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:3.1.30.2 (endonuclease)
18,621 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

Cytochrome P450 (CYP) 2C9 catalyses the metabolism of a wide range of drugs. Previous studies have shown the differences in the amino acid composition among CYP2C9 variants at Cys144/Arg, Tyr358/Cys, Leu359/Ile, and Gly417/Asp. PCR-endonuclease digestion methods have been developed to detect these four possible polymorphisms. The T416-->C mutation in exon 3 of CYP2C9 (Cys144-->Arg) creates an Ava II site. In the 135 subjects we tested, all leukocyte DNA samples showed a complete Ava II digestion indicating homozygous C416 (Arg144). A Tyr358-->Cys mutation will create a Nsi I site at codon 1057-1063 in exon 7. In 40 subjects tested, all samples showed negative results. DNA sequencing on a few samples showed Tyr358Ile359. A mismatched PCR primer pair was then designed to detect codon C1061-->A (Leu359-->Ile) mutation. In 115 subjects tested, 111 samples showed a complete Nsi I digestion (Ile359) and four samples showed heterozygous results. Another mismatched PCR primer pair was used to confirm the C1061 codon in heterozygous subjects. The four heterozygous subjects showed partial digestion with endonuclease Kpn I, which confirmed the heterozygous Ile/Leu at amino acid 359. The G1236-->A mutation in exon 8 of CYP2C9 (Gly417-->Asp) creates a Hph I site. In all 46 subjects, homozygous G1236 (Gly417) was found. Most Chinese subjects actually have Arg144 Tyr358 Ile359 Gly417 in CYP2C9 as previously reported human-2. Furthermore, we found an A-->T (+12 position in intron 2) mutation in our CYP2C9 sequencing process. The mutation creates a NIa III site.(ABSTRACT TRUNCATED AT 250 WORDS)
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PMID:Detection of CYP2C9 polymorphism based on the polymerase chain reaction in Chinese. 1196 81

Drosophila Rrp1 has several tightly associated enzymatic activities, including double-strand DNA 3'-exonuclease, apurinic/apyrimidinic endonuclease, 3'-phosphatase, and 3'-phosphodiesterase. The carboxyl-terminal third of Rrp1, homologous to Escherichia coli exonuclease III, is sufficient to repair oxidative and alkylation-induced DNA damage in vivo. Using a screen for partial complementation of repair-deficient E. coli, we isolated three mutants of the nuclease domain of Rrp1: T462A, K463Q, and L484P, that protect against methyl methanesulfonate (MMS)-induced but not t-BuO2H-induced DNA damage. Thr-462 and Lys-463 are highly conserved residues found in a cluster of 5 conserved amino acids (LQETK), while Leu-484 is poorly conserved. Gln-460 Glu-461, Thr-462, and Lys-463 and Leu-484 were altered by site-directed mutagenesis using a plasmid including the entire Rrp1 gene and mutant proteins were purified. Mutants of the three residues Glu-461, Thr-462, and Lys-463 demonstrate 8-200-fold lower phosphodiesterase specific activity than wild-type Rrp1. E461A has a 30-fold reduction in AP endonuclease and is MMS-sensitive, but all other mutants have near-normal AP endonuclease and are MMS-resistant. Glu-461 appears to be essential for the nuclease function for Rrp1. Lys-463 and, to a lesser extent, Thr-462 influence the substrate specificity of the Rrp1 nuclease.
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PMID:Single amino acid changes alter the repair specificity of Drosophila Rrp1. Isolation of mutants deficient in repair of oxidative DNA damage. 779 76

