Abstract
Ribonuclease A (RNase A; Ee 3.1.27.5) was perhaps the most studied enzyme of the 20th century and is the best characterized ribonuclease. The #x201C;A.#x201D; in its name refers not to its substrate specificity, but to the predominant form of the enzyme produced by the bovine pancreas. RNase A is unmodified, whereas RNase B, RNase e, and RNase D are mixtures of glycoforms. Because of its availability in large quantity and high purity, RNase A has been the object of landmark work in protein chemistry and enzymology (see Cuchillo et al. 1997; Raines 1998 and references therein). In addition, cytotoxic RNase A variants and homologues have demonstrated utility as chemotherapeutic agents (Leland and Raines 2001).
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References
Anfinsen CB (1973) Principles that govern the folding of protein chains. Science 181:223–230
Ballinger P, Long FA (1960) Acid ionization constants of alcohols. II. Acidities of some substituted methanols and related compounds. J Am Chem Soc 82:795–798
Barnard EA (1969) Ribonuci eases. Annu Rev Biochem 38:677–732
Barnard EA, Stein WD (1959a) The histidine in the active centre of ribonuclease. I.A specific reaction with brom oacet ic acid. J Mol Biol 1:339–349
Barnard EA, Stein WD (1959b) The histidine residue in the active centre of ribonuclease. II. The position of this residue in the primary protein chain. J Mol Biol 1:350–358
Bruix M, Rico M, González C, Neira JL, Santoro J, Nieto JL, Rüterjans H (1991) Two dimensional 1H-NMR studies of the solution structure of RNase A-pyrimidinenucleotide complexes. In: de Llorens R, Cuchillo CM, Nogues MV, Pares X (eds) Structure, mechanism and fFunction of ribonucleases. Universitat Autónoma de Barcelona, Bellaterra, Spain, pp 15–20
Carter P, Wells JA (1988) Dissecting the catalytic triad of a serine protease. Nature 332:564–568
Cederholm MT, Stuckey JA, Doscher MS, Lee L (1991) Histidine pKa shifts accompanying the inactivating Asp121 → Asn substitution in a semisynthetic bovine pancreatic ribonuclease. Proc Natl Acad Sci USA 88:8116–8120
Chatani E, Tanimizu N, Ueno H, Hayashi R (2001) Structural and functional changes in bovine pancreatic ribonuclease A by the replacement of Phe120 with other hydrophobic residues. J Biochem (Tokyo) 129:917–922
Chatani E, Hayashi R, Moriyama H, Ueki T (2002) Conformational strictness required for maximum activity and stability of bovine pancreatic ribonuclease A as revealed by crystallographic study of three Phe120 mutants at 1.4 Aresolution. Protein Sci 11:72–81
Corey DR, Craik CS (1992) An investigation into the minimum requirements for peptide hydrolysis by mutation of the catalytic triad of trypsin. J Am Chem Soc 114:1784–1790
Craik CS, Roczniak S, Largman C, Rutter WJ (1987) The catalytic role of the active site aspartic acid in serine proteases. Science 237:909–913
Crestfield AM, Stein WH, Moore S (1962) On the aggregation of bovine pancreatic ribonuclease. Arch Biochem Biophys Suppl 1:217–222
Cuchillo CM, Pares X, Guasch A, Barman T, Travers F, Nogues MV (1993) The role of2′,3′cyclic phosphodiesters in the bovine pancreatic ribonuclease A catalysed cleavage of RNA: Intermediates or products? FEBS Lett 333:207–210
Cuchillo CM, Vilanova M, Nogues MV (1997) Pancreatic ribonucleases. In: D’;Alessio G, Riordan JF (eds) Ribonucleases: structures and functions. Academic Press, New York, pp 271–304
