Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.30.1 (S1 nuclease)
 3,660 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The primary structure of nuclease P1, which cleaves both RNA and single-stranded DNA, from Penicillium citrinum was elucidated. The complete amino acid sequence consisting of 270 residues was determined by analysis of peptides obtained by digestion with Achromobacter protease I of the reduced and S-aminoethylated protein and by digestion with Staphylococcus aureus V8 protease of the reduced and S-carboxymethylated protein. Four half-cystine residues were assigned to Cys72-Cys217 and Cys80-Cys85. N-Glycosylated asparagine residues were identified at positions 92, 138, 184 and 197. Fast-atom-bombardment and laser-ionization MS were successfully used to confirm the determined amino acid sequences of peptides and to estimate the molecular mass of this glycoprotein having heterogenous sugar moieties, respectively. Comparison of the amino acid sequence of nuclease P1 with other nucleases revealed that the protein has a high degree of sequence identity (50%) with nuclease S1 from Aspergillus oryzae. The His-Phe-Xaa-Asp-Ala sequence (positions 60-64) is similar to the sequence (His-Phe-Asp-Ala) involving the active-site His119 of bovine pancreatic RNase A, and the Pro-Leu-His sequence (positions 124-126) is identical with the sequence involving the active-site His134 of porcine pancreatic DNase I.
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PMID:Primary structure of nuclease P1 from Penicillium citrinum. 191 39

Murine macrophage cell lines and resident macrophages showed various levels of expression of the murine osteopontin (OP) gene, and macrophage stimulating agents were found to enhance transcription of the gene with kinetics which are unique for each stimulator. The organization of the murine OP gene was determined. The gene comprises six exons and five introns and spans approximately 4.8 kilobases. Exon 1 contains the 16 amino acids of the leader sequence. Exons 2, 3, 4, 5, and 6 encode 12, 27, 14, 94, and 129 amino acid residues, respectively. Exon 5 encodes regions containing 10 consecutive Asp amino acid residues and a Gly-Arg-Gly-Asp-Ser peptide. Exon 6 encodes the C-terminal half of OP and contains no 15- and 54-base pair nucleotide sequences which are deleted in murine OP cDNA compared to that of rat OP cDNA. Since Southern blot analysis indicated that the OP gene is a single copy, it is obvious that the murine OP cDNA has the sequence previously determined (Miyazaki, Y., Setoguchi, M., Yoshida, S., Higuchi, Y., Akizuki, S., and Yamamoto, S. (1989) Nucleic Acids Res. 17, 3298). A comparison with the cDNA sequences reported previously suggested the presence of nucleotide sequence polymorphisms. The 5' end of the murine OP gene was defined by primer extension and S1 nuclease mapping. Sequence analysis of the 5'-flanking DNA revealed the presence of many potential regulatory motifs.
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PMID:The mouse osteopontin gene. Expression in monocytic lineages and complete nucleotide sequence. 238 63

Neuronal cells express a pp60c-src variant that displays an altered electrophoretic mobility and a different V8 peptide pattern relative to pp60c-src expressed in tissues of non-neuronal origin. To determine whether the neuronal form of pp60c-src is encoded by a brain-specific messenger RNA, a mouse brain complementary DNA (cDNA) library was screened with a chicken c-src probe and a 3.8-kilobase c-src cDNA clone was isolated. This clone encodes a 60-kilodalton protein that differs from chicken or human pp60c-src primarily in having six extra amino acids (Arg-Lys-Val-Asp-Val-Arg) within the NH2-terminal 16 kilodaltons of the molecule. S1 nuclease protection analysis confirmed that brain c-src RNA contains an 18-nucleotide insertion at the position of the extra six amino acids. This insertion occurs at a position that corresponds to a splice junction in the chicken and human c-src genes. The isolated c-src cDNA clone encodes a protein that displays an identical V8 peptide pattern to that observed in pp60c-src isolated from tissues of neuronal origin.
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PMID:Neuronal pp60c-src contains a six-amino acid insertion relative to its non-neuronal counterpart. 244 Jan 6

