The Bioinorganic Chemistry of Nickel

Chapter 1; The Coordination Chemistry of Nickel: An Introductory Survey; C. L. Coyle and E. I. Stiefel; 1.1. Introduction; 1.2. The Element; 1.3 Nickel(II) Complexes; 1.4. Structure and Bonding; 1.5. Ligand Effects; 1.6. Four--Coordinate Complexes; 1.7. Six--Coordinate Complexes; 1.8. Polynuclear Species; 1.9. Less Common Oxidation States; 1.9.1. Nickel(0); 1.9.2. Nickel(I); 1.9.3. Nickel(III) and Nickel(IV); 1.10. Non--Innocent Ligands; 1.11. Dithiolene Complexes; 1.12. Dynamic Properties; 1.13. Conclusions; References; Chapter 2; Nickel(III) Chemistry and Properties of the Peptide Complexes of Ni(II) and Ni(III); Dale W. Margerum and Sally L. Anliker; 2.1. Introduction; 2.2. Monopeptide Complexes of Nickel (III); 2.3. Bis(dipeptido) Complexes of Nickel(II) and Nickel(III); 2.4. Bis(tripeptido) Complexes of Nickel(III); 2.5. Nickel(III) Mixed--Ligand Complexes; 2.6. Electron Transfer and Redox Reactions; References; Chapter 3; The EPR Spectra of Odd--Electron Nickel Ions in Biological Systems: Theory for d 7 and d 9 Ions; J. C. Salerno; 3.1. EPR Spectra of Biological Nickel; 3.2. EPR of Nickel in Odd--Electron States; 3.2.1. EPR of d 7 Complexes; 3.2.2. EPR of d 9 Complexes; 3.3. Crystal Field Theory and the EPR Spectra of d 7 and d 9 Ions.; 3.4. Crystal Field Theory and Low--Symmetry Complexes; 3.5. Tetrahedral Complexes; 3.6. Conclusions; References; Chapter 4; Electronic and Molecular Structure of Biological Nickel as Studied by X--ray Absorption Spectroscopy; Marly K. Eidsness, Richard J. Sullivan, and Robert A. Scott; 4.1. Introduction; 4.1.1. X--ray Absorption Edge Spectroscopy; 4.1.2. What To Expect from Nickel; 4.1.3. Biological Nickel Before X--ray Absorption Spectroscopy; 4.2. Nickel Model Compounds; 4.2.1. Oxidation State; 4.2.2. Ligand Type; 4.2.3. Coordination Geometry; 4.3. Nickel Enzymes; 4.3.1. (Ni, Fe) Hydrogenases; 4.3.2. CO Dehydrogenase; 4.3.3. Factor F 430 of S--Methyl--Coenzyme--M Reductase; References; Chapter 5; Nickel in Biology: Nickel as an Essential Trace Element; Dorothe Ankel--Fuchs and Rudolf K. Thauer; 5.1. Introduction; 5.2. Role of Nickel in Bacteria; 5.2.1. Bacteria with Nickel Hydrogenase(s); 5.2.2. Anaerobic Bacteria with Carbon Monoxide Dehydrogenase; 5.2.3. Bacteria with Methyl--CoM Reductase; 5.2.4. Bacteria with Urease; 5.2.5. Growth Dependence of an Oscillatoria sp. on Nickel; 5.3. Role of Nickel in Plants; 5.3.1. Urease--Containing Plants and Fungi; 5.3.2. Nickel Dependence of Plants Not Containing Urease; 5.3.3. Nickel--Accumulating Plants; 5.4. Role of Nickel in Animals; References; Chapter 6; Biological Transport of Nickel; Harold L Drake; 6.1. Introduction; 6.2. Vertebrate Nickel Transport; 6.2.1. Role of Bound Nickel in Systemic Transport; 6.2.2. Cellular Nickel Transport; 6.2.3. Nickel Uptake by Phagocytosis; 6.2.4. Systemic Absorption and Excretion of Nickel; 6.2.5. Summary on Vertebrate Nickel Transport; 6.3. Nickel Transport in Plants; 6.3.1. Transport and Chelators in Nickel Hyperaccumulators; 6.3.2. Nickel in Nonhyperaccumulators; 6.3.3. Summary on Nickel Transport in Plants; 6.4. Microbial