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Ostendorf T, Zillinger T, Andryka K, Schlee-Guimaraes TM, Schmitz S, Marx S, Bayrak K, Linke R, Salgert S, Wegner J, Grasser T, Bauersachs S, Soltesz L, Hübner MP, Nastaly M, Coch C, Kettwig M, Roehl I, Henneke M, Hoerauf A, Barchet W, Gärtner J, Schlee M, Hartmann G, Bartok E. Immune Sensing of Synthetic, Bacterial, and Protozoan RNA by Toll-like Receptor 8 Requires Coordinated Processing by RNase T2 and RNase 2. Immunity 2020; 52:591-605.e6. [PMID: 32294405 DOI: 10.1016/j.immuni.2020.03.009] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 01/24/2020] [Accepted: 03/18/2020] [Indexed: 01/13/2023]
Abstract
Human toll-like receptor 8 (TLR8) activation induces a potent T helper-1 (Th1) cell response critical for defense against intracellular pathogens, including protozoa. The receptor harbors two distinct binding sites, uridine and di- and/or trinucleotides, but the RNases upstream of TLR8 remain poorly characterized. We identified two endolysosomal endoribonucleases, RNase T2 and RNase 2, that act synergistically to release uridine from oligoribonucleotides. RNase T2 cleaves preferentially before, and RNase 2 after, uridines. Live bacteria, P. falciparum-infected red blood cells, purified pathogen RNA, and synthetic oligoribonucleotides all required RNase 2 and T2 processing to activate TLR8. Uridine supplementation restored RNA recognition in RNASE2-/- or RNASET2-/- but not RNASE2-/-RNASET2-/- cells. Primary immune cells from RNase T2-hypomorphic patients lacked a response to bacterial RNA but responded robustly to small-molecule TLR8 ligands. Our data identify an essential function of RNase T2 and RNase 2 upstream of TLR8 and provide insight into TLR8 activation.
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Affiliation(s)
- Thomas Ostendorf
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Thomas Zillinger
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Katarzyna Andryka
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | | | - Saskia Schmitz
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Samira Marx
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Kübra Bayrak
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Rebecca Linke
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Sarah Salgert
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Julia Wegner
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Tatjana Grasser
- Axolabs GmbH, Fritz-Hornschuch-Strasse 9, 95326 Kulmbach, Germany
| | - Sonja Bauersachs
- Axolabs GmbH, Fritz-Hornschuch-Strasse 9, 95326 Kulmbach, Germany
| | - Leon Soltesz
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Marc P Hübner
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany
| | - Maximilian Nastaly
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Christoph Coch
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany; Miltenyi Biotech, Biomedicine Division, Bergisch Gladbach, Germany
| | - Matthias Kettwig
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Ingo Roehl
- Axolabs GmbH, Fritz-Hornschuch-Strasse 9, 95326 Kulmbach, Germany
| | - Marco Henneke
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Achim Hoerauf
- Institute of Medical Microbiology, Immunology and Parasitology (IMMIP), University Hospital Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Winfried Barchet
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Jutta Gärtner
- Department of Pediatrics and Adolescent Medicine, Division of Pediatric Neurology, University Medical Center Göttingen, Georg August University, Göttingen, Germany
| | - Martin Schlee
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany
| | - Gunther Hartmann
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany; German Center for Infection Research (DZIF), partner site Bonn-Cologne, Cologne, Germany
| | - Eva Bartok
- Department of Clinical Chemistry and Clinical Pharmacology, University Hospital Bonn, Bonn, Germany.
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2
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Parker KM, Barragán Borrero V, van Leeuwen DM, Lever MA, Mateescu B, Sander M. Environmental Fate of RNA Interference Pesticides: Adsorption and Degradation of Double-Stranded RNA Molecules in Agricultural Soils. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2019; 53:3027-3036. [PMID: 30681839 DOI: 10.1021/acs.est.8b05576] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Double-stranded RNA (dsRNA) pesticides are a new generation of crop protectants that interfere with protein expression in targeted pest insects by a cellular mechanism called RNA interference (RNAi). The ecological risk assessment of these emerging pesticides necessitates an understanding of the fate of dsRNA molecules in receiving environments, among which agricultural soils are most important. We herein present an experimental approach using phosphorus-32 (32P)-radiolabeled dsRNA that allows studying key fate processes of dsRNA in soils with unprecedented sensitivity. This approach resolves previous analytical challenges in quantifying unlabeled dsRNA and its degradation products in soils. We demonstrate that 32P-dsRNA and its degradation products are quantifiable at concentrations as low as a few nanograms of dsRNA per gram of soil by both Cerenkov counting (to quantify total 32P-activity) and by polyacrylamide gel electrophoresis followed by phosphorimaging (to detect intact 32P-dsRNA and its 32P-containing degradation products). We show that dsRNA molecules added to soil suspensions undergo adsorption to soil particle surfaces, degradation in solution, and potential uptake by soil microorganisms. The results of this work on dsRNA adsorption and degradation advance a process-based understanding of the fate of dsRNA in soils and will inform ecological risk assessments of emerging dsRNA pesticides.
