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Full Description
An authoritative and up-to-date collection of resources covering the ubiquitous iron-sulfur cluster-containing proteins
In Iron-Sulfur Clusters: Biogenesis and Biochemistry, a team of distinguished researchers delivers an incisive and practical discussion of the assembly and role of metalloproteins containing an iron atom in a mononuclear or binuclear metal-active site, or where the assembly and final activity of the enzyme depends on an Fe-S cluster containing protein.
The book examines the crosstalk in the assembly of metal-active sites and the roles played by various metal ions in polynuclear metalloclusters. It also describes metal homeostasis and trafficking in a cellular context and explains why the availability of metal ions is tightly regulated.
Of particular interest to chemists working with iron-sulfur (Fe-S) clusters in biology, biochemistry, pharmaceuticals, and drug synthesis, the book also contains:
A thorough introduction to the biosynthesis of hydrogenase cofactors and hydrogenase reaction mechanisms
Comprehensive explorations of the reaction mechanisms of molybdoenzymes, including sulfite oxidase, aldehyde oxidase, and formate dehydrogenase
Practical discussions of the biosynthesis of Fe-S clusters in prokaryotes and eukaryotes
Complete examinations of the insertion of Fe-S clusters and the biosynthesis of Moco and FeMoco
An overview of the chemical, crystallographic, spectroscopic and theoretical methods commonly used to characterize Fe-S clusters.
Perfect for biochemists and protein, pharmaceutical, bioinorganic, and organic chemists, Iron-Sulfur Clusters will also be useful for food and environmental chemists, as well as professionals working in the pharmaceutical industry.
Contents
Volume 1
Preface xv
1 ISC-based Fe-S Protein Biogenesis in Bacteria 1
Béatrice Py and Frédéric Barras
2 Unraveling the Complexity of the Suf-Based Fe-S
Biogenesis 25
Ingie Elchennawi, Claire E. Fisher, Franklin Wayne Outten, and Sandrine
Ollagnier de Choudens
3 Biogenesis of Mitochondrial Iron-Sulfur Proteins 57
Ulrich Mühlenhoff, Oliver Stehling, and Roland Lill
4 Iron-Sulfur Protein Maturation in the Cytosol of
Eukaryotes 87
Joseph J. Braymer and Antonio J. Pierik
5 Mammalian Aldehyde Oxidase 135
Maria Joao Romao, Guilherme Vilela-Alves, and Cristiano Mota
6 Biological Formation of Sulfide 159
Marion Jespersen and Tristan Wagner
7 The Molybdenum Cofactor, Its Biosynthesis, and Relation to
Fe-S Clusters in Bacteria 193
Paolo Olivieri and Silke Leimkühler
8 Molybdenum Cofactor Biosynthesis in Eukaryotes 227
Guenter Schwarz, Lukas Flohr, Emanuel Bruckisch, and Katrin
Fischer-Schrader
9 NifUS Is a Two-component Toolbox Involved in Assembling
Fe-S Clusters Associated with Nitrogen Fixation and
Beyond 257
Julia S. Martin del Campo, Shervin Shaybani, Dennis R. Dean, and Patricia C.
