Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.25.1 (deoxyribonuclease)
 1,471 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The activities of three human DNA metabolizing enzymes--uracil-DNA glycosylase, apurinic/apyrimidinic(AP)-DNA binding protein (an AP-DNA endonuclease) and the major cellular deoxyribonuclease (presumably DNase III and/or DNase IV)--were measured in logarithmic growing (diploid non-established) fibroblast strains, tumor-derived cell lines and SV40-transformed cell lines. The levels of activity of uracil-DNA glycosylase and DNase were increased, on average, 5- to 6-fold in tumor cell lines and 10-fold in SV40-transformed cell lines compared to those observed in normal fibroblast strains. AP-DNA binding activity was only 2- to 3-fold higher in both tumor-derived and SV40-transformed cell lines. Measurements in serum-deprived (and hence growth-retarded) SV40-transformed cells indicated that the observed increase in enzyme activity was only partially due to a higher proportion of S-phase cells in the rapidly growing transformed lines. Cell extract mixing experiments indicated that the relatively low levels of activity of the three enzymes in normal fibroblasts could not be ascribed to the presence of an inhibitory factor(s) in the crude extract.
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PMID:Increased uracil-DNA glycosylase, AP-DNA binding protein and deoxyribonuclease activities in tumor and SV40-transformed cell lines of human origin. 168 17

The paper is an outline review of the main aspects concerning the formation and repair of AP (apurinic/apyrimidinic) sites in DNA as well as some of the chemical properties allowing their quantitative determination. A new method for the measurement of AP sites based on their reaction with [14C]methoxyamine is described. It has been applied to the measurement of AP sites produced in DNA either by physical (gamma-rays) or chemical (methyl methanesulphonate, osmium tetroxide) agents. The method has also been used to quantify the excision of abnormal bases from DNA under the action of specific DNA glycosylases and to prevent the chemical or enzymatic degradation of DNA containing AP sites. The paper contains data about the purification and characterization of uracil-DNA glycosylase and AP endodeoxyribonuclease from carrot cells, two enzymes involved in the first steps of base excision repair through AP site intermediates. The biological effects of unrepaired AP sites are also discussed.
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PMID:Formation, detection and repair of AP sites. 244 77

This paper describes the use of methoxyamine to study the enzymatic reactions catalyzed by uracil-DNA glycosylase and by AP (apurinic/apyrimidinic) endodeoxyribonuclease isolated from mammalian cells. [14C]Methoxyamine permits one to follow the formation of AP sites in a uracil-containing polydeoxyribonucleotide incubated with calf thymus uracil-DNA glycosylase. The number of methoxyamine-reacted AP sites is equal to that of uracil released. Methoxyamine has no effect on the uracil-DNA glycosylase activity and may be added together with the enzyme in order to block the AP sites and prevent the degradation of the polynucleotide by the AP endonucleases that may be present in a crude preparation. Addition of methoxyamine to AP sites prevents not only the enzymatic hydrolysis of the adjacent phosphodiester bond but also the degradation of the polynucleotide by NaOH. This protective effect disappears after methoxyamine is removed by acetaldehyde.
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PMID:A new approach to the study of the base-excision repair pathway using methoxyamine. 258 Aug 33

Uracil-DNA glycosylase and apurinic/apyrimidinic (AP) endodeoxyribonuclease have been purified from cultured carrot cells. The two enzymes, separated by affinity chromatography on Sepharose-poly(rU), were found to have properties similar to those of the homologous bacterial and mammalian enzymes. The action of AP endodeoxyribonuclease on (dA)230 . (dT, dU)230 partially depyrimidinated by uracil-DNA glycosylase suggests that these two enzymes might act successively to initiate the repair of uracil-containing DNA.
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PMID:Base-excision repair in carrot cells. Partial purification and characterization of uracil-DNA glycosylase and apurinic/apyrimidinic endodeoxyribonuclease. 628 2

