Metalloenzymes in Denitrification

Isabel Moura; José J G Moura; Sofia R Pauleta; Luisa B Maia

BOOK

Metalloenzymes in Denitrification

Isabel Moura | José J G Moura | Sofia R Pauleta | Luisa B Maia

(2016)

Additional Information

Book Details

ISBN: 978-1-78262-376-2
Edition: 1
Language: English
Pages: 452
Subjects: Chemistry
Inorganic chemistry
Biochemistry
Chemical biology
Biotechnology

Abstract

The reduction of nitrate to nitrogen by metalloenzymes is a vital step in the nitrogen cycle. The importance of this pathway has inspired efforts to understand in greater depth the mechanisms involved. This book presents and discusses the latest information on multiple aspects of denitrification.

Written by recognized specialists in the field, this book describes the bioinorganic aspects and the key enzymes involved in denitrification, including their structure, function and mechanisms. Active site modelling, novel methodologies for monitoring denitrification in vivo and biotechnological methods for water treatment are discussed. The book also focusses on the environmental implications of denitrification, such nitrate accumulation and the release of nitrous oxide into the atmosphere from excessive fertiliser use.

An important topic in many biological, environmental and agricultural contexts, this book will aid teaching and help bioinorganic chemists and biotechnologists gain an up-to-date picture of the science behind the denitrification process.