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Affiliation(s)
- Kimberly M Parker
- Department of Energy, Environmental & Chemical Engineering , Washington University in St. Louis , St. Louis , Missouri 63130 , United States
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
| | - Verónica Barragán Borrero
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Daniël M van Leeuwen
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Mark A Lever
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
| | - Bogdan Mateescu
- Institute of Molecular Plant Biology, Department of Biology , ETH Zürich , 8092 Zürich , Switzerland
| | - Michael Sander
- Institute of Biogeochemistry and Pollutant Dynamics , ETH Zürich , 8092 Zürich , Switzerland
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3
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The inhibition of human tumor cell proliferation by RNase Pol, a member of the RNase T1 family, from Pleurotus ostreatus. Biosci Biotechnol Biochem 2013; 77:1486-91. [PMID: 23832341 DOI: 10.1271/bbb.130133] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
RNase Po1 is a guanylic acid-specific ribonuclease (a RNase T1 family RNase) from Pleurotus ostreatus. We determined the cDNA sequence encoding RNase Po1 and expressed RNase Po1 in Escherichia coli. A comparison of the enzymatic properties of RNase Po1 and RNase T1 indicated that the optimum temperature for RNase Po1 activity was 20 °C higher than that for RNase T1. An MTT assay indicated that RNase Po1 inhibits the proliferation of human neuroblastoma cells (IMR-32 and SK-N-SH) and human leukemia cells (Jurkat and HL-60). Furthermore, Hoechst 33342 staining showed morphological changes in HL-60 cells due to RNase Po1, and flow cytometry indicated the appearance of a sub-G1 cell population. The extent of these changes was dependent on the concentration of RNase Pol. We suggest that RNase Po1 induces apoptosis in tumor cells.
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Abstract
Ribonucleases (RNases) with different sequence or structural specificities are used for a variety of analytical purposes, including RNA sequencing, mapping, and quantitation. The development of RNase protection assays, structural determination assays, and the production of small interfering RNAs (siRNA) employed in RNA interference (RNAi) experiments has depended on the unique substrate specificities of commercially available RNases, including RNases A, I, T1, V1, HI, III, and Dicer. One very common application for high purity RNase A is also presented in this unit and involves hydrolyzing RNA that contaminates DNA preparations. RNase HII and the placental RNase inhibitor are also discussed.
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5
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Garcia-Ortega L, Masip M, Mancheño JM, Oñaderra M, Lizarbe MA, García-Mayoral MF, Bruix M, Martínez del Pozo A, Gavilanes JG. Deletion of the NH2-terminal beta-hairpin of the ribotoxin alpha-sarcin produces a nontoxic but active ribonuclease. J Biol Chem 2002; 277:18632-9. [PMID: 11897788 DOI: 10.1074/jbc.m200922200] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Ribotoxins are a family of highly specific fungal ribonucleases that inactivate the ribosomes by hydrolysis of a single phosphodiester bond of the 28 S rRNA. alpha-Sarcin, the best characterized member of this family, is a potent cytotoxin that promotes apoptosis of human tumor cells after internalization via endocytosis. This latter ability is related to its interaction with phospholipid bilayers. These proteins share a common structural core with nontoxic ribonucleases of the RNase T1 family. However, significant structural differences between these two groups of proteins are related to the presence of a long amino-terminal beta-hairpin in ribotoxins and to the different length of their unstructured loops. The amino-terminal deletion mutant Delta(7-22) of alpha-sarcin has been produced in Escherichia coli and purified to homogeneity. It retains the same conformation as the wild-type protein as ascertained by complete spectroscopic characterization based on circular dichroism, fluorescence, and NMR techniques. This mutant exhibits ribonuclease activity against naked rRNA and synthetic substrates but lacks the specific ability of the wild-type protein to degrade rRNA in intact ribosomes. The results indicate that alpha-sarcin interacts with the ribosome at two regions, i.e. the well known sarcin-ricin loop of the rRNA and a different region recognized by the beta-hairpin of the protein. In addition, this latter protein portion is involved in interaction with cell membranes. The mutant displays decreased interaction with lipid vesicles and shows behavior compatible with the absence of one vesicle-interacting region. In agreement with this conclusion, the deletion mutant exhibits a very low cytotoxicity on human rhabdomyosarcoma cells.