Dos Santos
10 Alternative Substrates of Nitrogenase 287
Frederik V. Schmidt and Johannes G. Rebelein
Volume 2
Preface xvii
11 Electron-Bifurcating Hydrogenases 317
Gregory E. Vansuch, Effie C. Kisgeropoulos, Jonathan R. Humphreys, Carolyn
E. Lubner, David W. Mulder, and Paul W. King
Chapter Goals 317
Main Chapter Points 317
11.1 Introduction 317
11.1.1 Hydrogenases: From "Simple" Prototypical Architectures to Not So
Simple Electron-Bifurcating Architectures 317
11.1.2 Electron Bifurcation: A Brief Overview 320
11.2 Physiology, Subunit Compositions, and Reactivity 321
11.2.1 Overview of Physiological Roles: Three Thematic Examples 321
11.2.2 Subunit Compositions and Reactivities 324
11.3 Structural and Biophysical Characterizations 337
11.3.1 Structures and Cofactors of Hyd-type Electron-Bifurcating
Hydrogenase 338
11.3.1.1 HydA and HydSL 339
11.3.1.2 HydB 340
11.3.1.3 HydC 341
11.3.2 Spectroscopy of HydABC and HndABCD 342
11.3.2.1 EPR Spectroscopy of the Fe-S Clusters in Tm HydABC 342
11.3.2.2 EPR Spectroscopy of HndABCD from S. fructosivorans 344
11.3.2.3 EPR and IR Spectroscopy of the H-Cluster in [FeFe]-HydABC 344
11.3.3 Structures and Cofactors of MvhAGD-HdrABC 346
11.3.3.1 Selenocysteine Considerations 348
11.3.4 Spectroscopy of MvhAGD 349
11.4 Mechanistic Proposals 349
11.4.1 Electron Bifurcation: General Mechanistic Considerations 350
11.4.2 [FeFe]- and [NiFe]--HydABC: Electron Transfer Pathways 352
11.4.3 [NiFe]-MvhAGD-HdrABC 356
11.4.3.1 Electron Transfer Pathways 356
11.4.3.2 CoM-S-S-CoB Binding and Reduction 359
11.5 Forefronts 360
11.6 Summary and Outlook 362
Acknowledgments 363
Author Contributions 363
References 364
12 Inhibition of [FeFe]-Hydrogenases by Small Molecules 381
Claudia Brocks and Thomas Happe
Chapter Goals 381
12.1 Historical Perspective of [FeFe]-Hydrogenase Research 381
12.2 Characteristics of [FeFe]-Hydrogenases: How They Do What They
Do 384
12.3 Small Molecules Inhibit [FeFe]-Hydrogenases 389
12.3.1 Diffusion of Small Molecules to the H-cluster 390
12.3.2 Irreversible Attack of O2 Molecules 392
12.3.3 Inhibitor Molecules that Protect [FeFe]-Hydrogenases Against O2 394
12.3.3.1 CO Protects Against the O2-Initiated H-Cluster Degradation 394
12.3.3.2 Formaldehyde Attacks Catalytically Important Sites of
[FeFe]-Hydrogenases 394
12.3.3.3 The Role of Sulfide in [FeFe]-Hydrogenases 396
12.3.3.4 Cba5H - A [FeFe]-Hydrogenase that Protects Itself by Its Own
Sulfide 396
12.3.4 Influences of Small Molecules on the Proton Transfer Pathway 398
12.4 Summary and Outlook 399
References 399
13 Biosynthesis of [NiFe]-Hydrogenase 407
Oliver Lenz and Giorgio Caserta
Chapter Goals and Main Chapter Points 407
13.1 [NiFe]-Hydrogenases and Their Function 407
13.2 The Inorganic Catalytic Center in the [NiFe]-Hydrogenase Basic
Module 409
13.3 Genetic Basis of [NiFe]-Hydrogenase Maturation 409
13.4 Cyanide Synthesis by HypE and HypF 412
13.5 Assembly of the Fe(CN)2CO Synthon on the HypCD Complex 414
13.6 Origin and Synthesis of the Carbon Monoxide Ligand 417
13.7 Transfer of the Fe(CN)2CO Synthon from the HypCD Complex to