Section Title	Page	Action	Price
Cover	Cover
Metalloenzymes in Denitrification Applications and Environmental Impacts	i
Preface	v
Contents	vii
Chapter 1 - A Bird’s Eye View of Denitrification in Relation to the Nitrogen Cycle	1
1.1 Introduction	1
1.2 The Nitrogen Cycle	2
1.3 Classic and New Pathways	2
1.3.1 Dissimilatory Nitrate Reduction to Ammonium and Nitrification	3
1.3.2 Anaerobic Oxidation of Ammonium to Dinitrogen	4
1.3.3 Anaerobic Reduction of Nitrate to Dinitrogen—Denitrification	4
1.3.4 New Avenues/New Challenges	5
1.4 Book Outlook	6
Acknowledgements	7
References	7
Chapter 2 - Nitric Oxide Production, Damage and Management During Anaerobic Nitrate Reduction to Ammonia	11
2.1 “Things Ain’t What They Used to Be!”	11
2.2 Overview of Enzymes that Catalyse Denitrification or Nitrite Reduction to Ammonia	13
2.3 Dissimilatory Reduction of Nitrate to Ammonia in the Cytoplasm of Gram-Negative Bacteria	17
2.4 Nitrate Reduction to Ammonia in the Periplasm of Gram-Negative Bacteria	18
2.5 Regulation of Nitrate Reduction to Ammonia by Enteric Bacteria	19
2.6 “Denitrification” by Enteric Bacteria that Mainly Reduce Nitrate to Ammonia	22
2.6.1 Nitrite Reductases Other than NirS and NirK Implicated in NO Formation	23
2.7 Defence Against NO Toxicity in Bacteria that Reduce Nitrate to Ammonia	24
2.7.1 Three Pathways for NO Reduction by Enteric Bacteria	25
2.7.2 Is There a High-Affinity But Previously Undiscovered NO Reductase in Anaerobic Bacteria	26
2.8 Controversial Claims that the Transcription Factors FNR, OxyR and Fur are Physiologically Relevant NO Sensors	28
2.9 Regulation of Gene Expression Under Conditions of Nitrosative Stress	29
2.10 Repair of Nitrosylation Damage by the YtfE Protein, also Known as RIC	31
Acknowledgements	32
References	32
Chapter 3 - Structure, Function and Mechanisms of Respiratory Nitrate Reductases	39
3.1 Introduction	39
3.2 Structural and Spectroscopic Properties of Respiratory Nars	43
3.2.1 The Catalytic Subunit NarG	44
3.2.1.1 The Mo-bisPGD Cofactor	44
3.2.1.2 The FeS0 Cluster	45
3.2.2 The ET Subunit NarH	46
3.2.3 The QH2-Oxidising Subunit NarI	47
3.3 Gene Expression Control and Maturation of Respiratory Nars	49
3.3.1 Regulation at the Transcriptional and Translational Levels	49
3.3.2 NarGHI Maturation and Assembly	50
3.4 Metabolic Role	51
3.5 Catalytic Mechanism	52
Acknowledgements	52
References	53
Chapter 4 - Nitrite Reductase – Cytochrome cd1	59
4.1 The Haem Nitrite Reductase Gene nirS	59
4.2 The cd1NIR Protein	61
4.3 Structure and Reactivity of cd1NIR	63
4.3.1 Structure Overview	63
4.3.2 Haem Pockets and Reactivity	64
4.3.3 Redox-Dependent Conformational Changes	68
4.4 Mechanistic Aspects of cd1NIR Catalysis	70
4.4.1 Substrate Binding	71
4.4.2 Electron Transfer From the c-Haem to the d1-Haem	73
4.4.3 Catalysis and Product Release	73
4.5 Biogenesis of the c-Haem and the d1-Haem	75
4.5.1 c-Haem	76
4.5.2 d1-Haem	77
4.6 Role of cd1NIR in Biofilm and Quorum Sensing	81
4.7 Haem NIR as a Bioresource	82
4.7.1 Nitrite Biosensing	82
4.7.2 Functional Markers in Metagenomic Analysis	82
References	83
Chapter 5 - Structure and Function of Copper Nitrite Reductase	91
5.1 Introduction	91
5.2 The T1Cu Site	93
5.3 Electron Transfer	98
5.3.1 Intramolecular ET	98
5.3.2 Intermolecular ET	100
5.4 The T2Cu Site and Nitrite Reduction	106
Acknowledgements	109
References	110
Chapter 6 - Structure and Function of Nitric Oxide Reductases	114
6.1 Introduction	114
6.2 Properties and Reactions of NO and Metal–NO Complexes	115
6.3 Bacterial NOR	116
6.4 Structural and Functional Knowledge Before Crystal Structures were Available	118
6.4.1 Metal Centres	118
6.4.2 Electron Transfer	120
6.4.3 Proton Transfer	122
6.5 Functional Characterisation Based on the Crystal Structures of NORs	123
6.5.1 Overall Structures	123
6.5.2 Electron Transfer Pathway	124
6.5.3 Active Site Structures	127
6.5.4 Molecular Mechanism of NO Reduction by NOR	128
6.5.5 Proton Transfer Pathway	132
6.6 Molecular Evolution of Proton Pumps in Respiratory Enzymes	135
References	136
Chapter 7 - Insights into Nitrous Oxide Reductase	141
7.1 Introduction	141
7.2 Biogenesis of N2OR	142
7.3 The Structure of N2OR	145
7.3.1 The Overall Structure	145
7.3.2 The Copper Centres—Structure and Coordination	145
7.4 Spectroscopic Properties	149
7.4.1 The CuA Centre	150
7.4.2 The “CuZ Centre”	153
7.4.2.1 CuZ*(4Cu1S)	154
7.4.2.2 CuZ(4Cu2S)	155
7.5 Kinetic Properties of N2OR	157
7.5.1 CuZ and CuZ*	158