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Affiliation(s)
- Lucia Garcia-Ortega
- Departamento de Bioquimica y Biologia Molecular I, Universidad Complutense, Madrid 28040, Spain
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Affiliation(s)
- S Loverix
- Dienst Ultrastructuur, Instituut voor Moleculaire Biologie, Vrije Universiteit Brussel, B-1640 Sint-Genesius-Rode, Belgium
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Irie M. Structure-function relationships of acid ribonucleases: lysosomal, vacuolar, and periplasmic enzymes. Pharmacol Ther 1999; 81:77-89. [PMID: 10190580 DOI: 10.1016/s0163-7258(98)00035-7] [Citation(s) in RCA: 95] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
It is surprising that only relatively recently has attention been directed to the characterization of the properties of acid ribonucleases (RNases), leading to some understanding of their biochemistry and their functional roles. The present review summarizes current progress in this field under the following general topics: (1) the wide distribution of acid RNases in organisms from viruses to animals; (2) recent findings concerning their primary and three-dimensional structure; (3) the structure-function relationship of acid RNases, with a fungal RNase from Rhizopus niveus as a model enzyme; (4) the unique localization of acid RNases in the periplasm of bacteria, vacuoles in plants, and lysosomes of animals and protozoa; and (5) the diversity of physiological roles, depending on the organism, such as self-incompatibility factors and defense proteins in some plants, the surface protein of an animal virus related to pathogenicity, and possible relationship to human cancer.
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Affiliation(s)
- M Irie
- Department of Microbiology, Hoshi College of Pharmacy, Tokyo, Japan
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8
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Chacko R, Shankar V. Extracellular ribonuclease from Rhizopus stolonifer: characteristics of an atypical--guanylic acid preferential--enzyme from ribonuclease T2 family. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1379:264-72. [PMID: 9528662 DOI: 10.1016/s0304-4165(97)00103-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
An extracellular ribonuclease from Rhizopus stolonifer (designated as RNase Rs) was purified to homogeneity by chromatography on DEAE-cellulose followed by CM-cellulose. The Mr of the purified enzyme determined by gel filtration and SDS-PAGE is 25,000 and 28,200, respectively. RNase Rs is a glycoprotein and contains 10.5% neutral sugar. It is an acidic protein with a pI of 5.0 and has a blocked N-terminus. The optimum pH and temperature are 5.5 and 45 degrees C, respectively. RNase Rs shows high stability between pH 6.0-10.0. Divalent cations like Zn2+, Hg2+ and Cu2+ inhibit the enzyme activity whereas, mononucleotides does not have any significant effect. The enzyme cleaves RNA to 3'-mononucleotides via 2',3'-cyclic nucleotides, with preferential liberation of 2',3'-cyclic GMP, suggesting that RNase Rs is a guanylic acid preferential cyclizing RNase. Moreover, cyclic nucleotides generated are highly resistant to further hydrolysis.
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Affiliation(s)
- R Chacko
- Division of Biochemical Sciences, National Chemical Laboratory, Pune, India
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9
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Steyaert J. A decade of protein engineering on ribonuclease T1--atomic dissection of the enzyme-substrate interactions. EUROPEAN JOURNAL OF BIOCHEMISTRY 1997; 247:1-11. [PMID: 9249002 DOI: 10.1111/j.1432-1033.1997.t01-1-00001.x] [Citation(s) in RCA: 90] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
During the last decade, protein engineering has been used to identify the residues that contribute to the ribonuclease-T1-catalyzed transesterification. His40, Glu58 and His92 accelerate the associative nucleophilic displacement at the phosphate atom by the entering 2'-oxygen downstream guanosines in a highly cooperative manner. Glu58, assisted by the protonated His40 imidazole, abstracts a proton from the 2'-oxygen, while His92 protonates the leaving group. Tyr38, Arg77 and Phe100 further stabilize the transition state of the reaction. A functionally independent subsite, including Asn36 and Asn98, contributes to chemical turnover by aligning the substrate relative to the catalytic side chains upon binding of the leaving group. An invariant structural motive, involving residues 42-46, renders ribonuclease T1 guanine specific through a series of intermolar hydrogen bonds. Tyr42 contributes significantly to guanine binding through a parallel face-to-face stacking interaction. Tyr45, often referred to as the lid of the guanine-binding site, does not contribute to the binding of the base.
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Affiliation(s)
- J Steyaert
- Dienst Ultrastruktuur, Vlaams Interuniversitair instituut Biotechnologie, Vrije Universiteit Brussel, Belgium.