[3H]Thymine-labeled poly(dA) . poly(dT) carrying many apyrimidinic (AP) sites has been prepared by treating an enzymatically synthesized poly(dA) . poly(dT, dU) with uracil-DNA glycosylase. Incubation of the polymer with a homogeneous preparation of T4 endonuclease V resulted in conversion of the labeled material into acid-soluble forms. Native DNA with apurinic sites was also cleaved by the enzyme. Single-stranded polymers, poly(dT) carrying AP sites or poly(dT) with thymine dimers, were barely attacked by T4 endonuclease V. The polymer whose aldehyde moieties at AP sites were reduced to alcoholic forms was not susceptible to the enzyme. The site of endonucleolytic cleavage was determined by using alternating copolymers whose phosphate groups were differentially labeled. The result is consistent with the view that T4 endonuclease V cleaves a phosphodiester linkage on the 3'-side of AP sites, producing chains terminated at their 3'-ends with base-free deoxyribose and at their 5'-ends with phosphate.
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PMID:Action of T4 endonuclease V on polydeoxyribonucleotides with apyrimidinic or apurinic sites. 711 62

Any uracil bases in DNA, a result of either misincorporation or deamination of cytosine, are removed by uracil-DNA glycosylase (UDG), one of the most efficient and specific of the base-excision DNA-repair enzymes. Crystal structures of human and viral UDGs complexed with free uracil have indicated that the enzyme binds an extrahelical uracil. Such binding of undamaged extrahelical bases has been seen in the structures of two bacterial methyltransferases and bacteriophage T4 endonuclease V. Here we characterize the DNA binding and kinetics of several engineered human UDG mutants and present the crystal structure of one of these, which to our knowledge represents the first structure of any eukaryotic DNA repair enzyme in complex with its damaged, target DNA. Electrostatic orientation along the UDG active site, insertion of an amino acid (residue 272) into the DNA through the minor groove, and compression of the DNA backbone flanking the uracil all result in the flipping-out of the damaged base from the DNA major groove, allowing specific recognition of its phosphate, deoxyribose and uracil moieties. Our structure thus provides a view of a productive complex specific for cleavage of uracil from DNA and also reveals the basis for the enzyme-assisted nucleotide flipping by this critical DNA-repair enzyme.
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PMID:A nucleotide-flipping mechanism from the structure of human uracil-DNA glycosylase bound to DNA. 890 Feb 70

A wide range of cytotoxic and mutagenic DNA bases are removed by different DNA glycosylases, which initiate the base excision repair pathway. DNA glycosylases cleave the N-glycosylic bond between the target base and deoxyribose, thus releasing a free base and leaving an apurinic/apyrimidinic (AP) site. In addition, several DNA glycosylases are bifunctional, since they also display a lyase activity that cleaves the phosphodiester backbone 3' to the AP site generated by the glycosylase activity. Structural data and sequence comparisons have identified common features among many of the DNA glycosylases. Their active sites have a structure that can only bind extrahelical target bases, as observed in the crystal structure of human uracil-DNA glycosylase in a complex with double-stranded DNA. Nucleotide flipping is apparently actively facilitated by the enzyme. With bacteriophage T4 endonuclease V, a pyrimidine-dimer glycosylase, the enzyme gains access to the target base by flipping out an adenine opposite to the dimer. A conserved helix-hairpin-helix motif and an invariant Asp residue are found in the active sites of more than 20 monofunctional and bifunctional DNA glycosylases. In bifunctional DNA glycosylases, the conserved Asp is thought to deprotonate a conserved Lys, forming an amine nucleophile. The nucleophile forms a covalent intermediate (Schiff base) with the deoxyribose anomeric carbon and expels the base. Deoxyribose subsequently undergoes several transformations, resulting in strand cleavage and regeneration of the free enzyme. The catalytic mechanism of monofunctional glycosylases does not involve covalent intermediates. Instead the conserved Asp residue may activate a water molecule which acts as the attacking nucleophile.
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PMID:DNA glycosylases in the base excision repair of DNA. 922 23