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PubMed1977

The structure and function of ribonuclease T1 XXIV. Preparation and properties of a stable water-insoluble polyacrylamide derivative of ribonuclease T1.

Ribonuclease T1 [EC 3.1.4.8] was coupled to a water-insoluble cross-linked polyacrylamide (Enzacryl AH) by the acid azide method. The immobilized enzyme exhibited about 45% and 77% of the original activity toward yeast RNA and 2', 3-cyclic GMP, respectively, as substrates. Although the specific activity was lowered by the coupling, the immobilized enzyme was found to be far more stable to heat and extremes of PH than the native enzyme. The immobilized enzyme was active toward RNA even above pH 9 (at 37 degree C) or above 60 degree C (at pH 7.5), where the native enzyme was inactive. The immobilized enzyme retained much of its activity as assayed at 37 degree C after incubation in the range of pH 1 to 10 at 37 degree C, or after heating at 100 degree C (at pH 7.5) under conditions where the native enzyme was inactivated to a considerable extent. The enzyme derivative could be repeatedly recovered and reused without much loss of activity. The active site glutamic acid-58 in the immobilized enzyme appeared to be nearly as reactive with iodoacetate as that in the native enzyme.

Enzymes, Immobilized↗

PubMed1981

Nuclear location of ribonuclease H and increased level of magnesium-dependent ribonuclease H in rat liver on thioacetamide treatment.

Rat liver nuclei were isolated in aqueous solutions of low ionic strength or anhydrous glycerol. The presence of ribonuclease H (RNase H) [EC 3.1.4.34] activity in the cytoplasm is due to extraction of the nuclear enzyme by buffer and inorganic salts. Two forms of RNase H were separated from rat liver nuclei by affinity chromatography using a DNA-cellulose column. When the RNase H in the wash solution of nuclei with 0.3 M sucrose and in nuclear solution extracted with 0.15 M NaCl were fractionated on a single-stranded DNA-cellulose column, two peaks corresponding to Mn2+- and Mg2+-dependent RNases H were eluted at 0.1 M and 0.2 M NaCl, respectively, and a peak having both RNase H activities was recovered in the wash-through fraction from the column. Among the enzymes from these two fractions in the nuclei, the activity of the Mg2+-dependent RNase H which binds to DNA-cellulose increased several-fold within 24 h of a single injection of thioacetamide. The activities of Mg2+-dependent RNase H extracted with higher-salt solution from the nuclei and recovered in the flow-through fraction from the DNA-cellulose column and the Mn2+-dependent RNase H activities were relatively unaffected by an injection of thioacetamide.

Acetamides↗

PubMed2004

Crystal structure of archaeal ribonuclease P protein Ph1771p from Pyrococcus horikoshii OT3: an archaeal homolog of eukaryotic ribonuclease P protein Rpp29.

Ribonuclease P (RNase P) is the endonuclease responsible for the removal of 5' leader sequences from tRNA precursors. The crystal structure of an archaeal RNase P protein, Ph1771p (residues 36-127) from hyperthermophilic archaeon Pyrococcus horikoshii OT3 was determined at 2.0 A resolution by X-ray crystallography. The structure is composed of four helices (alpha1-alpha4) and a six-stranded antiparallel beta-sheet (beta1-beta6) with a protruding beta-strand (beta7) at the C-terminal region. The strand beta7 forms an antiparallel beta-sheet by interacting with strand beta4 in a symmetry-related molecule, suggesting that strands beta4 and beta7 could be involved in protein-protein interactions with other RNase P proteins. Structural comparison showed that the beta-barrel structure of Ph1771p has a topological resemblance to those of Staphylococcus aureus translational regulator Hfq and Haloarcula marismortui ribosomal protein L21E, suggesting that these RNA binding proteins have a common ancestor and then diverged to specifically bind to their cognate RNAs. The structure analysis as well as structural comparison suggested two possible RNA binding sites in Ph1771p, one being a concave surface formed by terminal alpha-helices (alpha1-alpha4) and beta-strand beta6, where positively charged residues are clustered. A second possible RNA binding site is at a loop region connecting strands beta2 and beta3, where conserved hydrophilic residues are exposed to the solvent and interact specifically with sulfate ion. These two potential sites for RNA binding are located in close proximity. The crystal structure of Ph1771p provides insight into the structure and function relationships of archaeal and eukaryotic RNase P.