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10
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Pe'ery T, Mathews MB. Synthesis and purification of single-stranded RNA for use in experiments with PKR and in cell-free translation systems. Methods 1997; 11:371-81. [PMID: 9126552 DOI: 10.1006/meth.1996.0435] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
The biosynthesis of RNA in vitro using bacteriophage RNA polymerases has opened up many avenues of research. Large amounts of specific RNA species can be readily produced but small amounts of contaminants that are simultaneously generated can interfere with biological assays, PKR, a ribosome-associated and double-stranded (ds) RNA-dependent protein kinase, is an important regulator of the initiation of protein synthesis. It can be activated by very low concentrations of dsRNA and inhibited by small structured RNAs or high concentrations of dsRNA. The best-studied inhibitor of PKR activation is adenovirus VA RNA1. Its gene was cloned into a plasmid under the control of the T7 RNA polymerase promoter, and the optimization of VA RNA transcription is described. A dsRNA by-product of the transcription reaction activates PKR in kinase autophosphorylation assays, and hence a purification protocol that allows the separation and removal of dsRNA contaminants was developed. A scheme to analyze the RNA product with specific nucleases is discussed. In a reticulocyte cell-free translation system the activation of PKR by dsRNA contaminating a synthetic mRNA preparation is likely to lead to shut-off of translation. An assay to directly visualize and measure the level of PKR phosphorylation in the lysate is detailed.
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Affiliation(s)
- T Pe'ery
- Cold Spring Harbor Laboratory, New York 11724, USA.
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11
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Narlikar GJ, Khosla M, Usman N, Herschlag D. Quantitating tertiary binding energies of 2' OH groups on the P1 duplex of the Tetrahymena ribozyme: intrinsic binding energy in an RNA enzyme. Biochemistry 1997; 36:2465-77. [PMID: 9054551 DOI: 10.1021/bi9610820] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Binding of the Tetrahymena ribozyme's oligonucleotide substrate (S) involves P1 duplex formation with the ribozyme's internal guide sequence (IGS) to give an open complex, followed by docking of the P1 duplex into the catalytic core via tertiary interactions to give a closed complex. The overall binding energies provided by 2' OH groups on S and IGS have been measured previously. To obtain the energetic contribution of each of these 2' OH groups in the docking step, we have separately measured their contribution to the stability of a model P1 duplex using "substrate inhibition". This new approach allows measurement of duplex stabilities under conditions identical to those used for ribozyme binding measurements. The tertiary binding energies from the individual 2' OH groups include a small destabilizing contribution of 0.7 kcal/mol and stabilizing contributions of up to -2.9 kcal/mol. The energetic contributions of specific 2' OH groups are discussed in the context of considerable previous work that has characterized the tertiary interactions of the P1 duplex. A "threshold" model for the open and closed complexes is presented that provides a framework to interpret the energetic effects of functional group substitutions on the P1 duplex. The sum of the tertiary stabilization provided by the conserved G x U wobble at the cleavage site and the individual 2' OH groups on the P1 duplex is significantly greater than the observed tertiary stabilization of S (11.0 vs 2.2 kcal/mol). It is suggested that there is an energetic cost for docking the P1 duplex into the active site that is paid for by the "intrinsic binding energy" of groups on the P1 duplex. Substrates that lack sufficient tertiary binding energy to overcome this energetic barrier exhibit reduced reactivities. Thus, the ribozyme appears to use the intrinsic binding energy of groups on the P1 duplex for catalysis. This intrinsic binding energy may be used to position reactants within the active site and to induce electrostatic destabilization of the substrate, relative to its interactions in solution.
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Affiliation(s)
- G J Narlikar
- Department of Chemistry, Stanford University, California 94305, USA
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12
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Weinstein LB, Earnshaw DJ, Cosstick R, Cech TR. Synthesis and Characterization of an RNA Dinucleotide Containing a 3‘-S-Phosphorothiolate Linkage. J Am Chem Soc 1996. [DOI: 10.1021/ja9616903] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lara B. Weinstein
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - David J. Earnshaw
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Richard Cosstick
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
| | - Thomas R. Cech
- Contribution from the Howard Hughes Medical Institute, Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado 80309-0215, and Robert Robinson Laboratory, Department of Chemistry, University of Liverpool, Liverpool L69 3BX, U.K
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13
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Query CC, Moore MJ, Sharp PA. Branch nucleophile selection in pre-mRNA splicing: evidence for the bulged duplex model. Genes Dev 1994; 8:587-97. [PMID: 7926752 DOI: 10.1101/gad.8.5.587] [Citation(s) in RCA: 157] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Selection of the nucleophile for the first step of nuclear pre-mRNA splicing was probed by site-specific incorporation into splicing substrates of nucleotides modified at the 2' position. The differing abilities of ribose, 2'-deoxyribose, and arabinose nucleotides to base-pair within an RNA.RNA duplex and to contribute a nucleophilic 2'-OH group were exploited to analyze the paired/unpaired disposition of the branch site nucleotide. The results provide direct evidence for a bulged duplex model in which either of two adjacent purines within the consensus branch site sequence may shift into a bulged position and contribute the 2'-OH group for the first step of splicing. Furthermore, the presence of a consensus branch site that cannot present a reactive nucleophile suppresses splicing, including the use of cryptic branch sites elsewhere. We conclude that the branch site region base-pairing with U2 snRNA determines the first step nucleophile and persists at the time of the first transesterification reaction.
