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1.
Nat Rev Chem ; 8(10): 762-775, 2024 10.
Artigo em Inglês | MEDLINE | ID: mdl-39223400

RESUMO

From the reduction of dinitrogen to the oxidation of water, the chemical transformations catalysed by metalloenzymes underlie global geochemical and biochemical cycles. These reactions represent some of the most kinetically and thermodynamically challenging processes known and require the complex choreography of the fundamental building blocks of nature, electrons and protons, to be carried out with utmost precision and accuracy. The rate-determining step of catalysis in many metalloenzymes consists of a protein structural rearrangement, suggesting that nature has evolved to leverage macroscopic changes in protein molecular structure to control subatomic changes in metallocofactor electronic structure. The proton-coupled electron transfer mechanisms operative in nitrogenase, photosystem II and ribonucleotide reductase exemplify this interplay between molecular and electronic structural control. We present the culmination of decades of study on each of these systems and clarify what is known regarding the interplay between structural changes and functional outcomes in these metalloenzyme linchpins.


Assuntos
Metaloproteínas , Prótons , Transporte de Elétrons , Metaloproteínas/química , Metaloproteínas/metabolismo , Ribonucleotídeo Redutases/química , Ribonucleotídeo Redutases/metabolismo , Complexo de Proteína do Fotossistema II/química , Complexo de Proteína do Fotossistema II/metabolismo , Nitrogenase/química , Nitrogenase/metabolismo , Conformação Proteica , Modelos Moleculares
2.
J Phys Chem B ; 128(40): 9699-9705, 2024 Oct 10.
Artigo em Inglês | MEDLINE | ID: mdl-39344806

RESUMO

Nitrogenase converts nitrogen in the air to ammonia. It is often regarded as the second most important enzyme in nature after photosystem II. The mechanism for how nitrogenase is able to perform the difficult task of cleaving the strong bond in N2 is debated. It is known that for every electron that is donated to N2, two ATP are hydrolyzed. In the experimentally suggested mechanism, the activation occurs after four reductions of the ground state, but there is no suggestion for how the enzyme uses the hydrolysis energy to perform catalysis. In the theoretical mechanism, it is suggested that hydrolysis is used to reduce the electron donor. In previous papers, the steps leading to the activation of N2 in the so-called E4 state has been investigated, using both the experimental and theoretical mechanism, showing that only the theoretical one leads to agreement with EPR observations for E4. In the present paper, the four steps following E4, leading to the release of two ammonia molecules, are described using the same methodology as used in the previous studies.


Assuntos
Amônia , Fixação de Nitrogênio , Nitrogenase , Nitrogenase/química , Nitrogenase/metabolismo , Amônia/química , Amônia/metabolismo , Hidrólise , Espectroscopia de Ressonância de Spin Eletrônica , Nitrogênio/química , Nitrogênio/metabolismo
3.
Angew Chem Int Ed Engl ; 63(45): e202412740, 2024 Nov 04.
Artigo em Inglês | MEDLINE | ID: mdl-39107257

RESUMO

The production of ammonia (NH3) from nitrogen sources involves competitive adsorption of different intermediates and multiple electron and proton transfers, presenting grand challenges in catalyst design. In nature nitrogenases reduce dinitrogen to NH3 using two component proteins, in which electrons and protons are delivered from Fe protein to the active site in MoFe protein for transfer to the bound N2. We draw inspiration from this structural enzymology, and design a two-component metal-sulfur-carbon (M-S-C) catalyst composed of sulfur-doped carbon-supported ruthenium (Ru) single atoms (SAs) and nanoparticles (NPs) for the electrochemical reduction of nitrate (NO3 -) to NH3. The catalyst demonstrates a remarkable NH3 yield rate of ~37 mg L-1 h-1 and a Faradaic efficiency of ~97 % for over 200 hours, outperforming those consisting solely of SAs or NPs, and even surpassing most reported electrocatalysts. Our experimental and theoretical investigations reveal the critical role of Ru SAs with the coordination of S in promoting the formation of the HONO intermediate and the subsequent reduction reaction over the NP-surface nearby. Such process results in a more energetically accessible pathway for NO3 - reduction on Ru NPs co-existing with SAs. This study proves a better understanding of how M-S-Cs act as a synthetic nitrogenase mimic during ammonia synthesis, and contributes to the future mechanism-based catalyst design.