Amino Acid Sequence↗

PubMed2000

Analysis of the interactions of human ribonuclease inhibitor with angiogenin and ribonuclease A by mutagenesis: importance of inhibitor residues inside versus outside the C-terminal "hot spot".

Ribonuclease inhibitor (RI) binds diverse mammalian RNases with extraordinary avidity. Here, we have investigated the structural basis for this tight binding and broad specificity by mutational analysis of the complexes of RI with angiogenin (Ang) and RNase A (K(D)=0.5 fM and 43 fM, respectively). Both crystal structures are known; the interfaces are large, and the ligands dock similarly, although few of the specific interactions formed are analogous. Our previous mutagenesis studies focused primarily on one contact region, containing RI 434-438 and the enzymatic active site. Many single-residue replacements produced extensive losses of binding energy (2.3-5.9 kcal/mol), suggesting that this region constitutes a "hot spot" in both cases. We have now explored the roles of most of the remaining RI residues that interact with Ang and/or RNase A. One major cluster in each complex lies in a Trp-rich area of RI, containing Trp261, Trp263, Trp318, and Trp375. Although the energy losses from individual replacements in this portion of the Ang complex were small-to-moderate (0-1.5 kcal/mol), the changes from multiple substitutions were much greater than additive, and the binding energy provided by this region is estimated to be approximately 6 kcal/mol (30 % of total). Effects of replacing combinations of hot spot components had also been found to be superadditive, and this negative cooperativity is now shown to extend to the neighboring contact residue RI Ser460. The overall contribution of the hot spot, taking superadditivity into account, is then approximately 14-15 kcal/mol. The hot spot and Trp-rich regions, although spatially well separated, are themselves functionally linked. No other parts of the RI-Ang interface appear to be energetically important. Binding of RNase A is more sensitive to substitutions throughout the interface, with free energy losses>/=1 kcal/mol produced by nearly all replacements examined, so that the sum of losses greatly exceeds the binding energy of the complex. This discrepancy can be explained, in part, by positive cooperativity, as evident from the subadditive effects observed when combinations of residues in either the hot spot or Trp-rich region are replaced. These findings suggest that the binding energy may be more widely distributed in the RNase A complex than in the Ang complex.

Amino Acid Motifs↗

PubMed1996

Purification of mammalian ribonuclease using immobilized human ribonuclease inhibitor.

Affinity chromatography on immobilized ribonuclease (RNase) inhibitor was developed for purification of mammalian RNase. Human placental RNase inhibitor was conjugated to CNBr-activated Sepharose in the presence of dithiothreitol. About 80% of the immobilized RNase inhibitor was capable of binding bovine pancreatic RNase A. The bound RNase A was eluted with 3 M NaCl at pH 5.0. Two 25-kDa and 18-kDa RNases, which were obtained from human liver using a cellulose phosphate column, were bound to the immobilized RNase inhibitor and recovered in a pure and active form after treatment of the resin with p-hydroxymercuribenzoate. These enzymes were considered to be nonsecretory-type RNases with different sugar contents.

Amidohydrolases↗

PubMed1983

Ribonuclease and ribonuclease inhibitor in the human pancreas.

Previous investigations have failed to confirm any specificity of elevated serum ribonuclease (RNase) in the diagnosis of pancreatic cancer. Although RNase had been known to be present in two forms (free and inhibitor-bound) in various rat tissues, little was known about its presence in the human pancreas. This report investigates the presence of RNase inhibitor in the human pancreas through the assay of both active (=free) and total (=sum of free and inhibitor-bound) RNases. Inhibitor-bound RNase was also named as latent RNase. RNase was classified into three types according to pH (acid, neutral, and alkaline RNases) in the pancreatic supernatant fraction. An inhibitor was separated from latent RNase by p-chloromercuribenzoic acid (PCMB), and the latent RNase was changed to an active form. Latent RNase was more active on the alkaline side with a maximum at pH 7.5. Hence, the presence of RNase inhibitor was highly suggested in the pancreatic supernatant fraction. RNase inhibitor is most likely a protein, which binds with both neutral and alkaline RNases. The presence of RNase inhibitor has not yet been demonstrated in the normal human serum.

