The Biological Chemistry of Nickel

Deborah Zamble; Magdalena Rowińska-Żyrek; Henryk Kozlowski

BOOK

The Biological Chemistry of Nickel

Deborah Zamble | Magdalena Rowińska-Żyrek | Henryk Kozlowski

(2017)

Additional Information

Book Details

ISBN: 978-1-78801-058-0
Edition: 1
Language: English
Pages: 380
Subjects: Inorganic chemistry
Biochemistry
Molecular biology
Chemical biology

Abstract

Metal ions play key roles in biology. Many are essential for catalysis, for electron transfer and for the fixation, sensing, and metabolism of gases. Others compete with those essential metal ions or have toxic or pharmacological effects.

This book is structured around the periodic table and focuses on the control of metal ions in cells. It addresses the molecular aspects of binding, transport and storage that ensure balanced levels of the essential elements. Organisms have also developed mechanisms to deal with the non-essential metal ions. However, through new uses and manufacturing processes, organisms are increasingly exposed to changing levels of both essential and non-essential ions in new chemical forms. They may not have developed defenses against some of these forms (such as nanoparticles).

Many diseases such as cancer, diabetes and neurodegeneration are associated with metal ion imbalance. There may be a deficiency of the essential metals, overload of either essential or non-essential metals or perturbation of the overall natural balance.

This book is the first to comprehensively survey the molecular nature of the overall natural balance of metal ions in nutrition, toxicology and pharmacology. It is written as an introduction to research for students and researchers in academia and industry and begins with a chapter by Professor R J P Williams FRS.

