wild-type RT. The average length of translocated minus-strand DNA was shorter for the deletion mutant than for wild type, suggesting that mutations in the RNase H domain of RT also affect DNA polymerase activity.
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PMID:Defects in Moloney murine leukemia virus replication caused by a reverse transcriptase mutation modeled on the structure of Escherichia coli RNase H. 137 May 51

In situ transcription (IST) was shown to be useful for the detection of human enteroviral RNA in cultured cells. A primer to detect a wide variety of enteroviral genomes and a coxsackievirus type B3 genome-specific primer were demonstrated to be efficient in IST assays. Transcription times greater than 10 to 30 min did not significantly improve the acquisition of a specific signal, whereas the signal-to-noise ratio decreased with time. Inclusion of actinomycin D to suppress DNA-dependent DNA polymerase activity in reverse transcriptase decreased the signal that was obtained without improving the signal-to-noise ratio. Use of RNase H-free murine leukemia virus reverse transcriptase in the IST reaction increased the signal versus that obtained by use of the avian myeloblastosis virus enzyme, which contains endogenous RNase H activity. Exogenous RNase H added to the transcription reaction ablated the signal. Background transcription because of poorly hybridized (mismatched) primers was reduced after primer hybridization and prior to the transcription reaction by rinsing fixed cells with 3 M tetramethylammonium chloride at temperatures which dissociate mismatched primer-template duplexes. The rapid detection time and the simplicity of application suggest that IST can be performed with a high specificity for the detection of enteroviral genomic sequences in cultured cells and may be more useful than in situ hybridization for the detection of enteroviral genomes.
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PMID:Detection of enteroviruses in cell cultures by using in situ transcription. 137 Aug 49

Early events in the retroviral replication cycle include the conversion of viral genomic RNA into linear double-stranded DNA. This process is mediated by the reverse transcriptase (RT), a multifunctional enzyme that possesses RNA-dependent DNA polymerase, DNA-dependent DNA polymerase, and RNase H activities. In the course of studies of a recombinant RT of human immunodeficiency virus type 1 (HIV-1), we observed an additional, unexpected activity of the enzyme. The purified RT catalyzes a specific cleavage in HIV-1 RNA hybridized to tRNALys, the primer for HIV-1 reverse transcription. The cleavage at the primer binding site (PBS) of HIV RNA is dependent on the double-stranded structure of the HIV RNA-tRNALys complex. This RNase activity appears to be distinct from the RNase H activity of HIV-1 RT, as the substrate specificity and the products of the two activities are different. Moreover, Escherichia coli RNase H and avian myeloblastosis virus RT are unable to cleave the HIV RNA-tRNALys complex. We refer to this unusual activity as RNase D. Two lines of evidence indicate that the specific RNase D activity is an integral part of recombinant HIV RT. The specific RNase D activity comigrates with the other RT activities, DNA polymerase, and RNase H upon filtration on a Superose 6 gel column or chromatography on a phosphocellulose column. Moreover, three recombinant HIV-1 RT preparations expressed and purified in different laboratories by various procedures exhibit RNase D activity. Sequence analysis indicated that RNase D activity cleaves the substrate HIV-1 RNA-tRNALys at two distinct sites within the PBS sequence 5'-UGGCGCCCGA decreases ACAG decreases GGAC-3'. The sequence specificity of RNase D activity suggests that it might be involved in two stages during the reverse transcription process: displacement of the PBS to enable copying of tRNALys sequences into plus-strand DNA or to facilitate the second template switch, which was postulated to occur at the PBS sequence.
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PMID:Double-stranded RNA-dependent RNase activity associated with human immunodeficiency virus type 1 reverse transcriptase. 137 Oct 14