Humans↗

PubMed1990

Purification and characterization of three ribonucleases from human kidney: comparison with urine ribonucleases.

Three ribonucleases (RNases) with different molecular masses were isolated from human kidney. The enzymes were purified to an electrophoretically homogeneous state, and their respective molecular masses were found to be 18,000 (tentatively named RNase HK-1), 20,000 (RNase HK-2A), and 22,000 (RNase HK-2B) on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Analysis of the amino acid compositions, amino-terminal sequences, and enzymological properties of the enzymes indicate that RNase HK-1 is related to "nonsecretory" RNase, and that RNases HK-2A and HK-2B are both related to "secretory" RNase. Furthermore, RNase HK-1 showed cross-reactivity with an antibody specific to nonsecretory RNase from human urine, whereas RNases HK-2A and HK-2B showed cross-reactivity with another antibody specific to human urine secretory RNase. However, the carbohydrate compositions of RNases HK-2A and HK-2B were markedly different from that of the secretory urine RNase. This finding seems to indicate that the kidney is not the origin of the urine enzyme.

Adult↗

PubMed1990

Purification and characterization of two ribonucleases from human erythrocytes: immunological and enzymological comparison with ribonucleases from human urine.

Two ribonucleases (RNases), one active against RNA as well as poly(C) and the other more markedly against poly(C), were isolated from human erythrocytes by acetone fractionation in the presence of 0.25 M H2SO4, followed by a series of column chromatographies. The purified enzymes appeared homogeneous as judged by sodium dodecyl sulfate--polyacrylamide gel electrophoresis (SDS-PAGE), and were tentatively designated RNase HE-1 and RNase HE-2. The content of RNase HE-1 in erythrocytes was much higher than that of RNase HE-2. The molecular mass of RNase HE-1 was determined to be 18,000 and 16,000 Da, and that of RNase He-2 39,000 and 31,000 Da, by SDS-PAGE and gel filtration, respectively. The catalytic properties and structural features of RNase HE-1 including the amino acid composition and N-terminal amino acid sequence indicated that its protein moiety is strictly related to a nonsecretory RNase purified from human urine (Yasuda et al., 1988, Biochim. Biophys. Acta 965, 185-195). In particular, the N-terminal amino acid sequence up to the 32nd residue was identical with that of urine nonsecretory RNase reported recently (Beintema et al., 1988, Biochemistry 27, 4530-4538). Furthermore, RNase HE-1 was immunologically indistinguishable from urine nonsecretory RNase, but clearly differed from urine secretory RNase. On the other hand, erythrocyte RNase HE-2 was enzymologically and immunologically similar to urine secretory RNase.

Amino Acid Sequence↗

PubMed1978

Inhibition of ribonuclease. Efficacy of sodium dodecyl sulfate, diethyl pyrocarbonate, protein ase K and heparin using a sensitive ribonuclease assay.

The effectiveness of several commonly used inhibitors of ribonuclease (RNAase) has been studied using the removal of radio-labelled leucine from leucyl-tRNA as a sensitive assay for RNAase activity. The inhibitors were tested under a variety of conditions, varying the temperature, the pH, and the source of RNAase. When each inhibitor is udes separately in the presence of pancreatic RNAase, sodium dodecyl sulfate (SDS) is the most effective; but during long exposures to temperatures above 0 degrees C considerable amounts of RNA are still degraded. Combination of inhibitors are more effective in preserving RNA; with this assay, a combination of SDS with diethyl pyrocarbonate is the most effective. Proteinase K acts as an inhibitor when used in combination with SDS; however, it has RNAase activity when used by itself. Diethyl pyrocarbonate, when used at the high range of concentrations employed by others for RNAase inhibition, reacts with RNA changing its charge. However, when diethyl pyrocarbonate is used in smaller amounts the effects on RNA are minimal, and when used in combination with SDS it effectively inhibits RNAase.

Diethyl Pyrocarbonate↗

PubMed1985

Human seminal ribonuclease. A tool to check the role of basic charges and glycosylation of a ribonuclease in the action of the enzyme on double-stranded RNA.