Assuntos
Carbono , Nitrogenase , Enxofre , Nitrogenase/química , Nitrogenase/metabolismo , Catálise , Carbono/química , Enxofre/química , Rutênio/química , Amônia/química , Amônia/metabolismo , Oxirredução , Nitratos/química , Nitratos/metabolismo
4.
Dalton Trans ; 53(27): 11500-11513, 2024 Jul 09.
Artigo em Inglês | MEDLINE | ID: mdl-38916132

RESUMO

We have studied whether dissociation of the S2B sulfide ligand from one of its two coordinating Fe ions may affect the later parts of the reaction mechanism of nitrogenase. Such dissociation has been shown to be favourable for the E2-E4 states in the reaction mechanism, but previous studies have assumed that S2B either remains bridging or has fully dissociated from the active-site FeMo cluster. We employ combined quantum mechanical and molecular mechanical (QM/MM) calculations with two density-functional theory methods, r2SCAN and TPSSh. To make dissociation of S2B possible, we have added a proton to this group throughout the reaction. We study the reaction starting from the E4 state with N2H2 bound to the cluster. Our results indicate that half-dissociation of S2B is unfavourable in most steps of the reaction mechanism. We observe favourable half-dissociation of S2B only when NH or NH2 is bound to the cluster, bridging Fe2 and Fe6. However, the former state is most likely not involved in the reaction mechanism and the latter state is only an intermittent intermediate of the E7 state. Therefore, half-dissociation of S2B seems to play only a minor role in the later parts of the reaction mechanism of nitrogenase. Our suggested mechanism with a protonated S2B is alternating (the two N atoms of the substrate is protonated in an alternating manner) and the substrate prefers to bind to Fe2, in contrast to the preferred binding to Fe6 observed when S2B is unprotonated and bridging Fe2 and Fe6.


Assuntos
Nitrogenase , Nitrogenase/química , Nitrogenase/metabolismo , Ligantes , Modelos Moleculares , Sulfetos/química , Sulfetos/metabolismo , Teoria da Densidade Funcional , Teoria Quântica , Prótons
5.
mBio ; 15(7): e0127124, 2024 Jul 17.
Artigo em Inglês | MEDLINE | ID: mdl-38869277

RESUMO

Life depends on a conserved set of chemical energy currencies that are relics of early biochemistry. One of these is ATP, a molecule that, when paired with a divalent metal ion such as Mg2+, can be hydrolyzed to support numerous cellular and molecular processes. Despite its centrality to extant biochemistry, it is unclear whether ATP supported the function of ancient enzymes. We investigate the evolutionary necessity of ATP by experimentally reconstructing an ancestral variant of the N2-reducing enzyme nitrogenase. The Proterozoic ancestor is predicted to be ~540-2,300 million years old, post-dating the Great Oxidation Event. Growth rates under nitrogen-fixing conditions are ~80% of those of wild type in Azotobacter vinelandii. In the extant enzyme, the hydrolysis of two MgATP is coupled to electron transfer to support substrate reduction. The ancestor has a strict requirement for ATP with no other nucleotide triphosphate analogs (GTP, ITP, and UTP) supporting activity. Alternative divalent metal ions (Fe2+, Co2+, and Mn2+) support activity with ATP but with diminished activities compared to Mg2+, similar to the extant enzyme. Additionally, it is shown that the ancestor has an identical efficiency in ATP hydrolyzed per electron transferred to the extant of two. Our results provide direct laboratory evidence of ATP usage by an ancient enzyme.IMPORTANCELife depends on energy-carrying molecules to power many sustaining processes. There is evidence that these molecules may predate the rise of life on Earth, but how and when these dependencies formed is unknown. The resurrection of ancient enzymes provides a unique tool to probe the enzyme's function and usage of energy-carrying molecules, shedding light on their biochemical origins. Through experimental reconstruction, this research investigates the ancestral dependence of a nitrogen-fixing enzyme on the energy carrier ATP, a requirement for function in the modern enzyme. We show that the resurrected ancestor does not have generalist nucleotide specificity. Rather, the ancestor has a strict requirement for ATP, like the modern enzyme, with similar function and efficiency. The findings elucidate the early-evolved necessity of energy-yielding molecules, delineating their role in ancient biochemical processes. Ultimately, these insights contribute to unraveling the intricate tapestry of evolutionary biology and the origins of life-sustaining dependencies.