Apo-Hydrogenase 419
13.8 Mobilization and Insertion of Nickel by HypAB 421
13.9 Role of the C-Terminal Extension of the Premature Large Subunit 425
13.10 Hydrogenase Maturation Intermediates Isolated from Living Cells 427
13.11 Iron-Sulfur Cluster Insertion into the Small Subunit 429
13.12 Subunit Oligomerization and Transport Across the Cytoplasmic
Membrane 431
13.13 Special Case: Maturation of O2-Tolerant Membrane-Bound
[NiFe]-Hydrogenases 433
13.14 Conclusions 435
Acknowledgments 436
References 436
14 [Fe]-Hydrogenase and the FeGP Cofactor Involved in the
CO2-Reducing Hydrogenotrophic Methanogenic Pathway 447
Seigo Shima, Joao Pedro Fernandes-Queiroz, and Masanori Kaneko
Chapter Goals 447
Main Chapter Points 447
14.1 Introduction 447
14.2 Unique Coenzymes Found in Methanogens 448
14.3 Enzymes Involved in the Hydrogenotrophic Methanogenic
Pathway 449
14.4 [NiFe]-Hydrogenases Involved in the Hydrogenotrophic
Methanogenesis 452
14.5 Function of [Fe]-Hydrogenase (Hmd) 453
14.6 Reconstitution of the Hmd Holoenzyme with the Extracted
Cofactor 454
14.7 Light Sensitivity of Hmd and Finding of the Functional Iron in the
Cofactor 456
14.8 Structure and Properties of the FeGP Cofactor 457
14.9 Photolysis Mechanism 459
14.10 Crystal Structures of Hmd Apoenzymes 459
14.10.1 Crystal Structure of Reconstituted Hmd Holoenzymes 460
14.10.2 Crystal Structure of Reconstituted Hmd with the Substrate 460
14.10.3 The Other Crystal Structures of Hmd and its Homologs 461
14.11 ESI-MS Analysis for Detection of the CO/Acyl Ligands 462
14.12 Biosynthesis of the FeGP Cofactor 463
14.12.1 Stable Isotope Labeling Experiments 463
14.12.2 The hcg Gene Cluster, Sequence Similarities, and Mutational
Analysis 465
14.12.3 Structure to Function Analysis of Hcg Proteins 466
14.12.3.1 HcgA 467
14.12.3.2 HcgB 467
14.12.3.3 HcgC 468
14.12.3.4 HcgD 470
14.12.3.5 HcgE 471
14.12.3.6 HcgF 472
14.12.3.7 HcgG 473
14.12.4 In Vitro Biosynthesis 473
14.12.4.1 Design of the In Vitro Biosynthesis Assay 474
14.12.4.2 Confirmation of the Precursors by In Vitro Biosynthesis 475
14.12.4.3 Basis of the In Vitro Complementation Assay 476
14.12.4.4 In Vitro Complementation of HcgA 476
14.12.4.5 In Vitro Complementation of HcgG 477
14.12.5 Proposed Biosynthesis Sequence of the FeGP Cofactor 479
14.13 Conclusion 479
Acknowledgment 480
References 480
15 Catalysis by Hydrogenase 489
Seigo Shima, James A. Birrell, Sven T. Stripp, Giorgio Caserta, and Oliver Lenz
Chapter Goals and Main Chapter Points 489
15.1 Catalytic Cycle of [Fe]-Hydrogenase 490
15.1.1 Electronic Properties of the Iron Site of the FeGP Cofactor 490
15.1.2 Enzyme Reaction Kinetics 491
15.1.3 Hmd Inhibitors and Their Contribution to the Catalytic
Mechanism 492
15.1.3.1 CO and CN- 492
15.1.3.2 Isocyanides 492
15.1.3.3 Cu 493
15.1.3.4 Fe 494
15.1.3.5 H2O2 494
15.1.3.6 O2 is Reduced to H2O2 by the Hmd Reaction 495
15.1.4 Semisynthetic Hmd 496
15.1.4.1 Importance of the 2-OH Group of the Pyridinol Ring 498
15.1.4.2 Semisynthetic [Mn]-Hydrogenase 498
15.1.5 Circular Dichroism Spectroscopy 499
15.1.6 Crystal Structure of Hmd with the Substrate 499