Dantzman CL (1998) PhD Thesis, University of Wisconsin-Madison
Dantzman CL, Kiessling LL (1996) Reactivity of a 2′-thio nucleotide analog. J Am Chem Soc 118:11715–11719
Davis AM, Hall AD, Williams A (1988a) Charge description of base-catalyzed alcoholysis of aryl phosphodiesters: A ribonuclease model. J Am Chem Soc 110:5105–5108
Davis AM, Regan AC, Williams A (1988b) Experimental charge measurement at leaving oxygen in the bovine ribonuclease A catalyzed cyclization of uridine 3′-phosphate aryl esters. Biochemistry 27:9042–9047
del Rosario EJ, Hammes GG (1969) Kinetic and equilibrium studies of the ribonuclease-catalyzed hydrolysis of uridine 2′,3′-cyclic phosphate. Biochemistry 8:1884–1889
delCardayré SB, Ribo M, Yokel EM, Quirk DJ, Rutter WJ, Raines RT (1995) Engineering ribonuclease A: production, purification, and characterization of wild-type enzyme and mutants at Gln11. Protein Eng 8:261–273
deMel VSJ, Martin PD, Doscher MS, Edwards BFP (1992) Structural changes that accompany the reduced catalytic efficiency of two semisynthetic ribonuclease analogs. J Biol Chem 267:247–256
Evans TC Jr, Benner J, Xu M-Q (1998) Semisynthesis of cytotoxic proteins using a modified protein splicing element. Protein Sci 7:2256–2264
Fickling MM, Fischer A, Mann BR, Packer J, Vaughan J (1959) Hammett substituent constants for electron-withdrawing substituents: Dissociation of phenols, anilinium ions and dimethylanilinium ions. J Am Chem Soc 81:4226–4230
Findlay D, Herries DG, Mathias AP, Rabin BR, Ross CA (1961) The active site and mechanism of action of bovine pancreatic ribonuclease. Nature 190:781–784
Fisher BM, Ha J-H, Raines RT (1998) Coulombic forces in protein-RNA interactions: Binding and cleavage by ribonuclease A and variants at Lys7,ArglO and Lys66. Biochemistry 37:12121–12132
Gilliland GL (1997) Crystallographic studies of ribonuclease complexes. In: D’Alessio G, Riordan JF (eds) Ribonucleases: structures and functions. Academic Press, New York, pp 305–341
Gundlach HG, Stein WH, Moore S (1959) The nature of the amino acid residues involved in the inactivation of ribonuclease by iodoacetate. J Biol Chem 234:1754–1760
Herries DG, Mathias AP, Rabin BR (1962) The active site and mechanism of action of bovine pancreatic ribonuclease. 3. The pH-dependence of the kinetic parameters for the hydrolysis of cytidine 2′,3′-phosphate Biochem J 85:127-134
Jackson DY, Burnier J, Quan C, Stanley M, Tom J, Wells JA (1994) A designed peptide ligase for total synthesis of ribonuclease A with unnatural catalytic residues. Science 266:243–247
Jencks WP (1985) A primer for the Bema Hapothle. An empirical approach to the characterization of changing transition-state structures. Chem Rev 85:511–527
Kelemen BR, Klink TA, Behlke MA, Eubanks SR, Leland PA, Raines RT (1999) Hypersensitive substrate for ribonucleases. Nucleic Acids Res 27:3696–3701
Ladner JE, Wladkowski BD, Svensson LA, Sjölin L, Gilliland GL (1997) X-Ray structure of a ribonuclease A-uridine vanadate complex at l.3-Å resolution. Acta Crystallogr Sect D 53:290–301
Leland PA, Raines RT (2001) Cancer chemotherapy — ribonucleases to the rescue. Chem Biol 8:405–413
Lin MC, Gutte B, Moore S, Merrifield RB (1970) Regeneration of activity by mixture of ribonuclease enzymatically degraded from the COOH terminus and a synthetic COOH-terminal tetradecapeptide. J Biol Chem 245:5169–5170
