Introduction	5
	Contents	9
	Contributors	14
	Diversity of the Heme–Copper Superfamily in Archaea: Insights fromGenomics and Structural Modeling	17
	1 Introduction	17
	2 Introduction to the Heme–Copper Superfamily	18
	3 Classification of the Superfamily	19
	4 Heme-Copper Family Properties	21
	5 Heme–Copper Oxygen Reductases in Archaea	24
	6 Distribution and Evolution of the Heme–Copper Superfamily	42
	References	44
	Structure of Photosystems I and II	48
	1 Overview on Oxygenic Photosynthesis	48
	2 Photosystem I	50
	3 Photosystem II	65
	References	80
	Microbial Rhodopsins: Scaffolds for Ion Pumps, Channels, and Sensors	88
	1 Introduction	88
	2 Microbial ( Type 1) Rhodopsins	90
	3 Ion Transfer and Signal Transfer Mechanisms	106
	4 Phototaxis	116
	5 Outlook	126
	References	126
	Life Close to the Thermodynamic Limit: HowMethanogenic Archaea Conserve Energy	138
	1 Introduction	138
	2 The Process of Methanogenesis	140
	3 Reactions and Compounds of the Methanogenic Electron Transport Chains	143
	4 Structure and Function of Ion-Translocating Enzymes	148
	5 ATP Synthesis in Methanogens	154
	6 Concluding Remarks	159
	References	160
	ATP Synthesis by Decarboxylation Phosphorylation	168
	1 Introduction	168
	2 Fermentation Pathways with Na+- Transport Decarboxylases ( NaT- DC)	169
	3 Structure and Mechanism of the NaT-DC Enzymes	174
	4 ATP Synthesis Energized by an Electrochemical Na+ Ion Gradient	177
	5 Mechanism of the F0 Motor	186
	References	192
	The Three Families of Respiratory NADH Dehydrogenases	200
	1 Introduction	200
	2 “ Alternative” or NDH-2-Type NADH Dehydrogenases	202
	3 Sodium-Pumping NADH Dehydrogenases (Nqr)	211
	4 Proton-Pumping NADH:Ubiquinone Oxidoreductase (Complex I)	220
	References	228
	Hydrogenases and H+-Reduction in Primary Energy Conservation	238
	1 Introduction	238
	2 Diversity and Classification of Hydrogenases	239
	3 Modes of Energy Conservation by Hydrogenases	253
	4 Conclusions and Perspectives	258
	References	259
	A Structural Perspective onMechanism and Function of the Cytochrome bc1 Complex	268
	1 Introduction	268
	2 Structural Characterization of cyt	270
	3 Mechanistic Considerations	276
	4 Interaction of cyt c with cyt bc1	283
	5 Respiratory Supercomplexes	284
	References	285
	Regulatory Mechanisms of Proton- Translocating FOF1- ATP Synthase	294
	1 Introduction	294
	2 Structure and Rotary Catalysis: a Brief Summary	295
	3 ADP-Inhibition: a Common Regulatory Mechanism	299
	4 Subunit E in Bacterial and Chloroplast Enzyme	306
	5 Thiol Regulation in Chloroplast Enzyme	310
	6 Mitochondrial Inhibitor Protein IF1	312
	7 Conclusions	313
	References	314
	Subject Index	324