15.1.7 Proposed Catalytic Mechanism of Hmd 500
15.1.8 Conclusion 502
15.2 Toward the Catalytic Mechanism of [FeFe]-Hydrogenase 502
15.2.1 The Active Site Cofactor Is an Iron-Sulfur Cluster 503
15.2.2 The Electronic Structure of the H-cluster 504
15.2.3 Current State of the Catalytic Mechanism of [FeFe]-hydrogenase 507
15.2.4 Toward a Consensus Catalytic Mechanism 511
15.2.5 Conclusion 512
15.3 Catalytic Cycle of [NiFe]-Hydrogenase 512
15.3.1 Classification of [NiFe]-Hydrogenases: The Complex Trait of O2
Tolerance 514
15.3.2 [NiFe]-Hydrogenase Active Site States 516
15.3.2.1 CO-Bound States 517
15.3.2.2 Hydroxy-Bridged States 517
15.3.2.3 Unusual [NiFe] Site Arrangements 519
15.3.3 Catalytic Intermediates 520
15.3.3.1 Nia-S 520
15.3.3.2 Nia-SR 522
15.3.3.3 Nia-C 523
15.3.3.4 Nia-L 524
15.3.4 Conclusions 525
Acknowledgment 525
References 526
16 Macromolecular Crystallography 541
Konstantin Bikbaev and Ingrid Span
Chapter Goals 541
Main Chapter Points 541
16.1 Introduction 542
16.2 Crystallization of Macromolecules 544
16.3 Symmetry and the Unit Cell 548
16.4 Diffraction and Interpretation of Diffraction Patterns 550
16.5 Data Collection and Processing 552
16.6 X-ray structure analysis 554
16.6.1 Isomorphous Replacement 555
16.6.2 Anomalous Diffraction 556
16.6.3 Molecular Replacement 557
16.6.4 Structure Refinement 557
16.7 Time-Resolved Crystallography 562
16.8 Nuances of Fe-S Protein Crystallography 565
16.9 Conclusions 566
References 566
17 Vibrational and Mössbauer Spectroscopic Techniques to Study
Iron-Sulfur Clusters 571
Christian Lorent, Giorgio Caserta, Volker Schünemann, and Ingo Zebger
Chapter Goals 571
Main Chapter Points 571
17.1 Vibrational Spectroscopy 572
17.1.1 Normal Modes 573
17.1.2 Vibrational Spectroscopic Techniques 573
17.2 Infrared Spectroscopy 574
17.2.1 MIR Spectroscopy 575
17.2.2 FIR Spectroscopy 578
17.2.3 Conclusion 579
17.3 Raman Spectroscopy 579
17.3.1 Resonance Raman Spectroscopy 581
17.3.2 Studying [Fe-S] Clusters by Resonance Raman Spectroscopy 582
17.3.3 Rubredoxin 582
17.3.4 [2Fe-2S] Clusters 583
17.3.5 [3Fe-4S] Clusters 585
17.3.6 [4Fe-4S] Clusters 586
17.3.7 Studying Hydrogenases by Resonance Raman Spectroscopy 587
17.3.8 Conclusion 588
17.4 Mössbauer-Based Spectroscopic Techniques 588
17.4.1 Mössbauer Spectroscopy 588
17.4.2 Mössbauer Spectroscopy from Single Fe(S-Cys)4 Sites up to [4Fe-4S]
Clusters 592
17.4.3 Complex Iron-Sulfur Clusters: Hydrogenases and Nitrogenases 595
17.4.4 Conclusion 596
17.5 Nuclear Resonance Vibrational Spectroscopy 596
17.5.1 Theoretical Background 597
17.5.2 [Fe(S-Cys)4] Metal Site: The Case Study of Rubredoxin 599
17.5.3 [2Fe-2S] Clusters: 4xCys, 2xCys-2xHis, and 3xCys-1xHis Ligations 599
17.5.4 [3Fe-4S] Clusters 601
17.5.5 [4Fe-4S] Clusters 602
17.5.6 Binding of NO to [Fe-S] Clusters 602
17.5.7 The Nitrogenase FeMe Cofactor 603
17.5.8 [NiFe]- and [FeFe]-Hydrogenases 605
17.5.9 Conclusion 606
References 606
18 The Multisite Microstate Model: A Theoretical Approach for
Analyzing Charge Transfer in Proteins 617
G. Matthias Ullmann and Rajeev Ranjan Roy