Assuntos
Trifosfato de Adenosina , Azotobacter vinelandii , Trifosfato de Adenosina/metabolismo , Azotobacter vinelandii/enzimologia , Azotobacter vinelandii/genética , Azotobacter vinelandii/metabolismo , Nitrogenase/metabolismo , Nitrogenase/genética , Nitrogenase/química , Evolução Molecular , Fixação de Nitrogênio/genética , Oxirredução , Hidrólise
6.
Sci Adv ; 10(24): eado6169, 2024 Jun 14.
Artigo em Inglês | MEDLINE | ID: mdl-38865457

RESUMO

Nitrogenase plays a key role in the global nitrogen cycle; yet, the evolutionary history of nitrogenase and, particularly, the sequence of appearance between the homologous, yet distinct NifDK (the catalytic component) and NifEN (the cofactor maturase) of the extant molybdenum nitrogenase, remains elusive. Here, we report the ability of NifEN to reduce N2 at its surface-exposed L-cluster ([Fe8S9C]), a structural/functional homolog of the M-cluster (or cofactor; [(R-homocitrate)MoFe7S9C]) of NifDK. Furthermore, we demonstrate the ability of the L-cluster-bound NifDK to mimic its NifEN counterpart and enable N2 reduction. These observations, coupled with phylogenetic, ecological, and mechanistic considerations, lead to the proposal of a NifEN-like, L-cluster-carrying protein as an ancient nitrogenase, the exploration of which could shed crucial light on the evolutionary origin of nitrogenase and related enzymes.


Assuntos
Nitrogenase , Nitrogenase/metabolismo , Nitrogenase/química , Nitrogenase/genética , Filogenia , Nitrogênio/metabolismo , Nitrogênio/química , Molibdoferredoxina/química , Molibdoferredoxina/metabolismo , Modelos Moleculares , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/química , Fixação de Nitrogênio/genética
7.
FEBS J ; 291(15): 3454-3480, 2024 Aug.
Artigo em Inglês | MEDLINE | ID: mdl-38696373

RESUMO

The nitrogenase reductase NifH catalyses ATP-dependent electron delivery to the Mo-nitrogenase, a reaction central to biological dinitrogen (N2) fixation. While NifHs have been extensively studied in bacteria, structural information about their archaeal counterparts is limited. Archaeal NifHs are considered more ancient, particularly those from Methanococcales, a group of marine hydrogenotrophic methanogens, which includes diazotrophs growing at temperatures near 92 °C. Here, we structurally and biochemically analyse NifHs from three Methanococcales, offering the X-ray crystal structures from meso-, thermo-, and hyperthermophilic methanogens. While NifH from Methanococcus maripaludis (37 °C) was obtained through heterologous recombinant expression, the proteins from Methanothermococcus thermolithotrophicus (65 °C) and Methanocaldococcus infernus (85 °C) were natively purified from the diazotrophic archaea. The structures from M. thermolithotrophicus crystallised as isolated exhibit high flexibility. In contrast, the complexes of NifH with MgADP obtained from the three methanogens are superposable, more rigid, and present remarkable structural conservation with their homologues. They retain key structural features of P-loop NTPases and share similar electrostatic profiles with the counterpart from the bacterial model organism Azotobacter vinelandii. In comparison to the NifH from the phylogenetically distant Methanosarcina acetivorans, these reductases do not cross-react significantly with Mo-nitrogenase from A. vinelandii. However, they associate with bacterial nitrogenase when ADP· AlF 4 - is added to mimic a transient reactive state. Accordingly, detailed surface analyses suggest that subtle substitutions would affect optimal binding during the catalytic cycle between the NifH from Methanococcales and the bacterial nitrogenase, implying differences in the N2-machinery from these ancient archaea.