Lin MC, Gutte B, Caldi DG, Moore S, Merrifield RB (1972) Reactivation of des(119-124) ribonuclease A by mixture with synthetic COOH-terminal peptides; the role of phenylalanine-120. J Biol Chem 247:4768–4774
Lindquist RN, Lynn JL Jr, Lienhard GE (1973) Possible transition-state analogs for ribonuclease. The complexes of uridine with oxovanadium(IV) ion and vanadium(V) ion. J Am Chem Soc 95:8762–8768
Marchiori F, Borin G, Moroder L, Rocchi R, Scoffone E (1974) Relation between structure and function in some partially synthetic ribonucleases S′. II. Kinetic determinations on [Orn1O, Glu11]-, [Orn1O, Leu11]-and [Orn1O, Lys11]-RNase S′. Int J Pept Prot Res 6:337–345
Markley JL (1975) Correlation proton magnetic resonance studies at 250 MHz of bovine pancreatic ribonuclease. I. Reinvestigation of the histidine peak assignment. Biochemistry 14:3546–3553
Martin PD, Doscher MS, Edwards BFP (1987) The refined crystal structure of a fully active semisynthetic ribonuclease at 1.8-A resolution. J Biol Chem 262:15930–15938 Merrifield RB (1984) Solid phase synthesis. Science 232:341-347
Messmore JM (1999) PhD Thesis, University of Wisconsin, Madison
Messmore JM, Raines RT (2000a) Decavanadate inhibits catalysis by ribonuclease A. Bioconjug Chem 11:25–30
Messmore JM, Raines RT (2000b) Pentavalent organo-vanadates as transition state analogues for phosphoryl transfer reactions. J Am Chem Soc 122:9911–9916
Messmore JM, Fuchs DN, Raines RT (1995) Ribonuclease A: Revealing structure-function relationships with semisynthesis. J Am Chem Soc 117:8057–8060
Messmore JM, Holmgren SK, Grilley JE, Raines RT (2000) Sulfur shuffle: Modulating enzymatic activity by thiol-disulfide interchange. Bioconjug Chem 11:408–413
Moore S, Stein WH (1973) Chemical structures of pancreatic ribonuclease and deoxyribonuclease. Science 180:458–464
Muir TW, Sondhi D, Cole PA (1998) Expressed protein ligation: a general method for protein engineering. Proc Natl Acad Sci USA 95:6705–6710
Murdock AL, Grist KL, Hirs CHW (1966) On the dinitrophenylation of bovine pancreatic ribonuclease A. Kinetic s of the reaction in water and 8 M urea. Arch Biochem Biophys 114:375–390
Neurath H (1989) In: Beynon RJ, Bond JS (eds) Proteolytic enzymes: a practical approach. IRL Press, New York, pp 1–13
Panov KI, Kolbanovskaya EY, Okorokov AL, Panova TB, Terwisscha van Scheltinga AC, Karpeisky MYa, Beintema JJ (1996) Ribonuclease A mutant His119 Asn: The role of histidine in catalysis. FEBS Lett 398:57–60
Park C, Raines RT (2001) Quantitative analysis of the effect of salt concentration on enzymatic catalysis. J Am Chem Soc 123:11472–11479
Park C, Raines RT (2003) Catalysis by ribonuclease A is limited by the rate of substrate association. Biochemistry 42:3509–3518
Park C, Schultz LW, Raines RT (2001) Contribution of the active site histidine residues of ribonuclease A to nucleic acid binding. Biochemistry 40:4949–4956
Quirk DJ, Park C, Thompson JE, Raines RT (1998) His⋯Asp catalytic dyad of ribonuclease A: Conformational stability of the wild-type, D121 N, D121A, and H119A enzymes. Biochemistry 37:17985–17964
Quirk DJ, Raines RT (1999) His⋯Asp catalytic dyad of ribonuclease A: Histidine pKa values in the wild-type, D121 N, and D121A enzymes. Biophys J 76:1571–1579