Main Chapter Points 617
18.1 Introduction 617
18.2 Binding of Ligands to a Receptor 620
18.3 Analyzing Biomolecular Systems 622
18.3.1 General Considerations 622
18.3.2 Thermodynamic Analysis 624
18.3.3 Kinetic Analysis 625
18.4 Modeling Protein Electrostatics Using the Poisson-Boltzmann
Equation 626
18.4.1 Conceptual Model 626
18.4.2 The Mathematical Model 627
18.4.3 Electrostatic Potentials and Electrostatic Energies 629
18.4.4 Defining the Low-Dielectric Cavity of the Protein 631
18.4.5 Fitting Quantum Chemical Electrostatic Potentials to Point
Charges 633
18.4.6 Problems and Shortcomings of the Poisson-Boltzmann Model 635
18.5 Electrostatic Calculations of the Energy Parameter 636
18.6 Practical Hints to Construct a Multisite System 639
18.6.1 Molecular Structures as a Basis of Detailed Calculations 639
18.6.2 How to Choose Sites, Model Compounds, and Model Compound
Energies 640
18.7 Conclusions 642
Acknowledgement 643
References 643
19 Structural and Functional Bioinorganic Model Chemistry of
Fe-S Clusters - Synthesis and Analysis 649
Benedict Josua Elvers and Carola Schulzke
Chapter Goals and Main Chapter Points 649
19.1 Introduction 649
19.2 Fe-S Cluster Motifs: Natural Occurrence, Reactivity, and Artificial
Synthesis 652
19.3 [FeS4] 653
19.3.1 Biological Relevance 653
19.3.2 Synthetic Model Complexes 654
19.4 [Fe2S2] Clusters 657
19.4.1 Biological Relevance of [Fe2S2] Clusters 658
19.4.2 Synthetic Model Complexes of [Fe2S2] Clusters 658
19.5 [Fe4S4] and [Fe3S4] Clusters 665
19.5.1 Biological Relevance of [Fe4S4] and [Fe3S4] Clusters 665
19.5.2 Synthetic Model Complexes of [Fe4S4] 667
19.5.3 Synthetic Model Complexes of [Fe3S4] 676
19.6 Clusters of Higher Nuclearity 679
19.6.1 Hydrogenase and Nitrogenase 680
19.6.2 Model Chemistry for Clustersof Higher Nuclearity 683
19.7 Conclusion 691
References 692
20 Metal-Dependent Formate Dehydrogenases and Their
Interplay and Relationship to Iron-Sulfur Clusters 705
Benjamin R. Duffus
Chapter Goals 705
Main Chapter Points 705
20.1 Formate: General Considerations 706
20.2 Metal-Independent FDHs 707
20.3 Metal-Dependent FDHs 708
20.4 Metal-Dependent Formate Dehydrogenases: Common Modular Catalytic
Unit 711
20.5 FDH and Link of bis-MGD to a [4Fe-4S] Cluster 712
20.6 Link of the FDH bis-MGD Cofactor with Extended Fe-S Cluster Electron
Chains 714
20.7 FDH that Employ Ferredoxin as Electron Acceptor 715
20.8 E. coli Metal-Dependent Formate Dehydrogenases 715
20.9 Formate Hydrogenlyase Complex 716
20.10 NAD+-Reducing, Metal-Dependent FDHs 717
20.11 W-Containing FDHs from Sulfate-Reducing Bacteria 719
20.12 FDH: D. vulgaris Hildenborough 719
20.13 Tungsten vs. Molybdenum FDH 720
20.14 Metal-Dependent Formate Dehydrogenase from Moorella thermoacetica:
Variance and Codependence of Metal Ions 721
20.15 Formylmethanofuran Dehydrogenases 721
20.16 FDHs in Methanogens 722
20.17 FDH O2 Sensitivity: Inhibition and Enzymatic Activation 724
20.18 FDH and Electron Bifurcation vs. O2 Tolerance 725
20.19 FDH in H2-Dependent CO2 Reduction (HDCR) 727
20.20 Conclusion 728
Acknowledgments 729
References 729
Index 747
