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1.
Structure of ribonuclease H phased at 2 A resolution by MAD analysis of the selenomethionyl protein 总被引：32，自引：0，他引：32
Ribonuclease H digests the RNA strand of duplex RNA.DNA hybrids into oligonucleotides. This activity is indispensable for retroviral infection and is involved in bacterial replication. The ribonuclease H from Escherichia coli is homologous with the retroviral proteins. The crystal structure of the E. coli enzyme reveals a distinctive alpha-beta tertiary fold. Analysis of the molecular model implicates a carboxyl triad in the catalytic mechanism and suggests a likely mode for the binding of RNA.DNA substrates. The structure was determined by the method of multiwavelength anomalous diffraction (MAD) with the use of synchrotron data from a crystal of the recombinant selenomethionyl protein. 相似文献
2.
Two RNA-catalyzed reactions have been described, the Tetrahymena self-splicing ribosomal RNA and ribonuclease P. The Tetrahymena self-splicing reaction proceeds through a transesterification cascade that is dependent upon nucleophilic attacks by ribose 3'-OH groups. Periodate oxidation of the catalytic (or substrate) RNA, which destroys the nucleophilicity of RNA 3' termini, did not inhibit ribonuclease P activity. Thus, catalysis by ribonuclease P differs from the self-splicing reaction. 相似文献
3.
The intervening sequence RNA of Tetrahymena is an enzyme 总被引：40，自引：0，他引：40
A shortened form of the self-splicing ribosomal RNA (rRNA) intervening sequence of Tetrahymena thermophila acts as an enzyme in vitro. The enzyme catalyzes the cleavage and rejoining of oligonucleotide substrates in a sequence-dependent manner with Km = 42 microM and kcat = 2 min-1. The reaction mechanism resembles that of rRNA precursor self-splicing. With pentacytidylic acid as the substrate, successive cleavage and rejoining reactions lead to the synthesis of polycytidylic acid. Thus, the RNA molecule can act as an RNA polymerase, differing from the protein enzyme in that it uses an internal rather than an external template. At pH 9, the same RNA enzyme has activity as a sequence-specific ribonuclease. 相似文献
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Catalytic activity of an RNA molecule prepared by transcription in vitro 总被引：26，自引：0，他引：26
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Argonaute proteins and small interfering RNAs (siRNAs) are the known signature components of the RNA interference effector complex RNA-induced silencing complex (RISC). However, the identity of "Slicer," the enzyme that cleaves the messenger RNA (mRNA) as directed by the siRNA, has not been resolved. Here, we report the crystal structure of the Argonaute protein from Pyrococcus furiosus at 2.25 angstrom resolution. The structure reveals a crescent-shaped base made up of the amino-terminal, middle, and PIWI domains. The Piwi Argonaute Zwille (PAZ) domain is held above the base by a "stalk"-like region. The PIWI domain (named for the protein piwi) is similar to ribonuclease H, with a conserved active site aspartate-aspartate-glutamate motif, strongly implicating Argonaute as "Slicer." The architecture of the molecule and the placement of the PAZ and PIWI domains define a groove for substrate binding and suggest a mechanism for siRNA-guided mRNA cleavage. 相似文献
6.
Specific interactions in RNA enzyme-substrate complexes 总被引：27，自引：0，他引：27
Analysis of crosslinked complexes of M1 RNA, the catalytic RNA subunit of ribonuclease P from Escherichia coli, and transfer RNA precursor substrates has led to the identification of regions in the enzyme and in the substrate that are in close physical proximity to each other. The nucleotide in M1 RNA, residue C92, which participates in a crosslink with the substrate was deleted and the resulting mutant M1 RNA was shown to cleave substrates lacking the 3' terminal CCAUCA sequence at sites several nucleotides away from the normal site of cleavage. The presence or absence of the 3' terminal CCAUCA sequence in transfer RNA precursor substrates markedly affects the way in which these substrates interact with the catalytic RNA in the enzyme-substrate complex. The contacts between wild-type M1 RNA and its substrate are in a region that resembles part of the transfer RNA "E" (exit) site in 23S ribosomal RNA. These data demonstrate that in RNA's with very different cellular functions, there are domains with similar structural and functional properties and that there is a nucleotide in M1 RNA that affects the site of cleavage by the enzyme. 相似文献
7.
RNA required for import of precursor proteins into mitochondria 总被引：4，自引：0，他引：4
F A Firgaira J P Hendrick F Kalousek J P Kraus L E Rosenberg 《Science (New York, N.Y.)》1984,226(4680):1319-1322
A cytoplasmic RNA moiety is necessary for posttranslational uptake of nuclear-encoded mammalian proteins destined for the mitochondrial matrix. Post-translational addition of ribonuclease to a reticulocyte lysate-programmed cell-free translation mixture inhibited subsequent import of six different mitochondrial matrix enzyme precursors into rat liver mitochondria. The required RNA is highly protected, as indicated by the high concentrations of ribonuclease necessary to produce this inhibition. The dependence of the inhibitory effect on temperature, duration of exposure to ribonuclease, and availability of divalent cations is characteristic of the nuclease susceptibility of ribonucleoproteins. The ribonuclease-sensitive component was found in a 400-kilodalton fraction which contains the mitochondrial protein precursors. 相似文献
8.