Ninety-two and 33 methicillin-resistant Staphylococcus aureus (MRSA) strains were isolated in Japan and China respectively. They were categorised as ofloxacin-susceptible (MIC < 12.5 mg/L), moderately (MIC 12.5-25 mg/L) or highly (MIC > or = 50 mg/L) ofloxacin-resistant. 4-Quinolone concentrations required to inhibit purified DNA gyrase from the moderately and highly quinolone-resistant MRSA were at least 20 times higher than those required to inhibit the equivalent enzyme from quinolone-susceptible strains. Reconstitution assays demonstrated that the 4-quinolone-resistant MRSA had a mutation in subunit A of DNA gyrase. A portion of the gyrA gene from amino acids codons 40-115 was sequenced. Four moderately resistant and seven highly resistant MRSA contained a Ser-->Leu substitution at amino acid 84; one moderately and one highly resistant MRSA and one moderately resistant methicillin-susceptible S. aureus (MSSA) strain contained a Glu-->Lys substitution at amino acid 88. Eight MRSA, including one quinolone-susceptible strain and one MSSA contained a silent mutation at amino acid 86. Uptake of ofloxacin in moderately resistant strains was almost the same in the presence or absence of carbonyl cyanide m-chlorophenylhydrazone (CCCP), whereas in highly resistant strains, uptake increased when CCCP was added. Restriction fragment length analysis of the norA gene with the restriction endonuclease SfcI showed a mutation of nucleotide position 1085 in all MRSA strains tested except for one highly quinolone-resistant strain. Thus the mechanisms of 4-quinolone-resistance in these MRSA isolates involved alterations in both DNA gyrase and antimicrobial uptake and efflux.
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PMID:Mechanisms of 4-quinolone resistance in quinolone-resistant and methicillin-resistant Staphylococcus aureus isolates from Japan and China. 788 4

In this study, the endonuclease inhibitor aurintricarboxylic acid (ATA) was examined for its ability to attenuate both acute and delayed excitotoxicity mediated through NMDA and non-NMDA glutamate receptors. Ex vivo embryonic chick retina, a model system frequently used for studies of excitotoxicity, was exposed to either 100 microM NMDA or kainate (KA) +/- various concentrations of ATA for 60 min, then allowed to recover for 24 h. Lactate dehydrogenase release into the medium and histology were assessed as measures of delayed toxicity. ATA attenuated lactate dehydrogenase release due to NMDA or KA in a dose-dependent manner. Histology revealed that ATA decreased the number of pyknotic profiles in response to either glutamate agonist. The mechanism of ATA protection was addressed. ATA was found to block NMDA- but not KA-mediated 22Na+ influx and cyclic GMP formation. In membrane binding studies, ATA was relatively selective for displacement at the NMDA receptor. The IC50 values for displacement of [3H]CGS 19755, alpha-[3H]amino-3-hydroxy-5-methylisoxazole-4-propionic acid ([3H]AMPA), or [3H]KA were 29.9 +/- 1.3, 313 +/- 46, and > 1,000 microM +/- SEM, respectively. ATA also fully attenuated NMDA-induced and partially attenuated KA-induced acute excitotoxicity as monitored histologically by tissue swelling and by the increase in GABA in the medium. Temporal studies of ATA efficacy indicated that ATA needed to be present during NMDA exposure to afford protection but, versus KA, was equally effective if administered immediately after KA exposure. Questions regarding the cellular penetration of ATA were raised because incubation with 100 microM ATA for 60 min had no effect on lactate formation or [3H]leucine incorporation into trichloroacetic acid-precipitable material, even though, in cell-free systems, ATA is a potent inhibitor of phosphofructokinase activity and protein synthesis. These studies demonstrate that ATA can protect against excitotoxicity mediated through NMDA or non-NMDA glutamate receptors. The mechanism of protection versus NMDA is through interruption of NMDA receptor interactions. ATA has no direct effect at the KA receptor; thus, its mechanism of protection versus KA is distinct from that versus NMDA and is, at present, unknown.
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PMID:Excitotoxicity at both NMDA and non-NMDA glutamate receptors is antagonized by aurintricarboxylic acid: evidence for differing mechanisms of action. 789 Nov 4

Nae I endonuclease must bind to two DNA sequences for cleavage. Examination of the amino acid sequence of Nae I uncovered similarity to the active site of human DNA ligase I, except for leucine 43 in Nae I instead of the lysine essential for ligase activity. Changing leucine 43 to lysine 43 (L43K) changed Nae I activity: Nae I-L43K relaxed supercoiled DNA to yield DNA topoisomers and recombined DNA to give dimeric molecules. Interruption of the reactions of Nae I and Nae I-L43K with DNA demonstrated transient protein-DNA covalent complexes. These findings imply coupled endonuclease and ligase domains and link Nae I endonuclease to the topoisomerase and recombinase protein families.
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PMID:DNA topoisomerase and recombinase activities in Nae I restriction endonuclease. 789 5