Section Title	Page	Action	Price
Cover	Cover
The Biological Chemistry of Nickel	i
Preface	v
Contents	vii
Chapter 1 - Introduction to the Biological Chemistry of Nickel	1
1.1 Nickel Utilization	1
1.1.1 Nickel in Biology	1
1.1.2 Nickel in Humans	3
1.2 Nickel Enzymes	3
1.3 Nickel Availability and Distribution	6
1.4 Applications	8
1.5 Outstanding Questions	8
Acknowledgements	9
References	9
Chapter 2 - Oceanic Nickel Biogeochemistry and the Evolution of Nickel Use	12
2.1 Introduction	12
2.2 Nickel Geochemistry in Modern Oceans	13
2.2.1 Modern Oceanic Nickel Chemical Speciation, Sources and Sinks	13
2.2.2 Seawater Depth Profiles	13
2.2.3 Correlations with Other Elements	14
2.3 Modern Marine Microbial Nickel Enzyme Usage and Geochemical Signatures	15
2.3.1 The Oxic Surface Ocean	16
2.3.1.1 NiSOD	16
2.3.1.2 Urease	16
2.3.1.3 Nickel’s Role in Nitrogen Fixation	17
2.3.1.4 Imaging Nickel in Phytoplankton	17
2.3.2 The Deep Ocean	17
2.3.3 Anoxic Sediments and Seafloor Seeps	18
2.4 Microbial Growth Response to Varying Nickel Concentrations	18
2.5 Evolutionary Implications of Changes in Oceanic Nickel over Geologic Time	20
Acknowledgements	21
References	21
Chapter 3 - Nickel Toxicity and Carcinogenesis	27
3.1 Introduction	27
3.1.1 Toxicology	27
3.1.2 Epigenetics	29
3.1.3 Nickel Exposure	30
3.2 Nickel Carcinogenesis	31
3.2.1 Human, Animal, and In vitro Investigations	31
3.2.2 Nickel’s Effect on the DNA Methylome	34
3.2.3 Nickel’s Effect on Post-Translational Histone Modifications	36
3.2.4 Nickel’s Effect on microRNA Expression	37
3.3 Conclusions	38
Acknowledgements	38
References	39
Chapter 4 - Nickel Binding Sites – Coordination Modes and Thermodynamics	43
4.1 Coordination Chemistry of Nickel. Why and for Whom Did Nature Choose It	43
4.2 Nickel Complexes with Peptides Containing Amino Acid Residues with Non-Coordinating Side Chains	45
4.3 Tempting Nickel Binding Sites in Bacterial Enzymes	45
4.3.1 Cysteine-Rich Nickel Binding Sites	47
4.3.2 Polyhistidine Nickel-Binding Sites	51
Acknowledgements	55
References	55
Chapter 5 - Urease	60
5.1 Introduction	60
5.2 Biological Significance of Ureases	61
5.3 Enzymology	62
5.4 Urease Structures	63
5.5 Urease Inhibitors	71
5.5.1 Sulfur Compounds	71
5.5.2 Hydroxamic Acids	72
5.5.3 Phosphorus Compounds	73
5.5.4 Boric and Boronic Acids	75
5.5.5 Citrate	76
5.5.6 Fluoride	76
5.5.7 Heavy Metals	77
5.5.8 Quinones	78
5.5.9 Polyphenols	80
5.6 Mechanism	80
5.7 Non-Enzymatic Properties of Urease	85
5.8 Microbial Induced Calcite Preparation by Ureolytic Bacteria	85
5.9 Urease Maturation Process: The Role of Accessory Proteins	86
5.10 Conclusions	89
Acknowledgements	89
References	89
Chapter 6 - Crystallographic Analyses of the Active Site Chemistry and Oxygen Sensitivity of [NiFe(Se)]-Hydrogenases	98
6.1 Introduction	98
6.2 Structural Characterization of Ni–Fe Active Site Intermediates	101
6.3 Structural Characterization of Active Site Intermediates of [NiFeSe]-Hydrogenases	107
6.4 Active Site Reactivity with Molecular Oxygen	109
6.4.1 Naturally O2-Tolerant Hydrogenases	110
6.4.2 Artificially O2-Tolerant Hydrogenases: Variants at the V74 Position	111
6.4.3 O2-Resistant [NiFeSe]-Hydrogenases	114
6.4.4 Hydrophobic Tunnels in [NiFe]-Hydrogenases	115
6.5 Conclusions	116
References	117
Chapter 7 - One-Carbon Chemistry of Nickel-Containing Carbon Monoxide Dehydrogenase and Acetyl-CoA Synthase	121
7.1 Introduction	121
7.2 CODH and ACS in Microbial Metabolism	122
7.3 Carbon Monoxide Dehydrogenase (CODH)	125
7.3.1 Overall CODH Structure	125
7.3.2 The CODH C-Cluster	126
7.3.3 The CODH Catalytic Mechanism	129
7.4 Acetyl-CoA Synthase (ACS)	133
7.4.1 Overall ACS Structure	133
7.4.2 The ACS A-Cluster	135
7.4.3 The ACS Catalytic Mechanism	137
7.5 Bifunctional CODH/ACS	139
7.5.1 The CO Channel of MtCODH/ACS	139
7.5.2 Conformational Movements of Bifunctional CODH/ACS	142
7.6 Conclusions and Future Directions	143