Assuntos
Methanococcales , Modelos Moleculares , Oxirredutases , Cristalografia por Raios X , Oxirredutases/metabolismo , Oxirredutases/química , Oxirredutases/genética , Methanococcales/enzimologia , Methanococcales/genética , Sequência de Aminoácidos , Proteínas Arqueais/química , Proteínas Arqueais/metabolismo , Proteínas Arqueais/genética , Conformação Proteica , Nitrogenase/metabolismo , Nitrogenase/química , Nitrogenase/genética
8.
J Agric Food Chem ; 72(23): 12988-13000, 2024 Jun 12.
Artigo em Inglês | MEDLINE | ID: mdl-38820247

RESUMO

Biological nitrogen fixation is crucial for agriculture and improving fertilizer efficiency, but organic fertilizers in enhancing this process remain debated. Here, we investigate the impact of organic fertilizers on biological nitrogen fixation through experiments and propose a new model where bacterial interactions with complex carbon sources enhance nitrogen fixation. Field experiments showed that adding organic fertilizers increased the nitrogenase activity by 57.85%. Subculture experiments revealed that organic fertilizer addition enriched genes corresponding to complex carbon and energy metabolism, as well as nifJ involved in electron transfer for nitrogenase. It also enhanced bacterial interactions and enhanced connectors associated with complex carbon degradation. Validation experiments demonstrated that combinations increased nitrogenase activity by 2.98 times compared to the single. Our findings suggest that organic fertilizers promoted nitrogen fixation by enhancing microbial cooperation, improved the degradation of complex carbon sources, and thereby provided utilizable carbon sources, energy, and electrons to N-fixers, thus increasing nitrogenase activity and nitrogen fixation.


Assuntos
Carbono , Fertilizantes , Fixação de Nitrogênio , Nitrogenase , Fertilizantes/análise , Carbono/metabolismo , Carbono/química , Nitrogenase/metabolismo , Nitrogenase/química , Bactérias/metabolismo , Bactérias/genética , Nitrogênio/metabolismo , Microbiologia do Solo , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/genética , Proteínas de Bactérias/química
9.
Nat Commun ; 15(1): 4041, 2024 May 13.
Artigo em Inglês | MEDLINE | ID: mdl-38740794

RESUMO

Due to the complexity of the catalytic FeMo cofactor site in nitrogenases that mediates the reduction of molecular nitrogen to ammonium, mechanistic details of this reaction remain under debate. In this study, selenium- and sulfur-incorporated FeMo cofactors of the catalytic MoFe protein component from Azotobacter vinelandii are prepared under turnover conditions and investigated by using different EPR methods. Complex signal patterns are observed in the continuous wave EPR spectra of selenium-incorporated samples, which are analyzed by Tikhonov regularization, a method that has not yet been applied to high spin systems of transition metal cofactors, and by an already established grid-of-error approach. Both methods yield similar probability distributions that reveal the presence of at least four other species with different electronic structures in addition to the ground state E0. Two of these species were preliminary assigned to hydrogenated E2 states. In addition, advanced pulsed-EPR experiments are utilized to verify the incorporation of sulfur and selenium into the FeMo cofactor, and to assign hyperfine couplings of 33S and 77Se that directly couple to the FeMo cluster. With this analysis, we report selenium incorporation under turnover conditions as a straightforward approach to stabilize and analyze early intermediate states of the FeMo cofactor.


Assuntos
Azotobacter vinelandii , Molibdoferredoxina , Nitrogenase , Selênio , Enxofre , Espectroscopia de Ressonância de Spin Eletrônica/métodos , Azotobacter vinelandii/enzimologia , Azotobacter vinelandii/metabolismo , Nitrogenase/metabolismo , Nitrogenase/química , Molibdoferredoxina/metabolismo , Molibdoferredoxina/química , Selênio/metabolismo , Selênio/química , Enxofre/metabolismo , Enxofre/química , Proteínas de Bactérias/metabolismo , Proteínas de Bactérias/química
10.
FEBS J ; 291(14): 3233-3248, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38588274