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Affiliation(s)
- C C Query
- Center for Cancer Research, Massachusetts Institute of Technology, Cambridge 02139-4307
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14
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Nishimura N, Kitaoka Y, Niwano M. Utilization of copper ion as a ribonuclease inhibitor in a cell-free protein synthesis system. ACTA ACUST UNITED AC 1994. [DOI: 10.1016/0922-338x(94)90250-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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15
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Meiering EM, Bycroft M, Lubienski MJ, Fersht AR. Structure and dynamics of barnase complexed with 3'-GMP studied by NMR spectroscopy. Biochemistry 1993; 32:10975-87. [PMID: 8218163 DOI: 10.1021/bi00092a006] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
The binding of 3'-GMP to the ribonuclease, barnase, has been studied using heteronuclear 2D and 3D NMR spectroscopy. The 1H and 15N NMR spectra of barnase complexed with 3'-GMP have been assigned. 2D and 3D NOESY spectra have been used to identify inter- and intramolecular NOEs, and a solution structure for the barnase-3'-GMP complex has been calculated. The position of the guanine ring of the ligand is reasonably well defined in the structures. The guanine ring forms hydrogen bonds with the NH protons of Ser57 and Arg59. These residues are located in a loop that is conserved among the microbial guanine-specific ribonucleases. The 2'-hydroxyl of 3'-GMP is close to His102 and Glu73, which have been shown to be involved in catalysis. The phosphate group of 3'-GMP is close to a number of positively charged residues that have also been shown to be important for activity. The position of the sugar moiety of 3'-GMP is less well defined in the structures. Structures calculated for the complex could not simultaneously satisfy all the observed intermolecular NOEs for the sugar protons, suggesting that the sugar samples several conformations when bound to barnase. The binding of 3'-GMP to barnase in solution is similar to that observed in the crystal structures of nucleotides bound to related ribonucleases. 3'-GMP binding causes no major conformational change in barnase. In contrast to the small structural changes that occur, there is a significant decrease in the rates of hydrogen/deuterium exchange and aromatic ring rotation in the active site of barnase upon ligand binding.
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Affiliation(s)
- E M Meiering
- MRC Unit for Protein Function and Design, Cambridge IRC for Protein Engineering, U.K
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16
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Schmidt JM, Thüring H, Werner A, Rüterjans H, Quaas R, Hahn U. Two-dimensional 1H, 15N-NMR investigation of uniformly 15N-labeled ribonuclease T1. Complete assignment of 15N resonances. EUROPEAN JOURNAL OF BIOCHEMISTRY 1991; 197:643-53. [PMID: 1903106 DOI: 10.1111/j.1432-1033.1991.tb15954.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Uniformly 15N-enriched ribonuclease T1 (RNase T1) was obtained from Escherichia coli by recombinant techniques. Heteronuclear 1H, 15N-shift correlation spectra were recorded utilizing proton detection. Direct 1H, 15N connectivities were established applying the heteronuclear multiple-quantum coherence technique. Additional 1H, 1H-TOCSY or 1H, 1H-NOESY transfer steps allowed for sequential assignments. Nitrogen atoms without directly bonded protons were detected by means of the heteronuclear multiple-bond correlation experiment. Signals emerging from 15NH and 15NH2 groups were distinguished by heteronuclear triple-quantum filtering methods. 119 nitrogen resonances out of the expected 127 were assigned unambiguously; in addition, previously obtained proton assignments were extended. Preliminary 1H, 15N NMR investigation were performed on the RNase-T1-3'GMP inhibitor complex. Results were interpreted with respect to nucleotide binding.