The amino acid sequence of bovine somatotropin (bST) varies at position 127 where either valine or leucine is found. The frequencies of leucine127 and valine127 bST gene alleles in cows (n = 302) and sires (n = 70) from major dairy breeds (Holstein, Brown Swiss, Guernsey, Jersey, and Ayrshire) were determined using DNA extracted from whole blood or spermatozoa. A 428 base pair fragment of the bST gene was amplified using polymerase chain reaction (PCR) and variants of the bST gene were detected as polymorphisms by Alu I restriction endonuclease digestion of PCR products. Restriction enzyme DNA fragments for the leucine127 variant were 265, 96, 51, and 16 base pair and for the valine127 variant were 265, 147, and 16 base pair as a polymorphism of bST was present in the 147 base pair DNA fragment. Frequencies of leucine127 and valine127 alleles for cows (n = 302) were 1.0 and 0 for Brown Swiss, .93 and .07 for Holstein, .92 and .08 for Guernsey, .79 and .21 for Ayrshire, and .56 and .44 for Jersey, respectively. In Holstein sires used for artificial insemination (n = 70), the frequency of leucine127 and valine127 alleles was .96 and .04. Estimates of transmitting ability for milk production tended to be greater for Holstein cows that were homozygous for leucine127 bST and Jersey cows that were homozygous for valine127 bST whereas Holstein sires with different bST genotypes were similar. In summary, frequencies of alleles for the bST gene were not similar in different dairy breeds and estimates of milk production were correlated with bST gene variant in cows but not sires.
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PMID:Variants of somatotropin in cattle: gene frequencies in major dairy breeds and associated milk production. 790 13

The genes encoding the Neisseria lactamica restriction endonuclease IV (R.NlaIV) and its cognate DNA methyltransferase (M.NlaIV), both of which recognize the sequence GGNNCC, have been cloned in Escherichia coli and overexpressed using the T7 polymerase/promoter system. Analysis of a sequenced 3.58 kb fragment established the gene order, leuD-M.NlaIV-R.NlaIV-leuB. The predicted primary sequence of M.NlaIV (423 amino acids) shows the highest degree of identity to a pair of cytosine-specific methyltransferases, M.BanI (44.9%) and M.HgiCI (44.3%), which recognize the sequence GGYRCC (Y, pyrimidines; R, purines). In contrast, the R.NlaIV protein sequence (243 amino acids) is unique in the existing data-base, a situation that holds for most endonucleases. Flanking the NlaIV modification and restriction genes are homologues of the leuD and leuB genes of enteric bacteria, which code for enzymes in the leucine biosynthesis pathway. This gene context implies a possible new mode of gene regulation for the RM.NlaIV system, which would involve a mechanism similar to the recently discovered leucine/Lrp regulon in E. coli.
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PMID:The NlaIV restriction and modification genes of Neisseria lactamica are flanked by leucine biosynthesis genes. 819 68

The expression of Lewis fucosyltransferase (FT) mRNA was examined in gastric mucosa from two Lewis-positive [Le(+)] and two Lewis-negative [Le(-)] individuals. Northern blot analysis demonstrated that levels of mRNA were similar in both Le(+) and Le(-) gastric mucosa. We isolated the protein-coding region of the Lewis FT cDNA from Le(+) and Le(-) gastric mucosa by polymerase chain reaction (PCR) amplification. The sequence of cDNA from the Le(-) gastric mucosa shows two single-base substitutions of G for T at position 59 and of A for G at position 508 from the A of the initiation codon of cDNA. These substitutions may be the cause of changes in two amino acid residues, Arg for Leu at position 20 and Ser for Gly at position 170 from the N-terminal. To determine whether either or both of these base substitutions is responsible for the Le(-) gene, we constructed chimera cDNAs and expressed them in COS cells. Those COS cells transfected with a chimera cDNA containing a mutation of the 508th nucleotide did not express Lewis antigen, whereas those cells transfected with a chimera cDNA containing the 59th nucleotide mutation expressed Lewis antigen, indicating that a single-base change from G to A at position 508 is responsible for the Le(-) gene. The G to A transition at position 508 created a new site for PvuII endonuclease. The digestion by PvuII endonuclease of PCR products between the 386th and 612th nucleotides of Lewis FT cDNA from one of the Le(-) individuals proved to be homozygous for the PvuII site. However, the other Le(-) individual was heterozygous for the PvuII site, suggesting the presence of other Le(-) allele(s). Thus, we isolated one of the silent Lewis genes (le).
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PMID:Analysis of Lewis fucosyltransferase genes from the human gastric mucosa of Lewis-positive and -negative individuals. 821 40