RESUMO

Coenzyme F430 is a nickel-containing tetrapyrrole, serving as the prosthetic group of methyl-coenzyme M reductase in methanogenic and methanotrophic archaea. During coenzyme F430 biosynthesis, the tetrapyrrole macrocycle is reduced by the nitrogenase-like CfbC/D system consisting of the reductase component CfbC and the catalytic component CfbD. Both components are homodimeric proteins, each carrying a [4Fe-4S] cluster. Here, the ligands of the [4Fe-4S] clusters of CfbC2 and CfbD2 were identified revealing an all cysteine ligation of both clusters. Moreover, the midpoint potentials of the [4Fe-4S] clusters were determined to be -256 mV for CfbC2 and -407 mV for CfbD2. These midpoint potentials indicate that the consecutive thermodynamically unfavorable 6 individual "up-hill" electron transfers to the organic moiety of the Ni2+-sirohydrochlorin a,c-diamide substrate require an intricate interplay of ATP-binding, hydrolysis, protein complex formation and release to drive product formation, which is a common theme in nitrogenase-like systems.


Assuntos
Proteínas Ferro-Enxofre , Proteínas Ferro-Enxofre/metabolismo , Proteínas Ferro-Enxofre/genética , Proteínas Ferro-Enxofre/química , Oxirredutases/metabolismo , Oxirredutases/genética , Oxirredutases/química , Nitrogenase/metabolismo , Nitrogenase/química , Nitrogenase/genética , Proteínas Arqueais/metabolismo , Proteínas Arqueais/genética , Proteínas Arqueais/química , Cisteína/metabolismo , Enxofre/metabolismo , Enxofre/química , Metaloporfirinas
11.
Nat Protoc ; 19(7): 2026-2051, 2024 Jul.
Artigo em Inglês | MEDLINE | ID: mdl-38575747

RESUMO

Single-particle cryo-electron microscopy (cryoEM) provides an attractive avenue for advancing our atomic resolution understanding of materials, molecules and living systems. However, the vast majority of published cryoEM methodologies focus on the characterization of aerobically purified samples. Air-sensitive enzymes and microorganisms represent important yet understudied systems in structural biology. We have recently demonstrated the success of an anaerobic single-particle cryoEM workflow applied to the air-sensitive nitrogenase enzymes. In this protocol, we detail the use of Schlenk lines and anaerobic chambers to prepare samples, including a protein tag for monitoring sample exposure to oxygen in air. We describe how to use a plunge freezing apparatus inside of a soft-sided vinyl chamber of the type we routinely use for anaerobic biochemistry and crystallography of oxygen-sensitive proteins. Manual control of the airlock allows for introduction of liquid cryogens into the tent. A custom vacuum port provides slow, continuous evacuation of the tent atmosphere to avoid accumulation of flammable vapors within the enclosed chamber. These methods allowed us to obtain high-resolution structures of both nitrogenase proteins using single-particle cryoEM. The procedures involved can be generally subdivided into a 4 d anaerobic sample generation procedure, and a 1 d anaerobic cryoEM sample preparation step, followed by conventional cryoEM imaging and processing steps. As nitrogen is a substrate for nitrogenase, the Schlenk lines and anaerobic chambers described in this procedure are operated under an argon atmosphere; however, the system and these procedures are compatible with other controlled gas environments.


Assuntos
Microscopia Crioeletrônica , Nitrogenase , Microscopia Crioeletrônica/métodos , Nitrogenase/metabolismo , Nitrogenase/química , Anaerobiose , Ar , Oxigênio/metabolismo , Oxigênio/química
12.
Biosens Bioelectron ; 255: 116254, 2024 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-38569252

RESUMO

Nitrogen fixation is a key process that sustains life on Earth. Nitrogenase is the sole enzyme capable of fixing nitrogen under ambient conditions. Extensive research efforts have been dedicated to elucidating the enzyme mechanism and its artificial activation through high applied voltage, photochemistry, or strong reducing agents. Harnessing light irradiation to minimize the required external bias can lower the process's high energy investment. Herein, we present the development of photo-bioelectrochemical cells (PBECs) utilizing BiVO4/CoP or CdS/NiO photoanodes for nitrogenase activation toward N2 fixation. The constructed PBEC based on BiVO4/CoP photoanode requires minimal external bias (200 mV) and suppresses O2 generation that allows efficient activation of the nitrogenase enzyme, using glucose as an electron donor. In a second developed PBEC configuration, CdS/NiO photoanode was used, enabling bias-free activation of the nitrogenase-based cathode to produce 100 µM of ammonia at a faradaic efficiency (FE) of 12%. The ammonia production was determined by a commonly used fluorescence probe and further validated using 1H-NMR spectroscopy. The presented PBECs lay the foundation for biotic-abiotic systems to directly activate enzymes toward value-added chemicals by light-driven reactions.