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Affiliation(s)
- J M Schmidt
- Institut für Biophysikalische Chemie, Johann-Wolfgang-Goethe-Universität Frankfurt, Federal Republic of Germany
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17
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Vicente O, Filipowicz W. Purification of RNA 3'-terminal phosphate cyclase from HeLa cells. Covalent modification of the enzyme with different nucleotides. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 176:431-9. [PMID: 3416880 DOI: 10.1111/j.1432-1033.1988.tb14300.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
RNA 3'-terminal phosphate cyclase has been purified about 6000-fold to near homogeneity from HeLa cells. The purified protein is a single polypeptide with an Mr of 38,000-40,000 and a Stokes radius of 2.66 nm. The cyclase shows a pH optimum of 8.0-9.0. In the presence of Mg2+ and ATP this enzyme catalyzes the conversion of a 3'-phosphate group into the cyclic 2',3'-phosphodiester at the 3' end of RNA, through formation of a covalent cyclase-AMP intermediate. GTP, CTP and UTP (but not dATP or ADP) can also function as cofactors in the cyclization reaction, although less efficiently (apparent Km values for ATP and GTP are 6 microM and 200 microM, respectively). Consistent with this, the enzyme can be covalently labelled with the four [alpha-32P]NTPs.
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Affiliation(s)
- O Vicente
- Friedrich Miescher-Institut, Basel, Switzerland
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18
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Quaas R, McKeown Y, Stanssens P, Frank R, Blöcker H, Hahn U. Expression of the chemically synthesized gene for ribonuclease T1 in Escherichia coli using a secretion cloning vector. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 173:617-22. [PMID: 3131142 DOI: 10.1111/j.1432-1033.1988.tb14043.x] [Citation(s) in RCA: 80] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The gene for ribonuclease T1 from Aspergillus oryzae has been chemically synthesized using the segmental support technique. An Escherichia coli clone producing the ribonuclease at high levels was constructed by linking the gene downstream to the region coding for the signal peptide of the OmpA protein (a major outer membrane protein of E. coli), using the secretion cloning vector pIN-III-ompA2. This strategy was employed in order to circumvent a possible toxic effect of the gene product on the host cell. Active ribonuclease containing four additional amino acids at the N-terminus could be isolated from the periplasmic fraction of the host. The final yield after purification was 20 mg enzyme/l liquid culture. With respect to immunological, catalytic and specific behaviour, no qualitative differences could be detected between the enzyme from the over-producing E. coli strain and ribonuclease T1 isolated from A. oryzae.
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Affiliation(s)
- R Quaas
- Abteilung Saenger, Institut für Kristallographie, Freie Universität Berlin
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19
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Nishikawa S, Morioka H, Kimura T, Ueda Y, Tanaka T, Uesugi S, Hakoshima T, Tomita K, Ohtsuka E, Ikehara M. Increase in nucleolytic activity of ribonuclease T1 by substitution of tryptophan 45 for tyrosine 45. EUROPEAN JOURNAL OF BIOCHEMISTRY 1988; 173:389-94. [PMID: 3129293 DOI: 10.1111/j.1432-1033.1988.tb14011.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The preparation and analysis of a mutant ribonuclease (RNase) T1 which possesses higher nucleolytic activity than the wild-type enzyme are described. The gene for the mutant RNase T1 (Tyr45----Trp45), in which a single amino acid at the binding site of the guanine base has been changed, was constructed by the cassette mutangenesis method using a chemically synthesized gene [Ikehara, M. et al. (1986) Proc. Natl Acad. Sci. USA 83, 4695-4699]. In order to reduce the nucleolytic activity of the enzyme in vivo, this gene was expressed in Escherichia coli as a fused protein connected through methionine residues to other proteins at both the N- and C-termini. After liberation from the fused protein by cleavage with cyanogen bromide at the methionine junctions, the mutant RNase T1 was purified by column chromatography. The nucleolytic activity toward pGpC increased to 120% of that of wild-type RNase T1. The kinetic parameters of the mutant enzyme demonstrate that this higher nucleolytic activity is due to a higher affinity for the substrate, probably because of an increased stacking effect in the binding pocket for the guanine base. This mutant enzyme also possessed a higher nucleolytic activity against pApC than wild-type RNase T1.
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Affiliation(s)
- S Nishikawa
- Faculty of Pharmaceutical Sciences, Osaka University, Japan
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20
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Inoue H, Hayase Y, Iwai S, Ohtsuka E. Sequence-dependent hydrolysis of RNA using modified oligonucleotide splints and RNase H. FEBS Lett 1987; 215:327-30. [PMID: 2438160 DOI: 10.1016/0014-5793(87)80171-0] [Citation(s) in RCA: 208] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We found that, in the presence of chimeric oligonucleotides containing complementary deoxyribo- and 2'-O-methylnucleosides, a nonaribonucleotide, [5'-32P]pACUUACCUG, was cleaved specifically upon treatment with RNase H. When 3'm(UG)d(AATG)m(GAC)5' was used as a hybridization strand, pACUUACCUG was cleaved between C6 and C7 to yield pACUUAC. In the presence of 3'm(UGAA)d(TGGA)m(C)5', the nonaribonucleotide was hydrolyzed, mainly between U8 and C9, to give pACUUACCU. This method will have a variety of applications in the field of RNA engineering.