Human seminal ribonuclease (a basic protein occurring in a glycosylated and in a non-glycosylated form) is very active against double-stranded RNAs (De Prisco, R., Sorrentino, S., Leone, E. and Libonati, M. (1984) Biochim. Biophys. Acta 788, 356-363). The action of the two enzyme forms on single-stranded and double-stranded substrates was studied as a function of pH and ionic strength. Results indicate (1) that glycosylation of the RNAase molecule does not affect enzyme action on single-stranded RNAs, while (2) degradation of double-stranded RNAs is moderately increased by the presence of carbohydrates in the enzyme molecule. Human seminal RNAase shows a marked helix-destabilizing activity on poly(dA-dT) X poly(dA-dT). Under various conditions, this action (1) is definitely stronger than that of bovine RNAase A, and (2) seems to be less dependent on the glycosylation than on the basicity of the enzyme protein. The remarkable activity of human seminal RNAase on double-stranded RNA may, at least partly, be related to the enzyme properties mentioned above.

Glycoproteins↗

PubMed1992

Specific identification of human ribonucleases by antibodies produced against two synthetic peptides corresponding to the N- and C-terminal amino-acid sequences of human urinary secretory-type ribonuclease.

Antibodies were raised in rabbits by immunizing two synthetic peptides, which corresponded to the N- and C-terminal 15 residues, respectively, of human urinary secretory ribonuclease (RNase). These antibodies did not block the RNase activity, but reacted well with enzymes blotted onto a transfer membrane following electrophoresis, and discriminated strictly between secretory- and nonsecretory-type RNases. Therefore, these antibodies should to be valuable tools for the immunological identification of human RNases.

Amino Acid Sequence↗

PubMed2006

Ribonuclease revisited: structural insights into ribonuclease III family enzymes.

Ribonuclease III (RNase III) enzymes occur ubiquitously in biology and are responsible for processing RNA precursors into functional RNAs that participate in protein synthesis, RNA interference and a range of other cellular activities. Members of the RNase III enzyme family, including Escherichia coli RNase III, Rnt1, Dicer and Drosha, share the ability to recognize and cleave double-stranded RNA (dsRNA), typically at specific positions or sequences. Recent biochemical and structural data have shed new light on how RNase III enzymes catalyze dsRNA hydrolysis and how substrate specificity is achieved. A major theme emerging from these studies is that accessory domains present in different RNase III enzymes are the key determinants of substrate selectivity, which in turn dictates the specialized biological function of each type of RNase III protein.

Bacterial Proteins↗

PubMed2005

Crystal structure of a ribonuclease P protein Ph1601p from Pyrococcus horikoshii OT3: an archaeal homologue of human nuclear ribonuclease P protein Rpp21.

Ribonuclease P (RNase P) is a ribonucleoprotein complex involved in the removal of 5' leader sequences from tRNA precursors (pre-tRNA). The human protein Rpp21 is essential for human RNase P activity in tRNA processing in vitro. The crystal structure of Ph1601p from the hyperthermophilic archaeon Pyrococcus horikoshii OT3, the archaeal homologue of Rpp21, was determined using the multiple anomalous dispersion (MAD) method with the aid of anomalous scattering in zinc and selenium at 1.6 A resolution. Ph1601p comprises an N-terminal domain (residues 1-55), a central linker domain (residues 56-79), and a C-terminal domain (residues 80-120), forming an L-shaped structure. The N-terminal domain consists of two long alpha-helices, while the central and C-terminal domains fold in a zinc ribbon domain. The electrostatic potential representation indicates the presence of positively charged clusters along the L arms, suggesting a possible role in RNA binding. A single zinc ion binds the well-ordered binding site that consists of four Cys residues (Cys68, Cys71, Cys97, and Cys100) and appears to stabilize the relative positions of the N- and C-domains. Mutations of Cys68 and Cys71 or Cys97 and Cys100 to Ser destabilize the protein structure, which results in inactivation of the RNase P activity. In addition, site-directed mutagenesis suggests that Lys69 at the central loop and Arg86 and Arg105 at the zinc ribbon domain are strongly involved in the functional activity, while Arg22, Tyr44, Arg65, and Arg84 play a modest role in the activity.