Assuntos
Técnicas Biossensoriais , Nitrogenase , Nitrogenase/química , Nitrogenase/metabolismo , Amônia/química , Fixação de Nitrogênio , Nitrogênio/química
13.
Dalton Trans ; 53(18): 7996-8004, 2024 May 07.
Artigo em Inglês | MEDLINE | ID: mdl-38651170

RESUMO

In converting N2 to NH3 the enzyme nitrogenase utilises 8 electrons and 8 protons in the complete catalytic cycle. The source of the electrons is an Fe4S4 reductase protein (Fe-protein) which temporarily docks with the MoFe-protein that contains the catalytic active cofactor, FeMo-co, and an electron transfer cluster called the P cluster. The overall mechanism involves 8 repetitions of a cycle in which reduced Fe-protein docks with the MoFe-protein, one electron transfers to the P-cluster, and then to FeMo-co, followed by dissociation of the two proteins and re-reduction of the Fe-protein. Protons are supplied serially to FeMo-co by a Grotthuss proton translocation mechanism from the protein surface along a conserved chain of water molecules (a proton wire) that terminates near S atoms of the FeMo-co cluster [CFe7S9Mo(homocitrate)] where the multiple steps of the chemical conversions are effected. It is assumed that the chemical mechanisms use proton-coupled electron-transfer (PCET) and that H atoms (e- + H+) are involved in each of the hydrogenation steps. However there is neither evidence for, or mechanism proposed, for this coupling. Here I report calculations of cluster charge distribution upon electron addition, revealing that the added negative charge is on the S atoms of FeMo-co, which thereby become more basic, and able to trigger proton transfer from H3O+ waiting at the near end of the proton wire. This mechanism is supported by calculations of the dynamics of the proton transfer step, in which the barrier is reduced by ca. 3.5 kcal mol-1 and the product stabilised by ca. 7 kcal mol-1 upon electron addition. H tunneling is probable in this step. In nitrogenase it is electron transfer that triggers proton transfer.


Assuntos
Domínio Catalítico , Nitrogenase , Prótons , Nitrogenase/química , Nitrogenase/metabolismo , Transporte de Elétrons , Elétrons , Modelos Moleculares , Molibdoferredoxina/química , Molibdoferredoxina/metabolismo
14.
Angew Chem Int Ed Engl ; 63(21): e202400273, 2024 05 21.
Artigo em Inglês | MEDLINE | ID: mdl-38527309

RESUMO

Nitrogenase reduces N2 to NH3 at its active-site cofactor. Previous studies of an N2-bound Mo-nitrogenase from Azotobacter vinelandii suggest binding of three N2 species via asymmetric belt-sulfur displacements in the two cofactors of its catalytic component (designated Av1*), leading to the proposal of stepwise N2 reduction involving all cofactor belt-sulfur sites; yet, the evidence for the existence of multiple N2 species on Av1* remains elusive. Here we report a study of ATP-independent, EuII/SO3 2--driven turnover of Av1* using GC-MS and frequency-selective pulse NMR techniques. Our data demonstrate incorporation of D2-derived D by Av1* into the products of C2H2- and H+-reduction, and decreased formation of NH3 by Av1* concomitant with the release of N2 under H2; moreover, they reveal a strict dependence of these activities on SO3 2-. These observations point to the presence of distinct N2 species on Av1*, thereby providing strong support for our proposed mechanism of stepwise reduction of N2 via belt-sulfur mobilization.