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21
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Abstract
Production of extracellular RNase(s) by Yarrowia lipolytica CX161-1B was examined in media between pHs 5 and 7. RNase production occurred during the exponential growth phase. High-molecular-weight nitrogen compounds supported the highest levels of RNase production. Several RNases were detected in the supernatant medium. Based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis, the RNases had estimated molecular weights of 45,000, 43,000, and 34,000. It was found that Y. lipolytica secretes only one RNase (the 45,000-molecular-weight RNase) and that the 43,000 and 34,000-molecular-weight RNases are degradation products of this RNase. The alkaline extracellular protease secreted by Y. lipolytica was shown to have a major role in the 45,000- to 43,000-molecular-weight conversion, and it was demonstrated that the 45,000-molecular-weight RNase could be purified from a mutant which does not produce the alkaline extracellular protease. Purification of the RNase from a wild-type strain resulted in purification of the 43,000-molecular-weight RNase. This RNase was a glycoprotein with a molecular weight of 44,000 as estimated by gel filtration, an isoelectric point of pH 4.8, and a pH optimum between 6.5 and 7.0.
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22
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James DR, Demmer DR, Steer RP, Verrall RE. Fluorescence lifetime quenching and anisotropy studies of ribonuclease T1. Biochemistry 1985; 24:5517-26. [PMID: 3935161 DOI: 10.1021/bi00341a036] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The time-resolved fluorescence of the lone tryptophanyl residue of ribonuclease T1 was investigated by using a mode-locked, frequency-doubled picosecond dye laser. The fluorescence decay could be characterized by a single exponential function with a lifetime of 3.9 ns. The fluorescence was readily quenched by uncharged solutes but was unaffected by iodide ion. These observations are interpreted in terms of the electrostatic properties of the amino acid residues at the active site of the protein, which would appear to restrict the access of solute species to the tryptophanyl residue. The temperature dependence of the fluorescence lifetime and anisotropy decay time could be rationalized in terms of a model which postulates a significant ordering of the solvent layer immediately surrounding the surface of the protein.
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23
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Shelness GS, Williams DL. Secondary structure analysis of apolipoprotein II mRNA using enzymatic probes and reverse transcriptase. Evaluation of primer extension for high resolution structure mapping of mRNA. J Biol Chem 1985. [DOI: 10.1016/s0021-9258(17)39519-4] [Citation(s) in RCA: 35] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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24
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Lindberg RA, Drucker H. Characterization and comparison of a Neurospora crassa RNase purified from cultures undergoing each of three different states of derepression. J Bacteriol 1984; 157:375-9. [PMID: 6229528 PMCID: PMC215257 DOI: 10.1128/jb.157.2.375-379.1984] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Extracellular RNase N4 from Neurospora crassa is derepressible by limitation of any of the three nutrient elements obtainable from RNA. We have purified and characterized the enzyme from cultures grown under each of the three states of derepression. The purification procedure consisted of an ultrafiltration step, cation-exchange chromatography, and gel filtration. We found only one enzyme (N4) that hydrolyzed RNA at pH 7.5 in the presence of EDTA in culture filtrates from nitrogen-, phosphorus-, or carbon-limited cells. In all three cases, the enzymes were identical by polyacrylamide gel electrophoresis (Mr approximately 9,500) and by gel filtration (Mr approximately 10,000). There were no differences in thermal stability or pH optimum; all three cross-reacted with antibody to the nitrogen-depressed enzyme in interfacial ring and in Ouchterlony tests. Digestion of homopolyribonucleotides indicated that N4 preferentially cleaved phosphodiester bonds adjacent to guanine residues. Results indicate that the enzymes are very similar or identical and are probably products of the same gene. N4 appears to be homologous to guanine-specific RNases from other fungal sources.