7.5.2 CuZ0	160
7.5.3 Substrate Binding Site and Catalytic Cycle	161
7.6 Concluding Remarks	164
Acknowledgements	164
References	165
Chapter 8 - Model Compounds for Molybdenum Nitrate Reductases	170
8.1 Introduction	170
8.1.1 Nitrate Reduction and Its Implication in Biology	170
8.1.2 Classification and Active Site Structures of Nitrate Reductase	171
8.1.3 Mechanism of Nitrate Reduction	172
8.2 Model Chemistry	174
8.2.1 Introduction	174
8.2.2 Early Studies	175
8.2.3 Model Chemistry Using Non-Dithiolene Ligands	178
8.2.4 Model Chemistry Using Dithiolene Ligands	178
8.3 Problems, Strategies and Future Scope	182
References	183
Chapter 9 - Model Compounds for Nitric Oxide Reductase	185
9.1 Introduction	185
9.2 Synthetic Models of Haem/Non-Haem NOR	187
9.2.1 Design and Synthesis	187
9.2.1.1 Face Selection and Insertion of the Proximal Imidazole Ligand	188
9.2.1.2 Synthesis of the Glutamic Acid Mimic	191
9.2.1.3 Attachment of Distal Imidazole Ligands	192
9.2.1.4 Introduction of Metals	192
9.2.2 NO Reactivity of Synthetic Haem/Non-Haem NOR Models	192
9.2.3 Mechanism of NO Reduction by a Synthetic Haem/	197
9.3 Engineered Myoglobin-Based NOR Model	201
9.3.1 Synthesis	201
9.3.2 Mechanism	204
9.4 NOR versus CcO	208
9.4.1 O2 Reduction by a Synthetic Haem/Non-Haem NOR Model	208
9.4.2 Mechanism of O2 Reaction by a Synthetic Haem/Non-Haem NOR Model	211
9.4.3 NO Reactivity of a Synthetic Functional Model of CcO	211
9.5 Concluding Remarks	219
References	220
Chapter 10 - Model Compounds of Copper-Containing Enzymes Involved in Bacterial Denitrification	225
10.1 Introduction	225
10.2 Models Relevant to Nitrite Reductase	226
10.2.1 Key Aspects of the Enzymatic T2 Site to Model	226
10.2.2 Structural Models Relevant to the Nitrite-Bound T2 Site	227
10.2.3 Structural Models Relevant to the NO-Bound T2 Site	230
10.2.4 Functional Models with Nitrite Reductase Activity	232
10.3 Models Relevant to N2OR	235
10.3.1 Key Aspects of the CuZ Sites to Model	235
10.3.2 Structural Models Relevant to the CuZ* Site	237
10.3.3 Functional N2O Reactivity of Molecular Copper Complexes	241
Acknowledgements	244
References	244
Chapter 11 - Electron Transfer and Molecular Recognition in Denitrification and Nitrate Dissimilatory Pathways	252
11.1 Introduction	252
11.2 Electron Transfer Involved in Nitrate Reduction	253
11.2.1 Periplasmic Dissimilatory Nitrate Reductase	254
11.2.2 Respiratory Nitrate Reductase	257
11.3 Electron Transfer Involved in Nitrite Reduction	258
11.3.1 Direct Conversion of Nitrite to Ammonium by Dissimilatory NrfA	259
11.3.2 Cu-NiR	261
11.3.3 cd1-NiR	265
11.4 Electron Transfer Involved in Nitric Oxide Reduction	268
11.4.1 Intramolecular Electron Transfer	268
11.4.2 Intermolecular Electron Transfer	270
11.5 Electron Transfer Involved in Nitrous Oxide Reduction	272
11.5.1 Intramolecular Electron Transfer	273
11.5.2 Intermolecular Electron Transfer	274
11.6 Concluding Remarks	277
Acknowledgements	279
References	279
Chapter 12 - Channels and Transporters for Nitrogen Cycle Intermediates	287
12.1 Bioenergetics of Denitrification	287
12.1.1 The Compartmentalisation of the Nitrogen Cycle	288
12.1.2 Translocation of Ions Across Membranes	288
12.2 Nitrate Transport	290
12.2.1 Types of Nitrate Transporters	291
12.2.2 The NPF Family and the Plant Nitrate Transporter NRT1.1	292
12.2.3 NO3−/H+ Symport vs. NO3−/NO2− Antiport	293
12.2.4 The NNP Family	293
12.2.5 Structural Features of Bacterial NarK and NarU	294
12.2.6 Transport Mechanism of Nitrate/Nitrite Porters	295
12.3 Nitrite Transport	297
12.3.1 The Metabolic Role of Nitrite	297
12.3.2 The Formate/Nitrite Transporter Family of Ion Channels/Transporters	298
12.3.3 The Nitrite Channel NirC	299
12.3.4 The Transport Mechanism of NirC	300
12.4 Ammonium Transport	302
12.4.1 Amt/Rh/Mep Transporters	302
12.4.2 Passive vs. Active Transport of Reduced Nitrogen	303
12.4.3 Structures of Ammonium Transporters	304
12.4.4 Electrogenic NH4+ Transport by Amt Proteins	305
12.5 Conclusions	307
References	307
Chapter 13 - Regulation of Denitrification	312
13.1 Introduction	312
13.2 Regulation of Denitrification in Model Organisms	313
13.2.1 Pa. denitrificans	313
13.2.2 Ps. stutzeri and Ps. aeruginosa	317
13.2.3 Bra. japonicum	319
13.2.4 Rh. sphaeroides	320
13.2.5 Ra. eutropha	320
13.2.6 Brucella Species	321
13.2.7 Neisseria Species	321
13.3 NO Detoxification	322
13.4 Emerging Themes: Regulators and Signals	323
13.5 Conclusions and Future Prospects	325