The reverse transcriptases (RTs) from human immunodeficiency viruses types 1 and 2 (HIV-1 and HIV-2, respectively) are relatively highly related yet there are several significant differences in their catalytic activities. In an attempt to relate these functional dissimilarities to the differences in amino acid sequences, we have employed a novel approach of constructing chimeric molecules composed of complementary amino acid sequences derived from the two HIV RTs. These recombinant proteins were analyzed for their enzymatic activities and for their sensitivity to tetrahydroimidazo[4,5,1-jk][1,4]benzodiazepin-2[1H]-one and thione (TIBO), which selectively inhibits only HIV-1 RT. The active chimeric RTs were used to map the TIBO binding site on the HIV-1 RT molecules and to localize the putative sequences responsible for the high RNase H activity of HIV-1 RT relative to that of HIV-2 RT. The results suggest that TIBO interacts with amino acid residues located around residue 200 within the DNA polymerase domain of HIV-1 RT which shows a relatively low similarity to HIV-2 RT. The difference in the RNase H activity maps to a position in the DNA polymerase domain rather than to the RNase H domain. Out of the 12 chimeric RTs generated, four were either fully active or hyperactive, three others lost most of their catalytic activities, and the rest were totally inactive. The pattern of catalytic activities of these hybrid proteins can be explained by a model for the initial folding of HIV RTs, which entails the formation of three distinct and independently folded regions. Each region can be formed by amino acid sequences derived exclusively from either HIV-1 RT or HIV-2 RT.
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PMID:The catalytic functions of chimeric reverse transcriptases of human immunodeficiency viruses type 1 and type 2. 137 Dec 74

We have studied the effects of a natural carotenoid, identified as halocynthiaxanthin, on the enzymatic activities associated with the recombinant preparations of the reverse transcriptases (RTs) of human immunodeficiency viruses (HIV) types 1 and 2. The carotenoid was found to be a potent inhibitor of the RNA-dependent DNA polymerase activity (with 50% inhibition obtained at 5-7 microM halocynthiaxanthin), whereas the DNA-dependent DNA polymerase function of both RTs was significantly less sensitive to the inhibitor. Conversely, the ribonuclease H activity associated with the two HIV RTs was essentially insensitive to the carotenoid. The RNA-dependent DNA polymerase function of RT is the only unique activity found in this enzyme that is not expressed at significant levels in uninfected eukaryotic cells. Therefore, it is possible that this carotenoid may serve as a good candidate for the development of novel potent and specific inhibitors of HIV RT.
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PMID:The carotenoid halocynthiaxanthin: a novel inhibitor of the reverse transcriptases of human immunodeficiency viruses type 1 and type 2. 137 77

Phosphorothioate oligodeoxycytidine (S-dCn) was used as a model compound to examine the impact of the number of phosphorothioate linkages and their position on the inhibition of human DNA polymerases and RNase H in vitro. S-dCn with a chain length longer than 15 could inhibit human DNA polymerases and RNase H activities, in a linkage number-dependent manner. Longer oligomers were more potent inhibitors than shorter ones. Kinetic studies indicated that S-dC28 was a competitive inhibitor of DNA polymerase alpha and beta with respect to the DNA template, whereas it was a noncompetitive inhibitor of polymerases gamma and delta. S-dC28 was also a competitive inhibitor of RNase H1 and H2 with respect to RNA-DNA duplex. Susceptibility of these enzymes to inhibition by S-dC28 was in the order of delta approximately gamma greater than alpha greater than beta and RNase H1 greater than RNase H2. Structural-activity relationships were explored with a group of S-dC28 analogs that have phosphorothioate internucleotide linkages at various positions. The inhibitory effect depended on the total number of thioate linkages, rather than the position of the linkages within the oligomer or the chain length itself. No sequence specificity was found. In the presence of the complementary RNA, antisense phosphorothioates (S-oligos) exerted a biphasic effect on RNase H activity. At low concentrations S-oligos could enhance the cleavage of the RNA portion of S-oligo-RNA duplex, whereas at high concentrations (in excess of the complementary RNA) S-oligos could inhibit RNase H and protect the complementary RNA from degradation. Together, these results suggest that the non-sequence-specific inhibitory effect of S-oligos should be taken into consideration in designing antisense inhibitors. This inhibitory activity could be avoided by decreasing the number of phosphorothioate linkages at the backbone, and S-oligos of 15-20 residues are preferable in antisense molecule design.
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PMID:Phosphorothioate oligonucleotides are inhibitors of human DNA polymerases and RNase H: implications for antisense technology. 137 82

Luo and Taylor (J. Virol. 64:4321-4328, 1990) have previously shown that when, during RNA-directed DNA synthesis, a retroviral reverse transcriptase comes to a halt at the end of an RNA template, the associated RNase H produces a specific oligonucleotide that contains the 5' end of that template; in those studies the length of the oligonucleotide was predominantly 17 nucleotides. We have now investigated variables that might affect the formation and length of such a terminal oligonucleotide. We found small but significant variations in the length could be caused by the choice of reaction conditions and also the sources of reverse transcriptase and RNA template. Nevertheless, the general finding in all these situations was that RNase H acted at or about 14 to 18 nucleotides from the 5' end, thereby supporting the interpretation that in the reverse transcriptase, the cleavage site for the RNase H is held at around this distance behind the DNA polymerase activity. In other words, it appears that for the intact protein, the RNase H and reverse transcriptase activities may work in a coupled or coordinate manner. We also found that more than 80% of the residual 5' oligonucleotides remained base paired to the RNA-directed DNA product. Furthermore, under certain conditions, these short RNAs could act as efficient primers for an associated DNA-directed DNA synthesis in the reverse direction.
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PMID:When retroviral reverse transcriptases reach the end of their RNA templates. 137 69