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26
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Diadenosine 5',5"'-P1,P4-tetraphosphate and related adenylylated nucleotides in Salmonella typhimurium. J Biol Chem 1983. [DOI: 10.1016/s0021-9258(18)32297-x] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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27
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Purification and characterization of a novel UpN-specific endoribonuclease VI from Artemia larvae. J Biol Chem 1982. [DOI: 10.1016/s0021-9258(18)33552-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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28
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30
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Yasuda Y, Inoue Y. Evidence for the presence of two kinetically distinct active forms of ribonuclease T2. The pH dependence of the steady-state kinetic parameter, kcat, for transphosphorylation of both a natural and a synthetic substrate. EUROPEAN JOURNAL OF BIOCHEMISTRY 1981; 114:229-34. [PMID: 6260492 DOI: 10.1111/j.1432-1033.1981.tb05140.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
A kinetic study has been made of the RNase-T2-catalyzed transphosphorylation of two adenine nucleotides, adenylyl(3'-5')uridine and adenosine 3'-(1-naphthyl)phosphate. Rates were measured at pH values ranging from 2.6 to 8.2. The observed shape of the plot of log kcat against pH for both the natural and the synthetic substrate suggests that there exist two parallel rate-determining pathways. Two pH-independent rate constants and three ionization constants of the enzyme-substrate complexes were obtained by nonlinear iterative least-squares analysis. Detailed interpretation of the pH profiles was carried out and it is proposed that carboxylate anion is likely to deprotonate O-2' at 4 less than pH less than 6, but at pH greater than 6 an alternative general base would play this role more effectively than the carboxylate group. Another base in its protonated cationic form is responsible for the general acid catalysis.
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31
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Heinemann U, Wernitz M, Pähler A, Saenger W, Menke G, Rüterjans H. Crystallization of a complex between ribonuclease T1 and 2'-guanylic acid. EUROPEAN JOURNAL OF BIOCHEMISTRY 1980; 109:109-14. [PMID: 6250834 DOI: 10.1111/j.1432-1033.1980.tb04774.x] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Ribonuclease T1 was crystallized under various conditions. Form I crystals were produced by microdialysis against 53% (v/v) 2-methyl-2,4-pentanediol in 0.01 M sodium acetate, 0.05% 2'-guanylic acid (2'GMP) and 0.02% NaN3 (pH 6.2-7.2). These crystals are tetragonal, space group P41212 and contain two molecules per asymmetric unit; cell dimensions are a = b = 5.86 nm, c = 13.28 nm. Form IIa and form IIb crystals were obtained by microdialysis from a buffer of 0.01-0.05 M sodium acetate, 0.25-0.5% 2'GMP, 0.02% NaN3 and 2-5 mM calcium acetate (pH 4.0-4.4) in the presence of 50-75% (v/v) 2-methyl-2,4-pentanediol. These crystals are orthorhombic, space group P212121, and contain one molecule per asymmetric unit; cell dimensions are a = 4.66 nm, b = 5.02 nm, c = 4.04 nm (form I) and alpha = 4.44 nm, b = 5.00 nm, c = 4.03 nm (form II). Using high-performance liquid chromatography, it could be shown for all crystal forms that 2'-GMP is bound in the crystals. The molecular ratio between RNase T1 and 2'GMP was 0.9 for form II crystals and thus agreed with a 1:1 enzyme-nucleotide complex. Heavy-atom derivatives were produced with lead acetate for form IIa crystals and with uranyl acetate for from IIb crystals. Three-dimensional X-ray analysis of the RNase-T1 x 2'GMP complex is under way.
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33
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Ludwig W, Follmann H. The specificity of ribonucleoside triphosphate reductase. Multiple induced activity changes and implications for deoxyribonucleotide formation. EUROPEAN JOURNAL OF BIOCHEMISTRY 1978; 82:393-403. [PMID: 624279 DOI: 10.1111/j.1432-1033.1978.tb12034.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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34
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Satoh K, Inoue Y. SUBSTITUENT EFFECT ON RIBONUCLEASE T1-CATALYZED TRANSPHOSPHORYLATION OFpara-SUBSTITUTED BENZYL ESTERS OF GUANOSINE 3′-PHOSPHATE. CHEM LETT 1975. [DOI: 10.1246/cl.1975.551] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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Tolman GL, Barrio JR, Leonard NJ. Chloroacetaldehyde-modified dinucleoside phosphates. Dynamic fluorescence quenching and quenching due to intramolecular complexation. Biochemistry 1974; 13:4869-78. [PMID: 4373039 DOI: 10.1021/bi00721a001] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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36
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D'Alessio G, Zofra S, Libonati M. Action of dimeric ribonucleases on double-stranded RNA. FEBS Lett 1972; 24:355-358. [PMID: 11946706 DOI: 10.1016/0014-5793(72)80390-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Affiliation(s)
- G D'Alessio
- Laboratorio di Chimica Biologica, Facoltà di Sienze, Università di Napoli, Via Mezzoeannone 16, 80134, Napoli, Italy
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