Nickel Transport; 6.4.1. Bacterial Transport of Nickel; 6.4.2. Fungal Transport of Nickel; 6.4.3. Other Microbial Studies; 6.4.4. Summary on Microbial Nickel Transport; 6.5. Nickel Transport by Other Biological Systems; 6.6. Conclusions; References; Chapter 7; Urease - A Ni(II) Metalloenzyme; Robert K. Andrews, Robert L. Blakeley, and Burt Zerner; 7.1. Historical Perspective; 7.1.1. Urea; 7.1.2. Urease; 7.2. The Synthesis and Degradation of Urea; 7.2.1. Nonenzymatic Synthesis of Urea; 7.2.2. The Nonenzymatic Degradation of Urea; 7.2.3. Enzyme--Catalyzed Degradation of Urea; 7.3. The Nickel Content of Urease and Jackbeans; 7.3.1. The Nickel Content of Urease; 7.3.2. The Nickel Content of Jackbeans; 7.3.3. Why Nickel?; 7.4. Hydroxamic Acids and the Equivalent Weight of Urease; 7.4.1. The Equivalent Weight of Urease; 7.4.2. Complexes of Hydroxamic Acids with Metal Ions; 7.5. The Molecular Properties of Urease; 7.5.1. Amino Acid Composition; 7.5.2. Physicochemical Properties; 7.5.3. The Thiols of Urease; 7.6. Absorption Spectra; 7.7. On the Mechanism of Action of Urease; 7.7.1. Specificity; 7.7.2. The Role of the Metal Ion; 7.7.3. Differential Alteration of Charge; 7.7.4. A Possible Mechanism of Action; 7.7.5. Ni(II)--Promoted Hydrolysis of Amides; 7.8. Conclusion; References; Chapter 8; Nickel in Hydrogenases from Sulfate--Reducing, Photosynthetic, and Hydrogen--Oxidizing Bacteria; Richard Cammack, Victor M. Fernandez, and Klaus Schneider; 8.1. Introduction; 8.1.1. Evidence for the Involvement of Nickel in Hydrogenase; 8.1.2. Genetics of Hydrogenases; 8.2. Structure of Hydrogenases; 8.2.1. A General Model; 8.2.2. Subunit Composition and Prosthetic Groups; 8.3. Hydrogenase Activity; 8.3.1. Comparisons of Activity; 8.3.2. "Uptake" and "Production" Hydrogenases; 8.3.3. Stability; 8.3.4. Activation--Deactivation Phenomena; 8.4. Electron Paramagnetic Resonance Spectra; 8.4.1. Oxidized Hydrogenase; 8.4.2. Reduced Hydrogenase; 8.4.3. Coordination of the Nickel Site; 8.4.4. Interactions between Nickel and Iron--Sulfur Clusters; 8.4.5. Absent EPR Signals; 8.5. Redox Properties of Hydrogenases; 8.5.1. Activity; 8.5.2. Redox Centers; 8.6. The Role of Nickel in Hydrogenase Catalysis; 8.6.1. Evidence for Involvement in the H Site; 8.6.2. Possible Mechanisms of Hydrogenase Catalysis Involving Nickel; 8.7. Concluding Remarks: Toward a Classification of the Nickel--Containing Hydrogenases; 8.7.1. Composition; 8.7.2. Differences between Nickel Sites in Different Enzymes; References; Chapter 9; (Ni, Fe)Hydrogenases from Sulfate--Reducing Bacteria: Nickel Catalytic and Regulatory Roles; Jose J. G. Moura, Miguel Teixeira, Isabel Moura, and Jean LeGall; 9.1. Introductory Remarks; 9.2. Native (Ni, Fe)Hydrogenases; 9.2.1. Nickel EPR Signals; 9.2.2. Unambiguous Assignment of the Nickel EPR Signals by Isotopic Labeling Experiments Using 61 Ni; 9.2.3. Iron--Sulfur Centers; 9.3. Intermediate States Generated under H 2 Atmosphere; 9.4. Nickel Chemistry in the Context of Its Biological Role; 9.4.1. Oxidation States Involved; 9.4.2. Coordination and Redox Transitions; 9.4.3. EPR Information Concerning Ni(III) and