Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.30.2 (endonuclease)
 18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The accuracy with which Escherichia coli DNA polymerase I (Pol I) copies natural DNA in vitro has been determined. When phi X174 viral DNA containing an amber mutation (am3) is primed with a single restriction endonuclease fragment, copied in vitro with Pol I and then expressed in E. coli spheroplasts (Weymout, L. A., and Loeb, L. A. (1978) Proc. Natl. Acad. Sci. U. S. A. 75, 1924), the reversion frequency of this DNA is greater than that of uncopied DNA. This change in reversion frequency can be increased by selectively increasing the concentration of either dATP or dCTP relative to the other deoxyribonucleotide substrates. DNA sequence analyses of revertants obtained from substrate pool bias experiments demonstrates that the revertants contain the selectively biased nucleotide as an incorrect substitution at position 587 of the am3 codon. We have analyzed the product of the in vitro Pol I reaction using neutral and alkaline sucrose gradients. Fifty per cent of the input phi X174 DNA template molecules are copied past the am3 site. The phenotypic expression of the product (revertant) strand in the spheroplast assay was estimated using a model heteroduplex molecule similar in structure to the product of the reaction and containing a single base mismatch (A:A or A:C) at position 587. Using these data, and by extrapolation from pool bias experiments, we estimate the error rate of Pol I in Mg2+-activated reactions using equimolar concentrations of the four deoxynucleotide substrates is 1/680,000 for an A:C mispair and < 1/6,300,000 for an A:A mispair at position 587 of the am3 codon in phi X174 DNA.
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PMID:On the fidelity of DNA replication. The accuracy of Escherichia coli DNA polymerase I in copying natural DNA in vitro. 644 43

An enzyme activity to incorporate labeled dATP or dGTP preferentially into depurinated DNA, found in an extract of Escherichia coli, does not seem to represent "purine insertase," but may be ascribed to a combined action of DNA polymerase I and AP endonuclease(s) on the basis of the following findings. (1) The activity was found in polA+ but not in polA-cells. (2) The base moiety and the alpha-phosphate group of the nucleotide were equally incorporated into the DNA.
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PMID:Are purine bases enzymatically inserted into depurinated DNA in Escherichia coli? 675 12

A DNA ligase has been purified from a subnuclear soluble replication complex isolated from adenovirus type 2-infected human KB cells. DNA ligase activity could not be demonstrated using an exogenous template until the complex was dissociated, suggesting that the ligase activity may be a component of the complex. The purified enzyme was free of endonuclease, exonuclease, 5'-nucleotidase, and phosphatase activities, and had a molecular weight of 105 000, as estimated by sedimentation in a glycerol gradient. The ligase requires ATP and a divalent cation for activity. The optimum of the reaction is at pH 7.8 in 50--100 mM Tris-HCl buffer and 10--20 mM MgCl2. Monovalent salts greatly stimulate ligase activity and the optimum was found at 150 mM. The reaction is very sensitive to high temperature; maximum activity was observed at 25--30 degrees C. ATP is the sole required cofactor and NAD, dATP and GTP could not replace the requirement for ATP. The Km for ATP is 60 microM. The Km for DNA is 250 microgram/ml or 1.6 nmol of terminal phosphate/ml and thus the enzyme shows relatively weak affinity for exogenous DNA. The maximum conversion of 32P into a phosphatase-resistant form is approximately 1.3% of the total, whereas T4 ligase, under the same conditions, can convert more than 25% of phosphate into a resistant form.
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PMID:Purification and properties of a DNA ligase from a soluble DNA replication complex. 735 2