Part of the RNA synthesized from nucleoside triphosphate precursors by partially purified RNA synthetase, an enzyme induced in Escherichia coli by the RNA-containing phage MS 2, is resistant to hydrolysis by ribonuclease. Upon heating in 0.15M sodium chloride, 0.015M sodium citrate followed by fast cooling the material becomes ribonuclease-sensitive with a sharp transition at 102 degrees to 104 degrees C. The suggestion that the ribonuclease-resistant product is double-stranded RNA is reinforced by restoration of the ribonuclease resistance of the heat-denatured material by reannealing at temperatures just below the transition point and by its buoyant density in cesium sulfate. It is suggested that double-stranded RNA is the replicative form of MS 2 phage RNA. 相似文献
9.
A link between mRNA turnover and RNA interference in Arabidopsis 总被引：1，自引：0，他引：1
Gazzani S Lawrenson T Woodward C Headon D Sablowski R 《Science (New York, N.Y.)》2004,306(5698):1046-1048
In RNA interference (RNAi), double-stranded RNA (dsRNA) triggers degradation of homologous messenger RNA. In many organisms, RNA-dependent RNA polymerase (RdRp) is required to initiate or amplify RNAi, but the substrate for dsRNA synthesis in vivo is not known. Here, we show that RdRp-dependent transgene silencing in Arabidopsis was caused by mutation of XRN4, which is a ribonuclease (RNase) implicated in mRNA turnover by means of decapping and 5'-3' exonucleolysis. When both XRN4 and the RdRp were mutated, the plants accumulated decapped transgene mRNA. We propose that mRNAs lacking a cap structure become exposed to RdRp to initiate or maintain RNAi. 相似文献
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Selectivity of intracellular proteolysis: protein substrates activate the ATP-dependent protease (La) 总被引：19，自引：0，他引：19
A critical enzyme in protein breakdown in Escherichia coli is protease La (the lon gene product), which hydrolyzes proteins and adenosine triphosphate (ATP) in a coupled process. The mechanism of this process was studied with fluorogenic tripeptides. Although proteins and peptides are degraded at the same active site, protein substrates enhance the ability of the enzyme to degrade these peptides two- to tenfold. Proteins that are not substrates had little or no effect. Thus, protein substrates must bind to protease La at two sites, the active site and an allosteric site whose occupancy enhances proteolytic activity. This effect did not require that the proteins themselves be degraded. Proteins could induce peptide breakdown even in the absence of ATP, and proteins and ATP had additive effects in stimulating peptidase activity. A multistep cyclical mechanism is proposed in which the binding of the substrate and ATP activates the protease. The enzyme can then cleave a peptide bond, but is inactivated through ATP hydrolysis. Such a mechanism may help account for the selectivity of protein breakdown and prevent inappropriate or excessive proteolysis in vivo. 相似文献
12.
Internal protein dynamics are intimately connected to enzymatic catalysis. However, enzyme motions linked to substrate turnover remain largely unknown. We have studied dynamics of an enzyme during catalysis at atomic resolution using nuclear magnetic resonance relaxation methods. During catalytic action of the enzyme cyclophilin A, we detect conformational fluctuations of the active site that occur on a time scale of hundreds of microseconds. The rates of conformational dynamics of the enzyme strongly correlate with the microscopic rates of substrate turnover. The present results, together with available structural data, allow a prediction of the reaction trajectory. 相似文献
13.
Kowarik M Numao S Feldman MF Schulz BL Callewaert N Kiermaier E Catrein I Aebi M 《Science (New York, N.Y.)》2006,314(5802):1148-1150
N-linked protein glycosylation is found in all domains of life. In eukaryotes, it is the most abundant protein modification of secretory and membrane proteins, and the process is coupled to protein translocation and folding. We found that in bacteria, N-glycosylation can occur independently of the protein translocation machinery. In an in vitro assay, bacterial oligosaccharyltransferase glycosylated a folded endogenous substrate protein with high efficiency and folded bovine ribonuclease A with low efficiency. Unfolding the eukaryotic substrate greatly increased glycosylation. We propose that in the bacterial system, glycosylation sites are located in flexible parts of folded proteins, whereas the eukaryotic cotranslational glycosylation evolved to a mechanism presenting the substrate in a flexible form before folding. 相似文献
14.
