Gene/Protein Disease Symptom Drug Enzyme Compound
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Query: EC:3.1.26.9 (ribonuclease)
 6,589 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

A nuclease (RNase D) that can recognize structurally altered transfer RNA molecules has been partially purified from Escherichia coli. The enzyme acts poorly on intact tRNA and is inactive with the synthetic polyribonucleotides, poly(A), poly(U), or double-stranded poly(A).poly(U). The enzyme requires Mg2+ for activity and is stimulated by the monovalent cations, K+ and NH4+. The products of the reaction are 5'-mononucleotides. The molecular weight of the protein is about 60,000 as judged by Sephadex G-100 chromatography. The enzyme does not correspond to any known E. coli ribonuclease and may represent an intracellular scavenging mechanism for denatured tRNAs and other inactive RNA molecules.
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PMID:Identification of an Escherichia coli nuclease acting on structurally altered transfer RNA molecules. 34 22

We have extensively purified from Krebs II ascites cells, although not until homogeneity, a ribonuclease which preferentially cleaves natural or synthetic double-stranded RNA substrates (RNase D); this specificity is also supported by its sensitivity to inhibition by 10(-5) M ethidium bromide. It does not degrade RNA-DNA hybrids and is, therefore, clearly distinct from previously characterized RNases H (Cathala, G., Rech, J., Huet, J., and Jeanteur, Ph. (1979) J. Biol. Chem. 254, 7354-7361). It shows no requirement for a divalent cation and is inhibited by all kinds of nucleic acids regardless of their secondary structure. It acts exclusively as an endonuclease, as shown by the analysis of degradation products, and yields 5'-phosphate termini. This enzyme is able to introduce discrete nicks into purified HeLa 45 S preribosomal RNA as well as into HeLa heterogenous nuclear RNA packaged within naturally occurring nuclear ribonucleoprotein particles. It is, therefore, an interesting candidate for an RNA-processing enzyme.
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PMID:Isolation and characterization of a ribonuclease activity specific for double-stranded RNA (RNase D) from Krebs II ascites cells. 624 30

A new ribonuclease, RNase BN, has been identified and partially purified from a strain of Escherichia coli lacking RNase II and RNase D by using the artificial tRNA precursor tRNA-C-[14C]U as substrate. This enzyme is present in E. coli B but absent from the tRNA processing mutant strain BN which is unable to process extraneous 3' residues on certain phage T4-specified tRNA precursors. The properties of RNase BN clearly distinguish this enzyme from other known E. coli exoribonucleases. It is optimally active at pH 6.5 with 0.2 mM divalent cation and 0.2 M monovalent cation. It is most active against tRNA substrates containing nucleotide substitutions within the -C-C-A sequence and relatively inactive against other types of RNAs. This substrate specificity in vitro is consistent with a processing function in vivo. However, in contrast to the other processing enzymes whose function has been confirmed by mutation, RNase BN is an exoribonuclease. The presence of multiple RNases in E. coli and a strategy for their identification and separation are discussed.
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PMID:Ribonuclease BN: identification and partial characterization of a new tRNA processing enzyme. 634 80

Prior sequence analysis studies have suggested that bacterial ribonuclease (RNase) Ds comprise a complete domain that is found also in Homo sapiens polymyositis-scleroderma overlap syndrome 100 kDa autoantigen and Werner syndrome protein. This RNase D 3'-->5' exoribonuclease domain was predicted to have a structure and mechanism of action similar to the 3'-->5' exodeoxyibonuclease (proofreading) domain of DNA polymerases. Here, hidden Markov model (HMM) and phylogenetic studies have been used to identify and characterise other sequences that may possess this exonuclease domain. Results indicate that it is also present in the RNase T family; Borrelia burgdorferi P93 protein, an immunodominant antigen in Lyme disease; bacteriophage T4 dexA and Escherichia coli exonuclease I, processive 3'-->5' exodeoxyribonucleases that degrade single-stranded DNA; Bacillus subtilis dinG, a probable helicase involved in DNA repair and possibly replication, and peptide synthase 1; Saccharomyces cerevisiae Pab1p-dependent poly(A) nuclease PAN2 subunit, required for shortening mRNA poly(A) tails; Caenorhabditis elegans and Mus musculus CAF1, transcription factor CCR4-associated factor 1; Xenopus laevis XPMC2, prevention of mitotic catastrophe in fission yeast; Drosophila melanogaster egalitarian, oocyte specification and axis determination, and exuperantia, establishment of oocyte polarity; H.sapiens HEM45, expressed in tumour cell lines and uterus and regulated by oestrogen; and 31 open reading frames including one in Methanococcus jannaschii . Examination of a multiple sequence alignment and two three-dimensional structures of proofreading domains has allowed definition of the core sequence, structural and functional elements of this exonuclease domain.
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PMID:The proofreading domain of Escherichia coli DNA polymerase I and other DNA and/or RNA exonuclease domains. 939 23

In Xenopus oocytes, the deadenylation of a specific class of maternal mRNAs results in their translational repression. Here we report the purification, characterization, and molecular cloning of the Xenopus poly(A) ribonuclease (xPARN). xPARN copurifies with two polypeptides of 62 kDa and 74 kDa, and we provide evidence that the 62-kDa protein is a proteolytic product of the 74-kDa protein. We have isolated the full-length xPARN cDNA, which contains the tripartite exonuclease domain conserved among RNase D family members, a putative RNA recognition motif, and a domain found in minichromosome maintenance proteins. Characterization of the xPARN enzyme shows that it is a poly(A)-specific 3' exonuclease but does not require an A residue at the 3' end. However, the addition of 25 nonadenylate residues at the 3' terminus, or a 3' terminal phosphate is inhibitory. Western analysis shows that xPARN is expressed throughout early development, suggesting that it may participate in the translational silencing and destabilization of maternal mRNAs during both oocyte maturation and embryogenesis. In addition, microinjection experiments demonstrate that xPARN can be activated in the oocyte nucleus in the absence of cytoplasmic components and that nuclear export of deadenylated RNA is impeded. Based on the poly(A) binding activity of xPARN in the absence of catalysis, a model for substrate specificity is proposed.
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PMID:The mechanism and regulation of deadenylation: identification and characterization of Xenopus PARN. 1142 38

Poly(A)-specific ribonuclease (PARN) is the only mammalian exoribonuclease characterized thus far with high specificity for degrading the mRNA poly(A) tail. PARN belongs to the RNase D family of nucleases, a family characterized by the presence of four conserved acidic amino acid residues. Here, we show by site-directed mutagenesis that these residues of human PARN, i.e. Asp(28), Glu(30), Asp(292), and Asp(382), are essential for catalysis but are not required for stabilization of the PARN x RNA substrate complex. We have used iron(II)-induced hydroxyl radical cleavage to map Fe(2+) binding sites in PARN. Two Fe(2+) binding sites were identified, and three of the conserved acidic amino acid residues were important for Fe(2+) binding at these sites. Furthermore, we show that the apparent dissociation constant ((app)K(d)) values for Fe(2+) binding at both sites were affected in PARN polypeptides in which the conserved acidic amino acid residues were substituted to alanine. This suggests that these residues coordinate divalent metal ions. We conclude that the four conserved acidic amino acids are essential residues of the PARN active site and that the active site of PARN functionally and structurally resembles the active site for 3'-exonuclease domain of Escherichia coli DNA polymerase I.
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PMID:Identification of the active site of poly(A)-specific ribonuclease by site-directed mutagenesis and Fe(2+)-mediated cleavage. 1174 7