Ni(I) Oxidation States; 9.4.4. Nickel(I) and Nickel(III) Model Compounds; 9.4.5. Functional Model Systems; 9.5. Mechanism of Hydrogenase Action--Activation and Catalytic Cycles; 9.5.1. The Activation Cycle; 9.5.2. The Catalytic Cycle; References; Chapter 10; Hydrogenases of Methanobacterium thermoautotrophicum strain DELTAH; Neil R. Bastian, David A. Wink, Lawrence P. Wackett, David J. Livingston, Lynda M. Jordan, Judith Fox, William H. Orme--Johnson, and Christopher T. Walsh; 10.1. Introduction; 10.2. Methanogen Hydrogenases; 10.2.1. Purification and Properties; 10.2.2. Electron Microscopy; 10.2.3. Kinetics of F 420 --Reducing Hydrogenase; 10.2.4. Electron Paramagnetic Resonance Spectroscopy; 10.2.5. Electron Spin--Echo Spectroscopy; 10.2.6. EXAFS Spectroscopy; 10.2.7. Magnetic Circular Dichroism Spectroscopy; 10.2.8. Redox Potential; 10.3. Summary; References; Chapter 11; Methyl--S--Coenzyme--M Reductase: A Nickel--Dependent Enzyme Catalyzing the Terminal Redox Step in Methane Biogenesis; Lawrence P. Wackett, John F. Honek, Tadhg P. Begley, Spencer L. Shames, Eric C. Niederhoffer, Robert P. Hausinger, William H. Orme--Johnson, and Christopher T. Walsh; 11.1. Introduction; 11.2. In Vitro Methanogenesis; 11.2.1. Preparation and Properties of Cell--Free Extracts Containing Methyl Reductase Activity; 11.2.2. Fractionation of Cell Extract Compounds Active in Methyl--Coenzyme M Reduction; 11.3. F 430 ; 11.4. Electron Microscopy; 11.5. Mechanistic Studies of Methyl Reductase; 11.5.1. Alternative Substrates and Inhibitors; 11.6. Conclusions; References; Chapter 12; Structure and Properties of Coenzyme F 430 ; Andreas Pfaltz; 12.1. Introduction; 12.2. Structure of Coenzyme F 430 ; 12.2.1. Structure of the Porphinoid Ligand System; 12.2.2. Structure of the Protein--Free Cofactor; 12.3. Reactivity at the Ligand Periphery; 12.3.1. Epimerization to 12, 13--Diepi--F 430 ; 12.3.2. 12, 13--Didehydro--F 430 : Formation and Selective Reduction Back to F 430 ; 12.4. Reactivity at the Nickel Center; References; Chapter 13; Carbon Monoxide Dehydrogenase of Acetogens; Gabriele Diekert; 13.1. Introduction; 13.2. Properties of CO Dehydrogenase; 13.2.1. Kinetic Properties; 13.2.2. Molecular Properties; 13.2.3. Physiological Electron Acceptor; 13.3. Physiological Role of CO Dehydrogenase; 13.3.1. Oxidation of CO to CO 2 ; 13.3.2. Reduction of CO 2 to CO and Incorporation of CO into Acetate; 13.3.3. Physiological Role in Other Anaerobes; References; Chapter 14; Nickel in CO Dehydrogenase; Steve W. Ragsdale, Herland G. Wood, Tom A Morton, Lars G. Ljungdahl, and Dan V. DerVartanian; 14.1. Introduction; 14.2. CO Dehydrogenase: Physiological Role; 14.2.1. Acetyl--CoA Synthesis; 14.2.2. CO Dehydrogenase in CO Uptake in the Environment; 14.3. Nickel and CO Chemistry Relating to CO Dehydrogenase Reactions; 14.3.1. CO Chemistry; 14.3.2. Metal Carbonyl Chemistry; 14.3.3. Nickel Chemistry; 14.3.4. Nickel in Enzymes Other than CO Dehydrogenase; 14.4. Properties of Nickel in CO Dehydrogenase; 14.4.1. Nickel Content; 14.4.2. Geometry of the Nickel Site; 14.5. Why is Nickel in CO Dehydrogenase?; References; Index