The solution structure of Escherichia coli tRNA(3Thr) (anticodon GGU) and the residues of this tRNA in contact with the alpha 2 dimeric threonyl-tRNA synthetase were studied by chemical and enzymatic footprinting experiments. Alkylation of phosphodiester bonds by ethylnitrosourea and of N-7 positions in guanosines and N-3 positions in cytidines by dimethyl sulphate as well as carbethoxylation of N-7 positions in adenosines by diethyl pyrocarbonate were conducted on different conformers of tRNA(3Thr). The enzymatic structural probes were nuclease S1 and the cobra venom ribonuclease. Results will be compared to those of three other tRNAs, tRNA(Asp), tRNA(Phe) and tRNA(Trp), already mapped with these probes. The reactivity of phosphates towards ethylnitrosourea of the unfolded tRNA was compared to that of the native molecule. The alkylation pattern of tRNA(3Thr) shows some similarities to that of yeast tRNA(Phe) and mammalian tRNA(Trp), especially in the D-arm (positions 19 and 24) and with tRNA(Trp), at position 50, the junction between the variable region and the T-stem. In the T-loop, tRNA(3Thr), similarly to the three other tRNAs, shows protections against alkylation at phosphates 59 and 60. However, tRNA(3Thr) is unique as far as very strong protections are also found for phosphates 55 to 58 in the T-loop. Compared with yeast tRNA(Asp), the main differences in reactivity concern phosphates 19, 24 and 50. Mapping of bases with dimethyl sulphate and diethyl pyrocarbonate reveal conformational similarities with yeast tRNA(Phe). A striking conformational feature of tRNA(3Thr) is found in the 3'-side of its anticodon stem, where G40, surrounded by two G residues, is alkylated under native conditions, in contrast to other G residues in stem regions of tRNAs which are unreactive when sandwiched between two purines. This data is indicative of a perturbed helical conformation in the anticodon stem at the level of the 30-40 base pairs. Footprinting experiments, with chemical and enzymatic probes, on the tRNA complexed with its cognate threonyl-tRNA synthetase indicate significant protections in the anticodon stem and loop region, in the extra-loop, and in the amino acid accepting region. The involvement of the anticodon of tRNA(3Thr) in the recognition process with threonyl-tRNA synthetase was demonstrated by nuclease S1 mapping and by the protection of G34 and G35 against alkylation by dimethyl sulphate. These data are discussed in the light of the tRNA/synthetase recognition problem and of the structural and functional properties of the tRNA-like structure present in the operator region of the thrS mRNA.
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PMID:Tertiary structure of Escherichia coli tRNA(3Thr) in solution and interaction of this tRNA with the cognate threonyl-tRNA synthetase. 245

A genomic DNA clone encoding oryzacystatin (Oc), a cysteine proteinase inhibitor (cystatin) of rice, was isolated from a lambda EMBL3 phage library constructed with Sau3AI partial digests of rice chromosomal DNA, by screening with an oc cDNA as a probe. The restriction map of the isolated DNA fragment was consistent with the pattern of the genomic Southern-blot analysis using a cDNA probe, and consequently, the gene is considered to be a single-copy gene. The oc gene is about 1.4 kb long and composed of three exons and two introns. The first intron (336 bp) intervenes between Ala-38 and Asp-39. The second intron (372 bp) exists in the 3'-noncoding region at the G residue next to the stop codon. S1 nuclease mapping showed the major transcription start point (tsp) at A, 104 bp upstream from the start codon (ATG). Typical CAT and TATA box sequences were found in the 5'-upstream region of the tsp. The nucleotide sequences around the TATA box, the tsp, the start codon, and the stop codon essentially matched the consensus sequences of other higher plant genes. The intron boundaries of the oc gene were quite different from those of the human kininogen-encoding gene and the human salivary cystatin (cystatin S)-encoding gene.
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PMID:Cloning and sequence analysis of the genomic DNA fragment encoding oryzacystatin. 280 16

The amino terminus of glycine methyltransferase from rat liver is blocked. A hexapeptide containing the blocked amino-terminal residue was obtained from a tryptic digest of the purified enzyme and its amino acid sequence was determined to be Ac-Val-Asp-Ser-Val-Tyr-Arg by Edman degradation and fast-atom-bombardment mass spectrometry after fragmentation with Staphylococcus aureus protease V8. A full-length cDNA clone for the enzyme was isolated from a lambda gt11 rat liver cDNA library using the previously obtained pGMT A56 cDNA [Ogawa, H., Gomi, T., Horii, T., Ogawa, H. & Fujioka, M. (1984) Biochem. Biophys. Res. Commun. 124, 44-50] as a probe. The amino acid sequence deduced from the nucleotide sequence contained both amino- and carboxyl-terminal sequences. The predicted amino acid composition and molecular mass were also in agreement with the published data obtained with the purified protein. Five clones for the glycine methyltransferase gene were isolated from a Charon 4A library containing EcoRI digest of rat liver DNA by in situ plaque hybridization. All clones had inserts of 6500 base pairs, consistent with the size of EcoRI genomic DNA fragment determined by Southern blot hybridization. Sequence analysis of a 5400-bp fragment of the insert DNA lacking a 1100-bp 5' region and comparison of the sequence with that of the cDNA showed that the insert DNA entirely encoded glycine methyltransferase and the gene consisted of six exons and five introns. S1 nuclease protection mapping and primer extension analysis allowed us to propose that the A residue located 19 bp upstream from the translation initiation codon is the site of transcription initiation. TATA, CAAT and GC sequences, and the complementary sequence to the enhancer core element, were located upstream of the transcription initiation site.
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PMID:Rat glycine methyltransferase. Complete amino acid sequence deduced from a cDNA clone and characterization of the genomic DNA. 282 2