A typing method for bacteria was developed and applied to several species, including Escherichia coli and Actinobacillus actinomycetemcomitans. Total genomic DNA was digested with a restriction endonuclease, and fragments were enabled with [alpha-32P]dATP by using the Klenow fragment of DNA polymerase and separated by electrophoresis in 6% polyacrylamide/8 M urea (sequencing gel). Depending on the restriction endonuclease and the bacterium, the method produced approximately 30-50 well-separated fragments in the size range of 100-400 nucleotides. For A. actinomycetemcomitans, all strains had bands in common. Nevertheless, many polymorphisms could be observed, and the 31 strains tested could be classified into 29 distinct types. Furthermore, serotype-specific fragments could be assigned for the three serotypes investigated. The method described is very sensitive, allowing more distinct types to be distinguished than other commonly used typing methods. When the method was applied to 10 other clinically relevant bacterial species, both species-specific bands and strain-specific bands were found. Isolates from different locations of one patient showed indistinguishable patterns. Computer-assisted analysis of the DNA fingerprints allowed the determination of similarity coefficients. It is concluded that genomic fingerprinting by restriction fragment end labeling (RFEL) is a powerful and generally applicable technique to type bacterial species.
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PMID:Genomic DNA fingerprinting by restriction fragment end labeling. 777 50

16s and 23s ribosomal DNA (rDNA) genes were amplified form E. coli, labelled with [alpha- 32P] dATP by nick translation, and applied as conserved gene probes to detecting broad-spectrum rDNA. rDNA fingerprinting analysis of Enterobacter cloacae (E. cloacae) isolated form an outbreak of nosocomial infection and other hospital environmental sources was conducted with digestion by different restrictive endonuclease, such as Hind III, EcoRI, BamHI, Bgl I, et al. Results showed rDNA fingerprinting of E. cloacae strains isolated from 10 patients with nosocomial infection was the same as that from other sources. It suggested E. cloacae causing this outbreak was originated from one genetic clone, and its source of infection was the tubes and humidifying bottles for oxygenation. rDNA fingerprinting technique is accurate, reliable, specific and repeatable, and will plays important roles in identification and classification of bacteria, tracking the source of transmission of nosocomial infection.
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PMID:[Ribosomal DNA fingerprinting analysis of Enterobacter cloacae isolated from an outbreak of nosocomial infection]. 784 91

The bacteriophage lambda terminase is composed of two subunits, gpNu1 and gpA. In vitro, the holoenzyme is a site-specific endonuclease, helicase, ATPase, and can package lambda DNA into proheads. gpA possesses ATPase and helicase activities which are similar to those of the holoenzyme. Both terminase and gpA can hydrolyze a wide range of deoxyribo- and ribonucleoside triphosphates to inorganic phosphate and the corresponding diphosphate. Nucleoside diphosphates are not substrates for either protein. ATPase of both proteins is stimulated by double-stranded DNA. The ATPase of gpA is protein concentration-dependent, while that of terminase is not. Helicase activity of both proteins is not concentration-dependent, and requires a hydrolyzable triphosphate. ATP, dATP, and GTP supported helicase activity, while adenosine 5'-(beta, gamma-methylene)triphosphate, adenosine 5'-3-O-(thio)triphosphate, ADP, CTP, and UTP did not. The kinetic parameters of ATPase and helicase activities were similar for both proteins, but packaging with terminase was optimal only at a significantly higher level of ATP. Packaging was detectable at significant levels with CTP and UTP, but not with GTP. Packaging also differed from ATPase and helicase in the utilization of divalent metal cations and susceptibility to various inhibitors.
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PMID:The in vitro ATPases of bacteriophage lambda terminase and its large subunit, gene product A. The relationship with their DNA helicase and packaging activities. 817 94

Terminases are enzymes common to all of the complex double-stranded DNA viruses and are required for viral assembly. These enzymes function to excise a single viral genome from a concatemeric DNA precursor and package it into a preformed protective protein shell or capsid. ATP hydrolysis by these enzymes has been described and appears to be critical to the packaging process. We have previously characterized the endonuclease activity of purified terminase from bacteriophage lambda [Tomka, M. A., & Catalano, C. E. (1993) J. Biol. Chem. 268, 3056-3065], and we describe here a kinetic characterization of the ATPase activity of the enzyme. lambda Terminase possesses a DNA-stimulated ATPase activity and hydrolyzes ATP to ADP and Pi. This activity requires divalent metal and is supported by all of the group IIa metals examined, as well as Mn2+. The reaction is also stimulated by NaCl, GTP, and dGTP. Of note is that neither of the guanosine nucleotides is hydrolyzed by the enzyme, while dATP is hydrolyzed at a rate comparable to that of ATP. Kinetic analysis of the ATPase activity revealed two apparent binding sites for ATP hydrolysis. The high-affinity site (Km = 5 microM) and low-affinity site (Km approximately 1.3 mM) hydrolyze ATP with kcat = 3 and 16 min-1, respectively. While the high-affinity site is unaffected by the presence of DNA, ATP hydrolysis at the low-affinity site is stimulated by DNA, which results from both a decrease in the Km and a concomitant increase in the kcat of the reaction.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Kinetic characterization of the ATPase activity of the DNA packaging enzyme from bacteriophage lambda. 821 75