Tap-1 and Tap-2 genes code for a heterodimeric peptide transporter required for the normal maturation and surface expression of class I molecules. Polymorphic variants of these MHC encoded genes occur in rats and humans. After failing to amplify a 3' polymerase chain reaction (PCR) product from thymic and splenic cDNA of the nonobese nondiabetic (NON) strain, we considered it possible that Tap-1 polymorphism was present, since cDNA from CBA/J, C57BL/6, BALB/c, and NOD (nonobese diabetic) mice all yielded Tap-1 3' products. Overlapping PCR fragments spanning the highly conserved ATP-binding cassette (ABC) were generated for purposes of restriction endonuclease analysis, studies of IFN-gamma regulation, and sequencing. To avoid amplifying other members of the transporter family, we used a gel-purified 1670-bp Tap-1 PCR "long product" as template for nested PCR. Sequencing revealed three polymorphic alleles. The most divergent was for the NON strain and involved two non-conserved amino acid substitutions (Arg-->Cys397 and Leu-->Arg491) and three silent mutations. NON mice show an abnormal pattern of class I (Kb) expression and a sizeable reduction in the percentage of CD8+ cells in the blood and thymus. In F2 segregants, the low CD8 phenotype mapped to the MHC. Tap-1 genes of NON and C57BL/6 mice were equally sensitive to up-regulation by IFN-gamma. We conclude that the mouse Tap-1 transporter gene, like the Tap-2 of the rat and the Tap-1 and Tap-2 of the human, is polymorphic. The extensive variation and specific codon changes of Tap-1 in the NON mouse raise the possibility that this gene is the MHC locus responsible for altering the intrathymic development of CD8+ T cells.
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PMID:Polymorphism in the mouse Tap-1 gene. Association with abnormal CD8+ T cell development in the nonobese nondiabetic mouse. 822 29

The phenomenon of superinduction refers to the process by which high concentrations of protein synthesis inhibitors augment and stabilize mRNA transcript levels, e.g. 36-180 microM of Puromycin (PM) has been found to elicit c-myc mRNA superinduction. The expression of the proto-oncogene c-myc has been strongly variously implicated in the regulation of the apoptotic cascade. Since we recently found that a low dose of the protein synthesis inhibitor PM activated the apoptotic cascade in HL-60 leukaemic cells, the current study was undertaken to examine c-myc mRNA transcript levels in such cells, and to assess the relationship, if any, between PM-elicited c-myc mRNA superinduction and subsequent activation of the apoptotic cascade. PM was employed in vitro at doses of 0.9 microM and 2 microM. Dose-dependent c-myc mRNA superinduction was present at 1 hour of PM-exposure, and was associated with subsequent activation of the apoptotic cascade at 24 hours of exposure. Apoptosis was confirmed morphologically as evidenced by chromatin condensation, nuclear fragmentation and the formation of apoptotic bodies, and by DNA agarose gel electrophoresis which showed the pattern of double-stranded DNA fragments that result from the activation of an endogenous endonuclease. [C14]Leucine incorporation studies at 1 hour demonstrated minimal protein synthesis inhibition at doses used, suggesting that c-myc mRNA superinduction in this context may have been the result of mechanisms which were independent of the inhibition of synthesis of new proteins, such as interruptions in signal transduction.
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PMID:Puromycin-elicited c-myc mRNA superinduction precedes apoptosis in HL-60 leukaemic cells. 829 42


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