During senescence in the filamentous fungus Podospora anserina, specific regions of the mitochondrial genome, termed senDNA are excised, ligated and amplified. We have cloned in their entirety three such autonomously replicating plasmids, alpha, beta and epsilon senDNA. None of these plasmids displayed cross-hybridization nor did we detect any significant DNA homology by computer analysis. The complete DNA sequence of the 2.5 kb alpha, the 5.5 kb epsilon and about 3.4 kb of the 9.8 kb beta senDNA is presented (kb = 10(3) base-pairs). These sequences were analyzed for the presence of consensus sequences common to introns, and it was found that alpha senDNA has the characteristics of a group II intron, epsilon senDNA contains three group I introns, and beta senDNA did not show relevant sequences in the 3.4 kb examined. Comparison of the 5' and 3'-flanking sequences of alpha senDNA with oxi 3 (Co I) amino acid sequences from Neurospora crassa and Saccharomyces cerevisiae revealed significant homology and provided strong support that the excised alpha senDNA itself consists entirely of an intron. Upstream from the oxi 3 gene a transfer RNA cysteine sequence was detected. beta senDNA contained four tRNA sequences, aspartic acid, serine, valine and tryptophan, and sequences homologous to URFC (untranslated reading frame C) as well as two new URFs. epsilon senDNA contained sequences homologous to ATPase 8 and URFl; URFl was interrupted by three group I introns. The excision site sequences, as located by S1 nuclease mapping were unique for each senDNA. Analysis for repeated units showed that each plasmid contained elements which could be involved in secondary structure required for the alignment of distal ends preparatory to excision. These results are interpreted in terms of the structural requirements of mobile elements including the possible involvement of reverse transcriptase in the excision-ligation-amplification process.
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PMID:Excision-amplification of mitochondrial DNA during senescence in Podospora anserina. DNA sequence analysis of three unique "plasmids". 299 55

lambda gt11 cDNA libraries derived from human brain were screened with oligonucleotide probes for recombinants that code for alpha subunits of G signal transduction proteins. Eleven alpha s clones were detected with both probes and characterized. Four types of alpha s cDNA were cloned that differ in nucleotide sequence in the region that corresponds to amino acid residues 71-88. The clones differ in the codon for alpha s amino acid residue 71 (glutamic acid or aspartic acid), the presence or absence of codons for the next 15 amino acid residues, and the presence or absence of an adjacent serine residue. S1 nuclease protection experiments revealed at least two forms of alpha s mRNA. A mechanism for generating four species of alpha s mRNA by alternative splicing of precursor RNA is proposed.
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PMID:Human cDNA clones for four species of G alpha s signal transduction protein. 302 54

An alpha-tubulin gene of Physarum was isolated as a phage-lambda NM1149 recombinant (designated phage-lambda N alpha Tu). Phage-lambda N alpha Tu contained a 4700 base-pair HindIII nuclear DNA fragment of an allele of the altB locus of Physarum (one of four unlinked alpha-tubulin gene loci). Subfragments of the 4700 base-pair insert of phage-lambda N alpha Tu were cloned into phage M13 and the nucleotide sequence was determined by the dideoxy chain termination method. The start point of transcription was identified by primer extension and a putative polyadenylation site was located by S1 nuclease analysis. The 4650 base-pair HindIII insert into phage-lambda N alpha Tu spans the complete gene; sequences upstream from the 5' end contain the RNA transcription promoter elements (the TATA and CCAAT boxes). The nucleotide sequence encoding alpha-tubulin contains seven intervening sequences, ranging from 63 to 222 nucleotides in size. The exons have a sequence that is identical with a Physarum alpha-tubulin cDNA clone, except for three base changes, one leading to a Val codon in place of a Met codon, another leading to a Glu codon in place of an Asp codon, and the third change is silent. The genomic clone provides the nucleotide sequence coding for the last 26 amino acid residues missing from the cDNA clone. The new sequence data indicate that the alpha-tubulin gene has a C-terminal methionine codon and not a tyrosine codon, which has been found in all alpha-tubulin genes sequenced to date.
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PMID:Primary structure of an alpha-tubulin gene of Physarum polycephalum. 358 27

We have isolated a human gastrin gene from a genomic library by employing a human gastrin cDNA clone as a hybridization probe. The total length of the gene is approximately 4.0 kilobase pairs, and the gene is separated into three exons and two introns. A 130-base-pair intron interrupts the coding region and a 3.0-kilobase-pair intron is located in the 5' untranslated region. Nucleotide sequence analysis showed that all of the exon-intron boundaries follow the A-G/G-T consensus sequences. A putative transcription initiation site is assigned to the adenine 60 nucleotides upstream from the exon-intron junction on the basis of S1 nuclease protection mapping. A possible "TATA" equivalent sequence T-T-A-T-A-A is located 28 base pairs upstream from the transcription initiation site. A "CAT box" sequence, C-A-T-T, is located 99 nucleotides upstream of the transcription initiation site. A poly(A)-addition signal, A-A-U-A-A-A, is located 80 base pairs downstream from the termination codon. Comparison of the nucleotide sequences of the human cDNA and the genomic clone revealed that the aspartic acid codon at position 71 of preprogastrin is interrupted by the small intron (130 base pairs). The 3' region of the large intron contains a sequence of 300 nucleotides that is flanked by 15-nucleotide direct repeats. This sequence exhibits a striking homology to the human Alu-type sequence.
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PMID:Structural analysis of the gene encoding human gastrin: the large intron contains an Alu sequence. 608 40


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