Ribozymes and RNA Catalysis

• Preface: Foreword: Twenty-five years of ribozymes;Chapter 1: Ribozymes and RNA Catalysis Introduction and Primer;1.1. What are ribozymes?;1.2. What is the role of ribozymes in cells?;1.3. Ribozymes bring about significant rate enhancements;1.4. Why study ribozymes?;1.5. Folding RNA into the active conformation;1.6. The catalytic resources of RNA - making a lot of a little;1.7. Mechanisms and catalytic strategies of ribozymes;1.8. The impact of new methodologies to study ribozymes;1.9. Finally;Chapter 2: Proton Transfer in Ribozyme Catalysis;2.1 Scope of Chapter and Rationale;2.2 Overview of Proton Transfer Chemistry;2.3 General Considerations for Proton Transfer in RNA Enzymes;2.3.1 Classes of Protonation Sites in RNA;2.3.2 Driving Forces for pKa Shifting in RNA;2.3.3 Quantitative Contributions of Proton Transfer to RNA Catalysis;2.4 Proton Transfer in Small Ribozymes: 5 case studies;2.4.1 Why Small Ribozymes?;2.4.2 Proton Transfer in the Hepatitis Delta Virus Ribozyme;2.4.3 Proton Transfer in the Hairpin Ribozyme;2.4.4 Proton Transfer in the Hammerhead Ribozyme;2.4.5 Proton Transfer in the VS Ribozyme;2.4.6 Proton Transfer in the glmS Ribozyme;2.5 Conclusion and Perspectives;2.6 References and Footnotes;Chapter 3: Finding the hammerhead active site;3.1. Introduction;3.2. Background;3.3. Experimental data;3.1.1 Mechanistic Hypothesis Leads to Identification and Functional Test of Active Site Components;3.1.2. Structural Hypothesis-Large-scale Conformational Changes are Required for Catalysis;3.1.3. Molecular Modeling of a Hammerhead Active Fold that Satisfies Structural and Biochemical Constraints;3.4. Current Status and Future Prospects;Chapter 4: Hammerhead Ribozyme Crystal Structures and Catalysis;4.1 Introduction;4.2 A Catalytic RNA Prototype;4.3 A Small Ribozyme;4.4 The Chemistry of Phosphodiester Bond Isomerization;4.5 The Hammerhead Ribozyme Structure Nailed Down;4.6 Catalysis in the Crystal;4.7 Making Movies From Crystallographic Snapshots;4.8 An Ever-Growing List of Concerns;4.9 Occam's Razor Can Slit Your Throat;4.10 The Structure of a Full-Length Hammerhead Ribozyme;4.11 Do the Minimal and Full-Length Hammerhead Crystal Structures Have Anything in Common?;4.12 How the Does the Minimal Hammerhead Work?;4.13 A Movie Sequel with a Happy Ending;4.14 Concluding remarks;Chapter 5: The Hairpin and Varkud Satellite Ribozymes;5.1. The nucleolytic ribozymes;5.2. The hairpin ribozyme;5.2.1 The structure of the hairpin ribozyme;5.2.2 Metal ion-dependent folding of the hairpin ribozyme;5.2.3 Observing the cleavage and ligation activities of the hairpin ribozyme;5.2.4 The mechanism of the hairpin ribozyme;5.3. The VS ribozyme;5.3.1 The structure of the VS ribozyme;5.3.2 The structure of the substrate;5.3.3 The location of the substrate;5.3.4 The active site of the VS ribozyme;5.3.5 Candidate catalytic nucleobases;5.3.6 The mechanism of the VS ribozyme;5.4. Some striking similarities between the hairpin and VS ribozymes;Chapter 6: Catalytic Mechanism of the HDV Ribozyme;6.1. Introduction;6.1.1. Hepatitis Delta Virus Biology;6.1.2. Cleavage Reactions of Small Ribozymes;6.2. HDV structure;6.2.1. Determination of Crystal Structures;6.2.2. Structure Overview;6.2.3. Active Site;6.3. Catalytic Strategies for RNA Cleavage;6.4. The Active Site Nucleobase: C75;6.4.1. Exogenous Base Rescue Reactions;6.4.2. The Role of C75 in HDV Catalysis;6.4.3. Resolving the Kinetic Ambiguity;6.5. Metal ions in the HDV Ribozyme;6.5.1. Structural Metal Ions;6.5.2. Catalytic Metal Ions;6.6. Contributions of Non-active-site Structures to Catalysis;6.7. Dynamics in HDV Function;6.8. Varieties of Experimental Systems;6.9. Models for HDV Catalysis;6.10. Conclusion;Chapter 7: Mammalian self-cleaving ribozymes;7.1 