Raines RT (1998) Ribonuclease A. Chem Rev 98:1045–1065
Reese CB, Simons C, Zhang PZ (1994) The synthesis of 2′-thiouridylyl-(3′→5′)-uridine. J Chem Soc, Chem Commun:1809–1810
Richards FM, Wyckoff HW (1971) Bovine pancreatic ribonuclease. The Enzymes IV:647–806
Schowen RL (1988) Structural and energetic aspects of proteolytic catalysis by enzymes: Charge-relay catalysis in the function of serine proteases. In: Liebman JF, Greenberg A (eds) Mechanistic principles of enzyme activity. VCH, New York, pp 119–168
Schultz LW, Quirk DJ, Raines RT (1998) His⋯Asp catalytic dyad of ribonuclease A:Structure and function of the wild-type, D121 N, and D121A enzymes. Biochemistry 37:8886–8898
Sowa GA, Hengge AC, Cleland WW (1997) 18O isotope effects support a concerted mechanism for ribonuclease A. J Am Chem Soc 119:2319–2320
Sprang S, Standing T, Fletterick RJ, Stroud RM, Finer-Moore JF, Xuong NH, Hamlin R, Rutter WJ, Craik CS (1987) The three-dimensional structure of Asn102 mutant trypsin: Role of Asp102 in serine protease catalysis. Science 237:905–909
Sprang SR, Fletterick RJ, Graf L, Rutter WJ, Craik CS (1988) Studies of specificity and catalysis in trypsin by structural analysis of site-directed mutants. Crit Rev Biotechnol 8: 225–236
Stern MS, Doscher MS (1984) Aspartic acid-121 functions at the active site of bovine pancreatic ribonuclease. FEBS Lett 171:253–256
Tanimizu N, Ueno H, Hayashi R (1998) Role of Phe120 in the activity and structure of bovine pancreatic ribonuclease A. J Biochem 124:410–416
Thompson JE, Raines RT (1994) Value of general acid-base catalysis to ribonuclease A. J Am Chem Soc 116:5467–5468
Thompson JE, Kutateladze TG, Schuster MC, Venegas FD, Messmore JM, Raines RT (1995) Limits to catalysis by ribonuclease A. Bioorg Chem 23:471–481
Thompson JE, Venegas FD, Raines RT (1994) Energetics of catalysi s by ribonucleases: Fate of the 2′,3′-cyclic intermediate. Biochemistry 33:7408–7414
Trautwein K, Holliger P, Stackhouse J, Benner SA (1991) Site-directed mutagenesis of bovine pancreatic ribonuclease: Lysine-41 and aspartate-121. FEBS Lett 281:275–277
Usher DA, Erenrich ES, Eckstein F (1972) Geometry of the first step in the action of ribonuclease-A. Proc Natl Acad. Sci U.S.A. 69:115–118
Usher DA, Richardson DI Jr, Eckstein F (1970) Absolute stereochemistry of the second step of ribonuclease action. Nature 228:663–665
Velikyan I, Acharya S, Trifonova A, Földesi A, Chattopadhyaya J (2001) The pKa’s of 2′hydroxyl group in nucleosides and nucleotides. J Am Chem Soc 123:2893–2894
Witzel H (1963) The function of the pyrimidine base in the ribonuclease reaction. Progr Nucleic Acid Res 2:221–258
Wlodawer A, Miller M, Sjülin L (1983) Active site of RNase: Neutron diffraction study of a complex with uridine vanadate, a transition-state analog. Proc Natl Acad Sci USA 80:3628–3631
Wolfenden R (1976) Transition state analog inhibitors and enzyme catalysis. Annu Rev Biophys Bioeng 5:271–306
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Raines, R.T. (2004). Active Site of Ribonuclease A. In: Zenkova, M.A. (eds) Artificial Nucleases. Nucleic Acids and Molecular Biology, vol 13. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-18510-6_3
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DOI: https://doi.org/10.1007/978-3-642-18510-6_3
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