Assuntos
Azotobacter vinelandii , Nitrogênio , Nitrogenase , Nitrogenase/metabolismo , Nitrogenase/química , Azotobacter vinelandii/metabolismo , Azotobacter vinelandii/enzimologia , Nitrogênio/química , Nitrogênio/metabolismo , Trifosfato de Adenosina/metabolismo , Trifosfato de Adenosina/química
15.
Mol Biol Evol ; 41(4)2024 Apr 02.
Artigo em Inglês | MEDLINE | ID: mdl-38526235

RESUMO

Molecular innovations within key metabolisms can have profound impacts on element cycling and ecological distribution. Yet, much of the molecular foundations of early evolved enzymes and metabolisms are unknown. Here, we bring one such mystery to relief by probing the birth and evolution of the G-subunit protein, an integral component of certain members of the nitrogenase family, the only enzymes capable of biological nitrogen fixation. The G-subunit is a Paleoproterozoic-age orphan protein that appears more than 1 billion years after the origin of nitrogenases. We show that the G-subunit arose with novel nitrogenase metal dependence and the ecological expansion of nitrogen-fixing microbes following the transition in environmental metal availabilities and atmospheric oxygenation that began ∼2.5 billion years ago. We identify molecular features that suggest early G-subunit proteins mediated cofactor or protein interactions required for novel metal dependency, priming ancient nitrogenases and their hosts to exploit these newly diversified geochemical environments. We further examined the degree of functional specialization in G-subunit evolution with extant and ancestral homologs using laboratory reconstruction experiments. Our results indicate that permanent recruitment of the orphan protein depended on the prior establishment of conserved molecular features and showcase how contingent evolutionary novelties might shape ecologically important microbial innovations.


Assuntos
Fixação de Nitrogênio , Nitrogenase , Nitrogenase/genética , Nitrogenase/química , Nitrogenase/metabolismo , Fixação de Nitrogênio/genética , Nitrogênio/metabolismo
16.
J Phys Chem B ; 128(4): 985-989, 2024 02 01.
Artigo em Inglês | MEDLINE | ID: mdl-38237063

RESUMO

The mechanism for N2 activation in the E4 state of nitrogenase was investigated by model calculations. In the experimentally suggested mechanism, the E4 state is obtained after four reductions to the ground state. In a recent theoretical study, results for a different mechanism have been found in excellent agreement with available Electron Paramagnetic Resonance (EPR) experiments for E4. The two hydrides in E4 leave as H2 concertedly with the binding of N2. The mechanism suggested differs from the experimentally suggested one by a requirement for four activation steps prior to catalysis. In the present study, the experimentally suggested mechanism is studied using the same methods as those used in the previous study on the theoretical mechanism. The computed results make it very unlikely that a structure obtained after four reductions from the ground state has two hydrides, and the experimentally suggested mechanism does therefore not agree with the EPR experiments for E4. Another structure with only one hydride is here suggested to be the one that has been observed to bind N2 after only four reductions of the ground state.


Assuntos
Nitrogenase , Nitrogenase/química , Oxirredução , Espectroscopia de Ressonância de Spin Eletrônica , Catálise
17.
Biochemistry ; 63(1): 152-158, 2024 Jan 02.
Artigo em Inglês | MEDLINE | ID: mdl-38091601

RESUMO

Nitrogenase is the only enzyme that catalyzes the reduction of nitrogen gas into ammonia. Nitrogenase is tightly inhibited by the environmental gas carbon monoxide (CO). Many nitrogen fixing bacteria protect nitrogenase from CO inhibition using the protective protein CowN. This work demonstrates that a conserved glutamic acid residue near the C-terminus of Gluconacetobacter diazotrophicus CowN is necessary for its function. Mutation of the glutamic acid residue abolishes both CowN's protection against CO inhibition and the ability of CowN to bind to nitrogenase. In contrast, a conserved C-terminal cysteine residue is not important for CO protection by CowN. Overall, this work uncovers structural features in CowN that are required for its function and provides new insights into its nitrogenase binding and CO protection mechanism.


Assuntos
Ácido Glutâmico , Nitrogenase , Nitrogenase/química , Ácido Glutâmico/genética , Monóxido de Carbono/metabolismo
18.
Nat Struct Mol Biol ; 31(1): 150-158, 2024 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-38062208

RESUMO

Nitrogenases are best known for catalyzing the reduction of dinitrogen to ammonia at a complex metallic cofactor. Recently, nitrogenases were shown to reduce carbon dioxide (CO2) and carbon monoxide to hydrocarbons, offering a pathway to recycle carbon waste into hydrocarbon products. Among the three nitrogenase isozymes, the iron nitrogenase has the highest wild-type activity for the reduction of CO2, but the molecular architecture facilitating these activities has remained unknown. Here, we report a 2.35-Å cryogenic electron microscopy structure of the ADP·AlF3-stabilized iron nitrogenase complex from Rhodobacter capsulatus, revealing an [Fe8S9C-(R)-homocitrate] cluster in the active site. The enzyme complex suggests that the iron nitrogenase G subunit is involved in cluster stabilization and substrate channeling and confers specificity between nitrogenase reductase and catalytic component proteins. Moreover, the structure highlights a different interface between the two catalytic halves of the iron and the molybdenum nitrogenase, potentially influencing the intrasubunit 'communication' and thus the nitrogenase mechanism.