Introduction;7.2 General features of small self-cleaving sequences;7.3 Genome-wide selection of self-cleaving ribozymes;7.4 The CPEB3 ribozyme;7.4.1 Expression of the CPEB3 ribozyme;7.4.2 Structural features of the CPEB3 and HDV ribozymes;7.4.3 Linkage of HDV to the human transcriptome;7.5 Possible biological roles of self-cleaving ribozymes;7.6 Closing remarks;Chapter 8: The Structure and Action of glmS Ribozymes;8.1 Introduction;8.2 Biochemical characteristics of glmS ribozymes;8.2.1 Divalent metal ions support structure and not chemistry;8.2.2 Ligand specificity of glmS ribozymes;8.2.3 Evidence for a coenzyme role for GlcN6P;8.3 Atomic-resolution structure of glmS ribozymes;8.3.1 Secondary and tertiary structures of glmS ribozymes;8.3.2 Metabolite recognition by glmS ribozymes;8.4 Mechanism of glmS ribozyme self-cleavage;8.5 Can glmS ribozymes be drug targets?;8.6 Conclusions;Chapter 9: A Structural Analysis of Ribonuclease P. 9.1 Introduction;9.2 Chemistry of RNase P RNA;9.2.1 Universal;9.2.2 SN2-type reaction;9.2.3 pH-dependence of the reaction: hydroxide ion as the nucleophile;9.2.4 Metal ions in catalysis ;9.3 Phylogenetic variation and structure of RNase P RNA;9.4 Early studies of the RNase P RNA structure;9.5 Crystallographic studies of bacterial RNase P RNAs;9.6 Modeling an RNase P RNA:tRNA complex;9.7 Modeling the bacterial RNase P holoenzyme;9.8 Substrate recognition;9.9 Archaeal and Eucaryal holoenzymes - more proteins;9.10 Concluding remarks;Chapter 10: Group I Introns: Biochemical and Crystallographic Characterization of the Active Site Structure;10.1. Group I intron origins;10.2 Group I intron self-splicing;10.3 What has changed in group I intron knowledge in the last decade;10.4 The structure of group I introns;10.5 Crystallography of group I introns;10.5.1 The Tetrahymena LSU P4-P6 domain;10.5.2 The Tetrahymena intron catalytic core;10.5.3 The Twort orf142-I2 ribozyme;10.5.4 The Azoarcus sp. BBH72 tRNAile intron;10.6 The structural basis for group I intron self-splicing;10.6.1 Recognition of the 5' splice site;10.6.2 Does the ribozyme undergo conformational changes upon P1 docking?;10.6.3 A binding pocket for guanosine;10.6.4 Packed stacks;10.7 Biochemical characterization of the structure;10.7.1 Metal ion binding and specificity switches;10.7.2 Identification of ligands to the catalytic metal ions;10.7.3 Correlation with metal ion binding sites within the crystal structures;10.7.4 Nucleotide analog interference techniques;10.8 What makes a catalytic site?;10.9 Back to the origins;Chapter 10: Group II introns: catalysts for splicing, genomic change and evolution;11.1 Introduction: The place of group II introns among the family of ribozymes;11.2 The basic reactions of group II introns;11.3 The biological significance of group II introns;11.3.1 Evolutionary significance;11.3.2 Significance and prevalence in modern genomes;11.4 Domains and parts: the anatomy of a group II intron;11.4.1. Domain 1;11.4.2. Domain 2;11.4.3. Domain 3;11.4.4. Domain 4;11.4.5. Domain 5;11.4.6. Domain 6;11.4.7. Other domains and insertions;11.4.8. Alternative structural organization and split introns;11.5. A big, complicated family: the diversity of group II introns;11.6. Group II intron tertiary structure;11.7. Group II intron folding mechanisms;11.7.1. A slow, direct path to the native state:;11.7.2. A folding control element in the center of D1;11.7.3. Proteins and group II intron folding;11.8 Setting the stage for catalysis: proximity of the splice sites and branch-site;11.8.1. Recognition of exons and ribozyme substrates;11.8.2. Branch-site recognition and the coordination loop;11.9. A single active-site for group II intron catalysis;11.10 The group II intron active-site: what are the players?;11.10.1. Active-site