References	145
Chapter 8 - Biochemistry of Methyl-Coenzyme M Reductase	149
8.1 Introduction to Methanogenesis	149
8.2 Introduction to Methyl-CoM Reductase (MCR)	151
8.3 The MCR Mechanism	155
8.3.1 How MCR Enforces Strict Binding Order	155
8.3.2 Description of Three Proposed Mechanisms of Biological Methane Formation	157
8.3.3 Kinetic, Spectroscopic, and Computational Studies Resolve the MCR Mechanism	160
8.4 Looking Forward	164
Acknowledgements	165
References	165
Chapter 9 - Reinventing the Wheel: The NiSOD Story	170
9.1 General Features	170
9.1.1 Why Are Superoxide Dismutases Needed	170
9.1.2 Why Ni	172
9.1.3 The Role of Ni in Expression and Maturation of NiSOD	172
9.1.4 Structural Considerations	173
9.1.5 Mechanistic Considerations	177
9.2 Roles of the Nickel Ligands	180
9.2.1 Cysteine Ligands	180
9.2.2 Backbone N-Donor Ligands	183
9.2.2.1 H1*-NiSOD	183
9.2.2.2 Ala0-NiSOD	184
9.2.3 N-Donor Ligation and Stability Towards Thiolate Oxidation	186
9.2.4 Imidazole Ligation	187
9.3 Interactions Involving Second Coordination Sphere Residues	191
9.4 Conclusions	195
References	195
Chapter 10 - Nickel Glyoxalase I	200
10.1 Introduction	200
10.1.1 Methylglyoxal and Advanced Glycation End-Products (AGE)	200
10.1.2 MG Detoxification Enzymes	201
10.2 Glyoxalase Enzymes	201
10.2.1 Overview	201
10.2.2 Zn2+-Activated Glo1	202
10.2.3 Escherichia coli Ni2+-Activated Glo1	204
10.2.4 Additional Ni2+-Activated Glo1 Present in Nature	206
10.2.5 Pseudomonas aeruginosa Glo1 Enzymes	207
10.2.6 Insight into Key Structural Factors Controlling Metal Activation Profiles in Glo1	209
10.2.7 Half-of-Sites Enzymatic Activity in Glo1	210
10.2.8 Clostridium acetobutylicum Ni2+-Activated Glo1 and Quaternary Structure Variation in the Glo1 Enzymes	214
10.2.9 Glo1 and the βαβββ Superfamily	215
10.3 Conclusions	216
Acknowledgements	216
References	216
Chapter 11 - Lactate Racemase and Its Niacin-Derived, Covalently-Tethered, Nickel Cofactor	220
11.1 Introduction to Lactate Racemase – A Historical Perspective	220
11.2 Lactate Racemase in Lactobacillus plantarum	223
11.3 Biomimetic Nickel–Pincer Complexes	226
11.4 Potential Mechanism of Lactate Racemase	226
11.5 Biosynthetic Pathway for the Ni(SCS) Cofactor	228
11.6 Conclusions and Perspective	231
Note Added in Proof	234
Acknowledgements	234
References	234
Chapter 12 - Nickel in Microbial Physiology – from Single Proteins to Complex Trafficking Systems: Nickel Import/Export	237
12.1 Introduction	237
12.2 Nickel Uptake Systems	238
12.2.1 Crossing the Cytoplasmic Membrane	238
12.2.1.1 One-Step Importers	238
12.2.1.1.1\rNiCoTs.The nickel/cobalt transporters (NiCoTs) are widespread in the three domains of life.12 Members of this family are charact...	238
12.2.1.1.2\rUreH.The UreH group includes Ni-specific permeases encoded in the gene clusters of urease enzymes in the genomes of Bacillus sp....	239
12.2.1.1.3\rHupE/UreJ.HupE/UreJ proteins are widespread among bacteria, and the corresponding genes are usually localized within hydrogenase...	239
12.2.1.2 Multicomponent Nickel Uptake Systems	240
12.2.1.2.1\rABC Transporters.ABC transporters of transition metals are dedicated to the import of essential metals iron, zinc, copper, or ni...	240
12.2.1.2.2\rECF Transporters.The new class of ECF transporters was originally identified by functional genomics.10,54 It is present in appro...	242
12.2.2 Nickel Uptake in Gram-Negative Bacteria: Crossing the Outer Membrane	243
12.2.3 Nickel Speciation: The Flavors of Nickel	244
12.3 Nickel Efflux Systems	245
12.3.1 Functional Classification of Nickel Exporter Systems	245
12.3.1.1 Cation Diffusion Facilitators	245
12.3.1.2 RcnAB	246
12.3.1.3 Major Facilitator Protein Superfamily (MFS)	247
12.3.1.4 P-Type ATPases	247
12.3.1.5 Resistance, Nodulation, and Cell Division (RND) Pumps	248
12.3.2 Distribution and Dissemination of Exporter Genes in Bacteria	249