A 3.5 angstrom resolution electron density map of the HIV-1 reverse transcriptase heterodimer complexed with nevirapine, a drug with potential for treatment of AIDS, reveals an asymmetric dimer. The polymerase (pol) domain of the 66-kilodalton subunit has a large cleft analogous to that of the Klenow fragment of Escherichia coli DNA polymerase I. However, the 51-kilodalton subunit of identical sequence has no such cleft because the four subdomains of the pol domain occupy completely different relative positions. Two of the four pol subdomains appear to be structurally related to subdomains of the Klenow fragment, including one containing the catalytic site. The subdomain that appears likely to bind the template strand at the pol active site has a different structure in the two polymerases. Duplex A-form RNA-DNA hybrid can be model-built into the cleft that runs between the ribonuclease H and pol active sites. Nevirapine is almost completely buried in a pocket near but not overlapping with the pol active site. Residues whose mutation results in drug resistance have been approximately located.
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PMID:Crystal structure at 3.5 A resolution of HIV-1 reverse transcriptase complexed with an inhibitor. 137 3

A series of biochemical investigations to compare the DNA polymerase and RNase H functions of the reverse transcriptases (RTs) corresponding to azidothymidine (AZT)-sensitive and -resistant human immunodeficiency virus (HIV) strains are described. Steady-state kinetic studies with purified recombinant enzymes utilizing several templates and three inhibitors, 3' azido-3' deoxythymidine triphosphate (AZTTP), 3-amino-thymidine 5'-triphosphate, and 2',3'-didehydro-2',3'-dideoxythymidine 5'-triphosphate, found consistent 2-4-fold differences between the enzymes from the two strains over a wide pH range. A strong pH dependence for all three inhibitors was found at pH values below 7.4 and suggested an ionizable group on the enzyme with a pK of about 7. The sensitivities of the RNase H activities of the two enzymes to AZTTP and AZTMP were also compared and found to be similar. The nucleotide incorporation fidelities of recombinant RTs corresponding to AZT-sensitive and -resistant clinical isolates were compared and the error specificities determined. No significant differences were found. Both enzymes were equally able to incorporate AZTTP into an elongating M13 DNA strand with concomitant chain termination. Purified wild-type and mutant virions from cell-culture supernatants were compared in "endogenous" DNA synthesis reactions, and the sensitivities of this activity to AZTTP were found to be similar. The contrast between the small differences found in this study and the high level of viral resistance in tissue culture presumably reflects an incomplete understanding of AZT inhibition of HIV in the cell.
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PMID:Biochemical studies on the reverse transcriptase and RNase H activities from human immunodeficiency virus strains resistant to 3'-azido-3'-deoxythymidine. 137 38

The mobile element jockey is similar in structural organization and coding potential to the LINEs of various organisms. Current models of the mechanism of transposition involve reverse transcription of an RNA intermediate and utilization of element-encoded proteins. As it is demonstrated here, a 2.23 kb DNA fragment from the region of the jockey encoding the putative reverse transcriptase, was stably introduced into the expression system under inducible control of the Escherichia coli lac regulatory elements. We describe the expression of the 92 kDa protein and identify this polypeptide alone as authentic jockey reverse transcriptase based on some of its physical and enzymic properties. The jockey polymerase demonstrates RNA-directed and DNA-directed DNA polymerase activities, but lacks detectable RNase H, has a temperature optimum at 26 degrees C, requires Mg2+ or Mn2+ as a cofactor and is inactivated by sulfhydryl reagent. The enzyme prefers poly(rC) and poly(rA) as template and "activated" DNA is not effective. The results of this work suggest that the RNA-directed DNA polymerase coded by jockey elements may be involved in the transcription of the elements.
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PMID:[Cloning and expression in Escherichia coli of reverse transcriptase coded by the mobile genetic element jockey]. 138 Jun 45


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