players in D1 and surrounding linker regions;11.10.2. Domain 3 and the J2/3 linker;11.10.3. Domain 5: structural and catalytic regions;11.11 The chemical mechanism of group II intron catalysis;11.12 Proteins and group II intron function;11.12.1. Maturases;11.12.2. CRM-domain plant proteins;11.12.3. ATPase proteins;11.13 Group II introns and their many hypothetical relatives;11.14 Group II introns: RNA processing enzymes, transposons, or tiny living things?;Chapter 12: The GIR1 branching ribozyme;12.1 Introduction;12.2 Distribution and structural organization of twin-ribozyme introns;12.3 The biological context;12.3.1 Three processing pathways of a twin-ribozyme intron;12.3.2 Processing of the I-DirI mRNA;12.3.3 Conformational switching in GIR1;12.4 Biochemical characterization;12.4.1 GIR1 catalyzes three different reactions;12.4.2 Characterization of the branching reaction;12.4.3 The biochemistry of GIR1;12.5 Modelling the structure of GIR1;12.5.1 The overall structure;12.5.2 Coaxially stacked helices;12.5.3 The junctions and tertiary interactions involving peripheral elements;12.5.4 The active site;12.6 Phylogenetic considerations;12.7 Concluding remarks;Chapter 13: Is the spliceosome a ribozyme?;13.1 Similarity to group II self-splicing introns;13.2 Role of snRNA in the spliceosome active site;13.3 Conformation of the U2-U6 complex and parallels to group II intron structures;13.4 RNA-mediated regulation in the spliceosome;Chapter 14: Peptidyl Transferase Mechanism: The Ribosome as a Ribozyme;14.1 Introduction: Historical background;14.2 The ribosome;14.3 The peptidyl transfer reaction;14.3.1 Characteristics of the reaction off the ribosome;14.3.2 Enzymology of the peptidyl transfer reaction;14.3.2.1 Potential mechanisms of rate acceleration by the ribosome;14.3.2.2 Experimental approaches to reaction on the ribosome;14.3.2.3 pH-rate profiles;14.3.2.4 Activation parameters;14.4 The active site;14.4.1 Structures of the reaction intermediates;14.4.2 Conformational rearragements of the active site;14.4.2.1 Induced fit;14.4.2.2 Role of the P-site substrate;14.4.2.3 Conformational flexibility of the active site;14.4.3 Probing the catalytic mechanism: Effects of base substitutions;14.4.4. Importance of the 2?-OH of A76 of the P-site tRNA;14.5 Conclusions and evolutionary considerations;Chapter 15: Folding Mechanisms of Group I Ribozymes;15.1. The multi-domain architecture of group I ribozymes;15.2. RNA Folding Problem;15.2.1 Hierarchical Folding of tRNA;15.2.2 Coupling of Secondary and Tertiary Structure;15.3. Late events: Formation of Tertiary Domains in the Tetrahymena Ribozyme;15.3.1 Time-resolved Footprinting of Intermediates;15.3.2 Misfolding of the intron core;15.3.3 Peripheral Stability Elements;15.4. Kinetic Partitioning among Parallel Folding Pathways;15.4.1 Theory and Experiment;15.4.2 Single Molecule Folding Studies;15.4.3 Estimating the Flux through Footprinting Intermediates;15.4.4. Kinetic Partitioning in vivo;15.5. Early Events: Counterion-dependent RNA collapse;15.5.1 Compact Non-Native Form of bI5 Ribozyme;15.5.2 Small Angle X-ray Scattering of Tetrahymena Ribozyme;15.5.3 Native-like Folding Intermediates in the Azoarcus Ribozyme;15.5.4 Early Folding Intermediates of the P4-P6 RNA;15.6. Counterions and Folding of Group I Ribozymes;15.6.1 Metal Ions and RNA Folding;15.6.2 Valence and Size of Counterions Matter;15.6.3 Specific Metal Ion Coordination and Folding;15.7. Protein-dependent folding of group I ribozymes;15.7.1 Stabilization of RNA Tertiary Structure;15.7.2 Stimulation of Refolding by RNA Chaperones;15.8. Conclusion;

"...this is a book that certainly should be foundin every laboratory investigating RNA catalysis and can serveas a valuable reference for anyone teaching modern biochemistry."