1;Introduction;5 2;Contents;9 3;Contributors;14 4;Diversity of the Heme-Copper Superfamily in Archaea: Insights fromGenomics and Structural Modeling;17 4.1;1 Introduction;17 4.2;2 Introduction to the Heme-Copper Superfamily;18 4.3;3 Classification of the Superfamily;19 4.4;4 Heme-Copper Family Properties;21 4.5;5 Heme-Copper Oxygen Reductases in Archaea;24 4.6;6 Distribution and Evolution of the Heme-Copper Superfamily;42 4.7;References;44 5;Structure of Photosystems I and II;48 5.1;1 Overview on Oxygenic Photosynthesis;48 5.2;2 Photosystem I;50 5.3;3 Photosystem II;65 5.4;References;80 6;Microbial Rhodopsins: Scaffolds for Ion Pumps, Channels, and Sensors;88 6.1;1 Introduction;88 6.2;2 Microbial ( Type 1) Rhodopsins;90 6.3;3 Ion Transfer and Signal Transfer Mechanisms;106 6.4;4 Phototaxis;116 6.5;5 Outlook;126 6.6;References;126 7;Life Close to the Thermodynamic Limit: HowMethanogenic Archaea Conserve Energy;138 7.1;1 Introduction;138 7.2;2 The Process of Methanogenesis;140 7.3;3 Reactions and Compounds of the Methanogenic Electron Transport Chains;143 7.4;4 Structure and Function of Ion-Translocating Enzymes;148 7.5;5 ATP Synthesis in Methanogens;154 7.6;6 Concluding Remarks;159 7.7;References;160 8;ATP Synthesis by Decarboxylation Phosphorylation;168 8.1;1 Introduction;168 8.2;2 Fermentation Pathways with Na+- Transport Decarboxylases ( NaT- DC);169 8.3;3 Structure and Mechanism of the NaT-DC Enzymes;174 8.4;4 ATP Synthesis Energized by an Electrochemical Na+ Ion Gradient;177 8.5;5 Mechanism of the F0 Motor;186 8.6;References;192 9;The Three Families of Respiratory NADH Dehydrogenases;200 9.1;1 Introduction;200 9.2;2 " Alternative" or NDH-2-Type NADH Dehydrogenases;202 9.3;3 Sodium-Pumping NADH Dehydrogenases (Nqr);211 9.4;4 Proton-Pumping NADH:Ubiquinone Oxidoreductase (Complex I);220 9.5;References;228 10;Hydrogenases and H+-Reduction in Primary Energy Conservation;238 10.1;1 Introduction;238 10.2;2 Diversity and Classification of Hydrogenases;239 10.3;3 Modes of Energy Conservation by Hydrogenases;253 10.4;4 Conclusions and Perspectives;258 10.5;References;259 11;A Structural Perspective onMechanism and Function of the Cytochrome bc1 Complex;268 11.1;1 Introduction;268 11.2;2 Structural Characterization of cyt;270 11.3;3 Mechanistic Considerations;276 11.4;4 Interaction of cyt c with cyt bc1;283 11.5;5 Respiratory Supercomplexes;284 11.6;References;285 12;Regulatory Mechanisms of Proton- Translocating FOF1- ATP Synthase;294 12.1;1 Introduction;294 12.2;2 Structure and Rotary Catalysis: a Brief Summary;295 12.3;3 ADP-Inhibition: a Common Regulatory Mechanism;299 12.4;4 Subunit E in Bacterial and Chloroplast Enzyme;306 12.5;5 Thiol Regulation in Chloroplast Enzyme;310 12.6;6 Mitochondrial Inhibitor Protein IF1;312 12.7;7 Conclusions;313 12.8;References;314 13;Subject Index;324