Amino Acid Sequence↗

PubMed1998

Regeneration of three-disulfide mutants of bovine pancreatic ribonuclease A missing the 65-72 disulfide bond: characterization of a minor folding pathway of ribonuclease A and kinetic roles of Cys65 and Cys72.

The oxidative regeneration pathways of two three-disulfide mutants of bovine pancreatic ribonuclease A (RNase A) missing the 65-72 disulfide bond, [C65S,C72S] and [C65A,C72A], have been studied by using oxidized dithiothreitol (DTTox) as an oxidizing agent and 2-aminoethylmethanethiosulfonate (AEMTS) as a thiol-blocking agent at 25 degrees C and pH 8.0. These mutants are analogues of the des-[65-72] intermediate, which is one of the two major three-disulfide intermediates that follow after the transition states in the regeneration pathways of wild-type RNase A [Rothwarf, D. M., Li, Y.-J., and Scheraga, H. A. (1998) Biochemistry 37, 3760-3766, 3767-3776.]. Both mutants folded through the same pathway but at a rate lower than that of the wild-type protein. The major rate-determining step in the regeneration of these mutants was determined to be the oxidation from the two-disulfide intermediates (2S) to the post-transition-state three-disulfide intermediate (3S*), suggesting the existence of a minor oxidation pathway (2S --> 3S*, where 3S* is des-[65-72]) in the regeneration of the wild-type protein, in addition to one of the two major disulfide-rearrangement pathways (3S --> des-[65-72]). The regeneration intermediates of these mutants (R, 1S, 2S, and 3S) participate in a steady state with a kinetic behavior resembling that of the wild-type protein. However, the apparent equilibrium constants () in the steady state, averaged with statistical factors for these mutants, are significantly smaller than those for the wild-type protein, indicating that the intermediates in the regeneration of the mutants are relatively less stable by 0.32 kcal/mol. This difference is due to the decrease in the average rate constants for intramolecular disulfide-bond formation () for the mutant proteins. Loop entropy calculations indicate that the increase in the average length of all possible disulfide loops of the mutants due to the replacement of Cys65 and Cys72 is not sufficient to account for the observed reduction of the values of for the mutants. Therefore, it is the removal of energetic factors (arising from the loss of the 65-72 disulfide loop) that leads to deceleration of the regeneration of the mutant proteins. The formation of the 65-72 disulfide loop in the regeneration of wild-type RNase A appears to facilitate the subsequent folding events.

Animals↗

PubMed1999

Superadditive and subadditive effects of "hot spot" mutations within the interfaces of placental ribonuclease inhibitor with angiogenin and ribonuclease A.

Previous single-site mutagenesis studies on the complexes of ribonuclease inhibitor (RI) with angiogenin (Ang) and RNase A suggested that in both cases a substantial fraction of the binding energy is concentrated within one small part of the crystallographically observed interface, involving RI residues 434-438. Such energetic "hot spots" are common in protein-protein complexes, but their physical meaning is generally unclear. Here we have investigated this question by examining the detailed interactions within the RI.ligand hot spots and the extent to which they function independently. The effects of Phe versus Ala substitutions show that the key residue Tyr434 interacts with both ligands primarily through its phenyl ring; for Tyr437, the OH group forms the important contacts with RNase A, whereas the phenyl group interacts with Ang. Kinetic characterization of complexes containing multiple substitutions reveals striking, but distinctive, cooperativity in the interactions of RI with the two ligands. The losses in binding energy for the RNase complex associated with replacements of Tyr434 and Asp435, and Tyr434 and Tyr437, are markedly less than additive (i.e., by 2.4 and 1.3 kcal/mol, respectively). In contrast, the energetic effects of the 434 and 435, and 434 and 437, substitution pairs on binding of Ang are fully additive and 2.5 kcal/mol beyond additive, respectively. Superadditivities (0.9-2.4 kcal/mol) are also observed for several multisite replacements involving these inhibitor residues and two Ang residues, Arg5 and Lys40, from this part of the interface. Consequently, the decreases in binding energy for some triple-variant complexes are as large as 8.5-10.1 kcal/mol (compared to a total DeltaG of -21.0 kcal/mol for the wild-type complex). Potential explanations for these functional couplings, many of which occur over distances of >13 A and are not mediated by direct or triangulated contacts, are proposed. These findings show that the basis for the generation of hot spots can be complex, and that these sites can assume significantly more (as with Ang) or less (as with RNase) importance than indicated from the effects of single-site mutations.