Macrae IJ Zhou K Li F Repic A Brooks AN Cande WZ Adams PD Doudna JA 《Science (New York, N.Y.)》2006,311(5758):195-198
The specialized ribonuclease Dicer initiates RNA interference by cleaving double-stranded RNA (dsRNA) substrates into small fragments about 25 nucleotides in length. In the crystal structure of an intact Dicer enzyme, the PAZ domain, a module that binds the end of dsRNA, is separated from the two catalytic ribonuclease III (RNase III) domains by a flat, positively charged surface. The 65 angstrom distance between the PAZ and RNase III domains matches the length spanned by 25 base pairs of RNA. Thus, Dicer itself is a molecular ruler that recognizes dsRNA and cleaves a specified distance from the helical end. 相似文献
15.
A small RNA of Bacillus subtilis bacteriophage phi 29 is shown to have a novel and essential role in viral DNA packaging in vitro. This requirement for RNA in the encapsidation of viral DNA provides a new dimension of complexity to the attendant protein-DNA interactions. The RNA is a constituent of the viral precursor shell of the DNA-packaging machine but is not a component of the mature virion. Studies of the sequential interactions involving this RNA molecule are likely to provide new insight into the structural and possible catalytic roles of small RNA molecules. The phi 29 assembly in extracts and phi 29 DNA packaging in the defined in vitro system were strongly inhibited by treatment with the ribonucleases A or T1. However, phage assembly occurred normally in the presence of ribonuclease A that had been treated with a ribonuclease inhibitor. An RNA of approximately 120 nucleotides co-purified with the phi 29 precursor protein shell (prohead), and this particle was the target of ribonuclease action. Removal of RNA from the prohead by ribonuclease rendered it inactive for DNA packaging. By RNA-DNA hybridization analysis, the RNA was shown to originate from a viral DNA segment very near the left end of the genome, the end packaged first during in vitro assembly. 相似文献
16.
Pancreatic ribonuclease: enzymic and physiological properties of a cross-linked dimer 总被引：3，自引：0，他引：3
Monomeric ribonuclease A has very low activity toward typically double-stranded RNA's; the dimeric form of ribonuclease A obtained by cross linking the enzyme by dimethyl suberimidate has more than 78 times the activity of the monomer toward polyadenylate . polyuridylate and 440 times the activity of the monomer toward the double-stranded RNA of a virus from Penicillium chrysogenum. The half-life of the dimer in the bloodstream of the rat is 12 times that of the mononmer. 相似文献
17.
Chaperonin function: folding by forced unfolding 总被引：1，自引：0，他引：1
The ability of the GroEL chaperonin to unfold a protein trapped in a misfolded condition was detected and studied by hydrogen exchange. The GroEL-induced unfolding of its substrate protein is only partial, requires the complete chaperonin system, and is accomplished within the 13 seconds required for a single system turnover. The binding of nucleoside triphosphate provides the energy for a single unfolding event; multiple turnovers require adenosine triphosphate hydrolysis. The substrate protein is released on each turnover even if it has not yet refolded to the native state. These results suggest that GroEL helps partly folded but blocked proteins to fold by causing them first to partially unfold. The structure of GroEL seems well suited to generate the nonspecific mechanical stretching force required for forceful protein unfolding. 相似文献
18.
【目的】为了避免在制备基因治疗或基因免疫的质粒时使用动物源性的核糖核酸酶A（RNase A）。【方法】提取牛胰腺总RNA，利用RT-PCR扩增出牛核糖核酸酶A cDNA，RT-PCR产物克隆到pGEM-T载体测序验证后，将此cDNA亚克隆到大肠杆菌分泌型表达载体pEZZ18中。【结果】SDS-PAGE电泳显示其转化菌经温度诱导后能表达预计的大小为28 kD重组蛋白。用渗透法释放出表达产物，将其加入到经碱裂解粗提的质粒DNA中并孵育0.5 h，琼脂糖凝胶结果表明表达产物能很好地去除细菌的RNA并且不降解超螺旋质粒DNA。【结论】在质粒的纯化过程中，重组牛核糖核酸酶可以替代动物源性的RNase A。 相似文献
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几丁质酶中存在结合口袋及水解活性位点，关键氨基酸与底物几丁质的结合可调控酶的水解活性。以嗜热几丁质酶Chi304为研究材料，采用同源建模分析其高级结构，发现在其底物结合口袋附近存在2个色氨酸（W140与W272），将其定点突变为丙氨酸后，采用高效液相色谱检测酶的水解产物，并进一步分析水解产物三乙酰壳三糖（DP3）与二乙酰壳二糖（DP2）的比例（DP3/DP2），用于评估突变体的效果。结果表明，突变体W140A、W272A与W140/272A水解胶体几丁质产物DP3/DP2分别较野生型提升23.3%、45.7%与80.0%。由此表明，W140与W272是影响酶与底物结合的关键氨基酸，将其突变为丙氨酸可提升Chi304的内切活力，降低外切活力。 相似文献