Assuntos
Dióxido de Carbono , Ferro , Ferro/metabolismo , Dióxido de Carbono/química , Oxirredução , Nitrogenase/química , Nitrogenase/metabolismo , Hidrocarbonetos/metabolismo
19.
Phys Chem Chem Phys ; 26(2): 1364-1375, 2024 Jan 03.
Artigo em Inglês | MEDLINE | ID: mdl-38108422

RESUMO

Nitrogenase is the only enzyme that can cleave the strong triple bond in N2, making nitrogen available for biological lifeforms. The active site is a MoFe7S9C cluster (the FeMo cluster) that binds eight electrons and protons during one catalytic cycle, giving rise to eight intermediate states E0-E7. It is experimentally known that N2 binds to the E4 state and that H2 is a compulsory byproduct of the reaction. However, formation of H2 is also an unproductive side reaction that should be avoided, especially in the early steps of the reaction mechanism (E2 and E3). Here, we study the formation of H2 for various structural interpretations of the E2-E4 states using combined quantum mechanical and molecular mechanical (QM/MM) calculations and four different density-functional theory methods. We find large differences in the predictions of the different methods. B3LYP strongly favours protonation of the central carbide ion and H2 cannot form from such structures. On the other hand, with TPSS, r2SCAN and TPSSh, H2 formation is strongly exothermic for all structures and En and therefore need strict kinetic control to be avoided. For the E2 state, the kinetic barriers for the low-energy structures are high enough to avoid H2 formation. However, for both the E3 and E4 states, all three methods predict that the best structure has two hydride ions bridging the same pair of Fe ions (Fe2 and Fe6) and these two ions can combine to form H2 with an activation barrier of only 29-57 kJ mol-1, corresponding to rates of 7 × 102 to 5 × 107 s-1, i.e. much faster than the turnover rate of the enzyme (1-5 s-1). We have also studied H-atom movements within the FeMo cluster, showing that the various protonation states can quite freely be interconverted (activation barriers of 12-69 kJ mol-1).


Assuntos
Nitrogenase , Prótons , Nitrogenase/química , Oxirredução , Nitrogênio/química , Catálise
20.
Mol Cells ; 46(12): 736-742, 2023 Dec 31.
Artigo em Inglês | MEDLINE | ID: mdl-38052488

RESUMO

NifB, a radical S-adenosylmethionine (SAM) enzyme, is pivotal in the biosynthesis of the iron-molybdenum cofactor (FeMo-co), commonly referred to as the M-cluster. This cofactor, located within the active site of nitrogenase, is essential for the conversion of dinitrogen (N2) to NH3. Recognized as the most intricate metallocluster in nature, FeMo-co biosynthesis involves multiple proteins and a sequence of steps. Of particular significance, NifB directs the fusion of two [Fe4S4] clusters to assemble the 8Fe core, while also incorporating an interstitial carbide. Although NifB has been extensively studied, its molecular mechanisms remain elusive. In this review, we explore recent structural analyses of NifB and provide a comprehensive overview of the established catalytic mechanisms. We propose prospective directions for future research, emphasizing the relevance to biochemistry, agriculture, and environmental science. The goal of this review is to lay a solid foundation for future endeavors aimed at elucidating the atomic details of FeMo-co biosynthesis.


Assuntos
Compostos de Ferro , Nitrogenase , Nitrogenase/química , Nitrogenase/metabolismo , Molibdoferredoxina/química , Molibdoferredoxina/metabolismo , Compostos de Ferro/química , Compostos de Ferro/metabolismo , Estudos Prospectivos , Domínio Catalítico , Proteínas de Bactérias/metabolismo
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