Alanine↗

PubMed2006

Characterization of the tryptophan residues of human placental ribonuclease inhibitor and its complex with bovine pancreatic ribonuclease A by steady-state and time-resolved emission spectroscopy.

Human placental ribonuclease inhibitor (hRI) containing six tryptophan (Trp) residues located at positions 19, 261, 263, 318, 375, and 438 and its complex with RNase A have been studied using steady-state and time-resolved fluorescence (298 K) as well as low-temperature phosphorescence (77 K). Two Trp residues in wild-type hRI and also in the protein-protein complex with RNase A are resolved optically. The accessible surface area values of Trp residues in the wild-type hRI and its complex and consideration of inter-Trp energy transfer in the wild-type hRI reveal that one of the Trp residues is Trp19, which is located in a hydrophobic buried region. The other Trp residue is tentatively assigned as Trp375 based on experimental results on wild-type hRI and its complex. This residue in the wild-type hRI is more or less solvent exposed. Both the Trp residues are perturbed slightly on complex formation. Trp19 moves slightly toward a more hydrophobic region, and the environment of Trp375 becomes less solvent exposed. The complex formation also results in a more heterogeneous environment for both the optically resolved Trp residues.

Animals↗

PubMed1975

Alkaline ribonuclease and ribonuclease inhibitor in mammary gland during the lactation cycle and in the R3230AC mammary tumour.

Alkaline RNAase (ribonuclease) and RNAase inhibitor were assayed to determine the potential role of the degradative process in regulating the amount of RNA in the mammary gland and mammary tumour. Very little free alkaline RNAase activity was found in the cytosol fraction of the mammary gland of virgin, pregnant, lactating or involuting Fischer rats. However, addition of p-chloromercuribenzoate to the assay medium revealed latent RNAase which, when expressed on a DNA basis, decreased during pregnancy and lactation. The cytosol latent RNAase is stable in 0.125 M-H2SO4. The non-cytosol RNAase activity also decreased during pregnancy and lactation. Addition of Triton X-100 produced slightly higher activity at all stages tested. The inhibitor activity in rat mammary gland was very low before pregnancy, increased gradually during pregnancy and more dramatically at parturition, continued to increase throughout lactation and returned to resting-gland values by the sixth day of involution. The increase during pregnancy may be due to the increased cellularity of the gland, whereas the gain during lactation was more than could be accounted for by increases in cell number. The R3230AC transplantable mammary tumour resembles the normal gland in early lactation with respect to both its cytosol and non-cytosol alkaline RNAase activities and its moderately high content of RNAase inhibitor. The relatively high inhibitor and low RNAase activities in both the gland of the lactating rat and in the tumour are of potential significance in maintaining high amounts of RNA and increased rates of protein synthesis in these tissues.

Animals↗

PubMed1999

Crystal structure of a hybrid between ribonuclease A and bovine seminal ribonuclease--the basic surface, at 2.0 A resolution.

A variant of bovine pancreatic ribonuclease A has been prepared with seven amino acid substitutions (Q55K, N62K, A64T, Y76K, S80R, E111G, N113K). These substitutions recreate in RNase A the basic surface found in bovine seminal RNase, a homologue of pancreatic RNase that diverged some 35 million years ago. Substitution of a portion of this basic surface (positions 55, 62, 64, 111 and 113) enhances the immunosuppressive activity of the RNase variant, activity found in native seminal RNase, while substitution of another portion (positions 76 and 80) attenuates the activity. Further, introduction of Gly at position 111 has been shown to increase the catalytic activity of RNase against double-stranded RNA. The variant and the wild-type (recombinant) protein were crystallized and their structures determined to a resolution of 2.0 A. Each of the mutated amino acids is seen in the electron density map. The main change observed in the mutant structure compared with the wild-type is the region encompassing residues 16-22, where the structure is more disordered. This loop is the region where the polypeptide chain of RNase A is cleaved by subtilisin to form RNase S, and undergoes conformational change to allow residues 1-20 of the RNase to swap between subunits in the covalent seminal RNase dimer.

Endoribonucleases↗