Tyrosine hydroxylase (TH) cDNA has been characterized in rodents and primates, but only a few studies have been developed in ungulates, except in cows. Because sheep is a species used for many physiological studies, it was of interest to clone TH cDNA in this species. Ovine TH cDNA was purified from a library of sheep adrenal glands. The entire cDNA was 1,721 bp long. It presented a higher percentage of similarity with bovine TH cDNA (93%) than with rodent cDNAs (75%). The deduced amino acid sequence was 490 amino acids long and had 96% similarity with the bovine amino acid sequence. The entire cDNA and different fragments obtained with endonuclease restriction enzymes were cloned in plasmid pUC 18 and were labeled with 35S-dATP to detect TH mRNA by in situ hybridization. Strong labelings were observed on adrenal medulla and on noradrenergic and dopaminergic neurons in the sheep but also in the cow and pig. This labeling matched completely TH immunohistochemical staining obtained on the same sections with anti-TH antibodies. Ovine TH cDNA is a useful tool to study the variations of TH mRNA levels in sheep catecholaminergic neurons.
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PMID:Isolation and characterization of ovine tyrosine hydroxylase mRNA. 910 44

We have studied mutagenic specificity of an abasic site by the yeast-transformation procedure using an oligonucleotide containing a single furan-type abasic site. The recipient yeast used was deficient in the major AP endonuclease (apn1). Sequence analysis of the transformants suggested that dATP was incorporated most frequently opposite the abasic site, while dGTP seemed to be incorporated opposite the abasic site in the recipient proficient in apn1. To explore the mechanism of this oligonucleotide transformation, we have also analyzed the transformation with phosphorothioate oligonucleotides with mismatched 3'-end. The results are discussed.
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PMID:Yeast oligonucleotide transformation: its mechanism and application to analysis of mutations induced by defined DNA lesions. 958 13

To gain further insights into the biological functions of Dna2, previously known as a cellular replicative helicase in Saccharomyces cerevisiae, we examined biochemical properties of the recombinant Dna2 protein purified to homogeneity. Besides the single-stranded (ss) DNA-dependent ATPase activity as reported previously, we were able to demonstrate that ssDNA-specific endonuclease activity is intrinsically associated with Dna2. Moreover, Dna2 was capable of degrading duplex DNA in an ATP-dependent fashion. ATP and dATP, the only nucleotides hydrolyzed by Dna2, served to stimulate Dna2 to utilize duplex DNA, indicating their hydrolysis is required. Dna2 was able to unwind short duplex only under the condition where the endonuclease activity was minimized. This finding implies that Dna2 unwinds only partially the 3'-end of duplex DNA and generates a stretch of ssDNA of limited length, which is subsequently cleaved by the ssDNA-specific endonuclease activity. A point mutation at the conserved ATP-binding site of Dna2 inactivated concurrently ssDNA-dependent ATPase, ATP-dependent nuclease, and helicase activities, indicating that they all reside in Dna2 itself. By virtue of its nucleolytic activities, the Dna2 protein may function in the maintenance of chromosomal integrity, such as repair or other related process, rather than in propagation of cellular replication forks.
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PMID:Dna2 of Saccharomyces cerevisiae possesses a single-stranded DNA-specific endonuclease activity that is able to act on double-stranded DNA in the presence of ATP. 975 35


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