Ribonucleases (eBook)

Front Cover 1
Ribonucleases Structures and Functions 4
Copyright Page 5
Contents 6
Contributors 12
Preface 16
Chapter 1. Escherichia coli Ribonucleases: Paradigms for Understanding Cellular RNA Metabolism and Regulation 22
I. Introduction 23
II. Gallery of Escherichia Coli Ribonucleases 24
III. Endoribonucleases 24
IV. Exoribonucleases 40
V. Ribonuclease Functional Roles 44
VI. Other Ribonucleases 54
VII. Ribonuclease Regulation an RNA Metabolic Control 56
VIII. Conclusions and Prospects 58
References 59
Chapter 2. Barnase and Barstar 72
I. Introduction 72
II. Gene Structure 75
III. Activity and Structure 78
IV. Barnase, Barstar, and the Folding Problem 91
V. Barnase and Barstar Homologs 107
VI. Other Practical Applications of Barnase 110
VII. Concluding Remarks 111
References 112
Chapter 3. RNase T1/RNase T2 Family RNases 122
I. RNase T1 Family RNases 122
II. RNase T2 Family RNases 130
References 145
Chapter 4. Structure and Mechanism of Action of Cytotoxic Ribonuclease a-Sarcin 152
I. Discovery of a-Sarcin and Determination of Basis of Its Cytotoxicity 152
II. Substrate Specificity of a-Sarcin 153
III. a-Sarcin Cleavage Site Sequence 154
IV. Structure of a-Sarcin and of Related Aspergillus Toxins 157
V. Mechanism by Which a-Sarcin Enters Cells 159
VI. a-Sarcin Recognition Elements in 28S rRNA 159
VII. Conformation of Sarcin Domain in 28S rRNA 166
VIII. Effect of Mutations of Analog of G4319 in 28S rRNA on Recognition Oligoribonucleotides by a-Sarcin 169
IX. Phenotype of Mutations in G2655 in Escherichia coli 23S rRNA 170
X. Relationship of a-Sarcin RNA Identity Element to Selection by Toxin of Unique Site of Phosphodiester Bond Hydrolysis 173
XI. Three-Dimensional Structure of Restrictocin, a Homolog of a-Sarcin. Binding to a-Sarcin Domain RNA and Catalytic Mechanism 174
XII. Coda 180
References 180
Chapter 5. Plant Ribonucleases 184
I. Introduction 184
II. Classes of Plant RNases 185
III. Regulation and Functions of Plant RNases 194
IV.Conclusions and Future Prospects 203
References 204
Chapter 6. S-RNases and Other Plant Extracellular Ribonucleases 212
I. Introduction 213
II. Self-Incompatibility in the Solanaceae 213
III. S-RNases from the Rosaceae 223
IV. Extracellular Ribonucleases Associated with Stress 224
V. Seed RNases and Other RNases of Unknown Function and Location 226
VI. Plant Extracellular RNases: Enzymes in Search of a Substrate 227
References 229
Chapter 7. Evolutionary Reconstructions in the Ribonuclease Family 234
I. Introduction 235
II. Protein Engineering to Understand Evolution 236
III. Reconstructing Evolution of Biomolecular Behavior in RNase Superfamily 246
IV. Repair of Damaged Pseudogenes by Gene Conversion: A Mechanism for Obtaining Biomolecular Function in Proteins 253
V. Physiological Function of Seminal RNase 258
VI. Conclusions 259
References 260
Chapter 8. Evolution of Vertebrate Ribonucleases: Ribonuclease A Superfamily 266
I. The Ribonuclease Superfamily 266
II. Mammalian Ribonucleases 1: Pancreatic Type 273
References 286
Chapter 9. Pancreatic Ribonucleases 292
I. Introduction 293
II. Reaction Catalyzed by Pancreatic Ribonucleases 293
III. Specificity of Reaction and Catalytic Mechanism 297
IV. Substrate Binding Subsites: Structure and Function 305
V. The Carbohydrate Moiety: Structure and Function 308
VI. Folding/Unfolding of Ribonuclease A 311
References 318
Chapter 10. Crystallographic Studies of Ribonuclease Complexes 326
I. Introduction 327
II. Phosphate/Sulfate-Free RNase 329
III. Phosphate/Sulfate Binding Site 331
IV. Substrate Analog–RNase Complexes 332
V. Transition State Analog–RNase Complex 338
VI. Product-RNase Complexes 341
VII. Nonproductive Ligand–RNase Complexes 344
VIII. Other Ligand–RNase Complexes 345
IX. Semisynthetic RNases 350
X. Conclusions 354
References 358
Chapter 11. NMR Solution Structures of Ribonuclease A and Its Complexes with Mono- and Dinucleotides 364
I. Introduction 364
II. Structure of Bovine Pancreatic Ribonuclease A in Aqueous Solution 366
III. Ligand Binding Studies: Complexes with Mono- and Dinucleotides 379
IV. Structures of Other Animal Ribonucleases in Solution 394
References 399
Chapter 12. Seminal Ribonuclease: The Importance of Diversity 404
I. Introduction 404
II. Isolation and Production of Seminal RNase 406
III. Structures 409
IV. Functions 429
References 438
Chapter 13. Eosinophil-Associated Ribonucleases 446
I. Introduction 447
II. The Ribonuclease Superfamily 450
III. Eosinophil-Derived Neurotoxin 452
IV. Eosinophil Cationic Protein 457
V. Conclusion 460
References 461
Chapter 14. Structure and Function of Angiogenin 466
I. Introduction 467
II. Angiogenesis 468
III. Isolation of Angiogenin 471
IV. Characterization as Member of the Ribonuclease Family 474
V. Relationship of RNase Activity and Angiogenic Activity 488
VI. Interaction with Endothelial Cells 491
VII. Angiogenin Enhancement of Actin Acceleration of Plasminogen Activation 497
VIII. Angiogenin Support of Endothelial Cell Adhesion 498
IX. Mechanism of Action 499
X. Biology of Angiogenin 501
XI. Epilogue 504
References 504
Chapter 15. Antitumor RNases 512
I. Introduction 512
II. Bovine Seminal RNase 513
III. Amphibian RNases 520
IV. Concluding Remarks 529
References 530
Chapter 16. 2–5A-Dependent RNase L: A Regulated Endoribonuclease in the Interferon System 536
1. Perspectives on the 2–5A System 537
II. Structure and Function of RNase L 539
III. Biochemical Properties of RNase L 545
IV. Distribution, Localization, and Regulation of RNase L and Its Gene 553
V. Biological Activities of RNase L 557
References 562
Chapter 17. RNA-Processing RNases in Mammalian Cells 574
1. Introduction 574
II. rRNA-Processing Ribonucleases 575
III. mRNA-Degrading Ribonucleases 584
IV. Summary 597
References 598
Chapter 18. Messenger RNA Ribonucleases and mRNA Turnover in Saccharomyces cerevisiae 610
I. Introduction 610
II. Pathways of mRNA Decay 611
III. mRNA Ribonucleases 617
IV. Discussion and Future Directions 632
References 634
Chapter 19. Ribonuclease Inhibitor 642
I. Introduction 642
II. Biological Properties 643
III. Molecular Properties 653
IV. Applications 667
References 670
Index 680
Color Plate Section 692