References	326
Chapter 14 - Denitrification in Fungi	331
14.1 Introduction	331
14.2 Serendipitous P450	332
14.3 Fungal Denitrifying System	333
14.4 Eukaryotic nirK Genes: Originating from the Protomitochondrion	336
14.5 Co-Denitrification	337
14.6 P450nor (Fungal Nor)	338
14.7 Occurrence of Fungal Denitrification and Co-Denitrification in Ecosystems	343
14.8 Concluding Remarks	343
Acknowledgements	345
References	346
Chapter 15 - Denitrification and Non-Denitrifier Nitrous Oxide Emission in Gram-Positive Bacteria	349
15.1 Denitrification is Widespread but Underexplored in Gram-Positive Bacteria	349
15.2 Novel Features in the Denitrifier B. azotoformans	351
15.2.1 Membrane-Bound Enzymes and a Novel NO Reductase	351
15.2.2 High Genetic Redundancy and Potential Metabolic Versatility	353
15.3 N2O Emission by Non-Denitrifying Bacilli	355
15.3.1 N2O Emission Related to Nitrite Accumulation and DNRA	355
15.3.2 Mechanisms for N2O Production	357
15.4 Environmental Relevance of Bacilli and Related Methodological Issues	360
15.4.1 Their Ubiquitous Nature	360
15.4.2 Their Contribution to Denitrification	361
Acknowledgements	363
References	363
Chapter 16 - Denitrification Processes for Wastewater Treatment	368
16.1 Introduction	368
16.1.1 Nitrogen Removal from Wastewater	370
16.1.2 Overview of Denitrification Processes	371
16.2 Heterotrophic Denitrification	372
16.2.1 Heterotrophic Denitrifying Organisms	372
16.2.2 Stoichiometry and Kinetics of Heterotrophic Denitrification	373
16.2.3 Factors Affecting Heterotrophic Denitrification	373
16.2.3.1 Carbon Source	373
16.2.3.2 COD to N Ratio	374
16.2.3.3 Dissolved Oxygen Concentration	374
16.2.3.4 pH and Temperature	374
16.2.4 Denitrification Intermediate Accumulation and Electron Competition	375
16.2.5 Modelling the Heterotrophic Denitrification Processes	375
16.2.6 Nitrogen Removal Based on Heterotrophic Denitrification	377
16.2.6.1 Pre-Denitrification and Post-Denitrification	377
16.2.6.2 Modified Ludzack–Ettinger Configuration	378
16.2.6.3 Oxidation Ditch	378
16.2.6.4 Sequencing Batch Reactors	379
16.3 Anaerobic Ammonia Oxidation	379
16.3.1 AnAmmOx Organisms	379
16.3.2 Metabolic Pathways of AnAmmOx	380
16.3.3 Physiological Characteristics and Enrichment of AnAmmOx	380
16.3.4 Factors Affecting AnAmmOx	382
16.3.4.1 Dissolved Oxygen	382
16.3.4.2 Ammonia and Nitrite Levels	383
16.3.4.3 Temperature	383
16.3.4.4 Salinity	383
16.3.4.5 Fe(ii) Concentration	383
16.3.5 Modelling the AnAmmOx Processes	384
16.3.6 Autotrophic Nitrogen Removal by AnAmmOx	384
16.4 Denitrifying Anaerobic Methane Oxidation	386
16.4.1 Stoichiometry of DAMO	386
16.4.2 Enrichment and Characteristics of DAMO	387
16.4.3 Proposed Mechanisms of DAMO Microorganisms	387
16.4.3.1 DAMO Bacteria—Candidatus Methylomirabilis oxyfera	387
16.4.3.2 DAMO Archaea—Candidatus Methanoperedens nitroreducens	388
16.4.4 Factors Affecting DAMO	389
16.4.5 Emerging Technologies Based on DAMO Processes	389
16.4.6 Modelling DAMO Processes	392
16.5 Autotrophic Denitrification	393
16.5.1 Autotrophic Denitrifying Organisms	393
16.5.2 Stoichiometry of Autotrophic Denitrification	394
16.5.3 Key Factors Affecting Autotrophic Denitrification	394
16.5.3.1 pH	394
16.5.3.2 Temperature	395
16.5.3.3 Electron Acceptor	395
16.5.3.4 Electron Donor	395
16.5.4 Application of the Autotrophic Denitrification Processes	396
16.5.5 Modelling the Autotrophic Denitrification Processes	400
16.6 Bioelectrochemical Denitrification Processes	400
16.6.1 Bioelectrochemical Systems	400
16.6.2 Bioelectrochemical Denitrification	402
16.6.3 Bioelectrochemical System Configurations for Nitrogen Removal	403
16.6.4 Factors Affecting Bioelectrochemical Denitrification	405
16.6.5 Community Analyses in Denitrifying Biocathodes	406
16.7 Concluding Remarks	407
Acknowledgements	408
References	408
Chapter 17 - Lessons from Denitrification for the Human Metabolism of Signalling Nitric Oxide	419
17.1 “Classic” Metabolism of Signalling Nitric Oxide	419
17.2 Nitrite-Dependent NO Formation	421
17.2.1 A New Concept Emerged	421
17.2.2 Present Key Questions	422
17.2.2.1 Nitrite Homeostasis	422
17.2.2.2 “Non-Dedicated” Nitrite Reductases	423
17.2.3 Human Nitrite Reduction in the Cellular Context	427
17.3 Nitrate Reduction to Signalling NO in the Context of the Nitrogen Cycle	428
Acknowledgements	430
References	430
Subject Index	444

Metalloenzymes in Denitrification

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