12.3.3 Nickel Homeostasis in Host-Associated Bacteria	250
12.4 New Perspectives on Nickel Transport	251
12.5 Concluding Remarks	252
Acknowledgements	253
References	254
Chapter 13 - Nickel Regulation	259
13.1 Overview	259
13.2 Regulation of Transition Metals in Bacterial Systems	260
13.2.1 Metals as Allosteric Effectors of Regulator Function	261
13.2.2 Promoter Occupancy is Determined by the Coupling Free Energy	262
13.3 Bacterial Nickel Regulators	263
13.3.1 Cytoplasmic Protein Regulators of Nickel Import	264
13.3.1.1 NikR	264
13.3.1.2 Nur	267
13.3.2 Cytoplasmic Protein Regulators of Ni Efflux	268
13.3.2.1 RcnR	268
13.3.2.2 InrS	270
13.3.2.3 NmtR/KmtR	271
13.3.3 Periplasmic Protein Regulator of Ni Efflux	272
13.3.3.1 CnrX	272
13.3.4 RNA-Dependent Regulation of Ni Efflux	274
13.3.4.1 The NiCo Riboswitch	274
13.4 Indirect Mechanisms of Regulation of Ni-Uptake	275
13.5 Trends and Future Directions	276
References	277
Chapter 14 - Nickel Metallochaperones: Structure, Function, and Nickel-Binding Properties	284
14.1 Introduction	284
14.2 Urease and Metallochaperones	285
14.2.1 UreE	285
14.2.2 UreG/F/H	286
14.3 [Ni,Fe]-Hydrogenase and Metallochaperones	288
14.3.1 Iron Insertion	289
14.3.2 Nickel Insertion	289
14.3.3 HypA	290
14.3.4 HypB	291
14.3.5 SlyD	292
14.3.6 Nickel-Dependent Proteolysis	294
14.4 Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase and Metallochaperones	294
14.5 Other Nickel Enzymes and Related Metallochaperones	296
14.5.1 Nickel Superoxide Dismutase	296
14.5.2 Methyl-Coenzyme M Reductase	296
14.5.3 Glyoxalase I	297
14.5.4 Acireductone Dioxygenase	297
14.5.5 Lactate Racemase	297
14.6 Nickel Storage Proteins	298
14.7 Perspectives	298
Acknowledgements	299
References	299
Chapter 15 - Cross-Talk Between Nickel and Other Metals in Microbial Systems	306
15.1 Introduction	306
15.2 Availability of Nickel	308
15.3 Import of Nickel Ions	309
15.3.1 High-Rate, Low-Specificity Import of Transition Metal Cation Mixtures	309
15.3.2 Nickel Import Channels	312
15.4 Export of Nickel Ions	314
15.4.1 Export from the Periplasm to the Outside in Gram-Negative Bacteria	314
15.4.2 Export from the Cytoplasm	320
15.5 Nickel Ions in the Cytoplasm	323
15.6 Cytoplasmic Ni-Binding Proteins and Enzyme Metallation	324
15.6.1 Nickel-Binding Proteins	324
15.6.2 Ensuring Nickel Fidelity in [NiFe]-Hydrogenase Maturation	326
15.6.3 GTP-Driven Conformational Switches in Nickel Metalation	326
15.7 Interference Between Nickel and Other Transition Metal Cations	326
References	327
Chapter 16 - Nickel and Virulence in Bacterial Pathogens	339
16.1 Introduction	339
16.2 Metals and Virulence of Bacterial Pathogens	340
16.2.1 Nickel in Bacterial Pathogens	340
16.2.2 Diverse Functions of the Nickel-Enzyme Urease During Bacterial Pathogenesis	341
16.2.3 Nickel in Virulence Independent from Urease	342
16.3 Nickel in Helicobacter Pylori	343
16.3.1 Generalities	343
16.3.2 In Vivo Urease Activation and Accessory Protein Complexes in H. pylori	345
16.3.3 [NiFe]-Hydrogenase and Molecular Cross-Talk Between the Hydrogenase and Urease Maturation Machineries	345
16.3.4 Nickel Uptake and Efflux	346
16.3.5 Original Nickel Chaperones and Storage Proteins in H. pylori	348
16.3.5.1 HspA	348
16.3.5.2 Hpn and Hpn-2	348
16.3.6 NikR: The Coordinator of Nickel Transport and Trafficking in H. pylori	350
16.3.7 Other Roles of Urease in H. pylori Virulence	350
16.4 Nickel in Staphylococcus aureus	351
16.5 Conclusion	352
Acknowledgements	352
References	352
Chapter 17 - Application of Ni2+-Binding Proteins	357
17.1 Introduction	357
17.2 Purification of Recombinant His-Tagged Proteins and Their Application as Biosensors	357
17.3 Ni2+-Binding Proteins as Targets for Antibacterial Compounds	360
17.4 Ni2+-Binding Proteins in Bioremediation	361
17.5 Concluding Remarks	362
References	362
Subject Index	365

The Biological Chemistry of Nickel

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