Biochemical and Structural Characterization of the Cross-Linked Complex of Nitrogenase:  Comparison to the ADP-AlF4--Stabilized Structure,

Schmid, Benedikt; Einsle, Oliver; Chiu, Hsiu‐Ju; Willing, A.; Yoshida, Mika; Howard, James B.; Rees, Douglas C.

doi:10.1021/bi026642b

Cited by 92 publications

(98 citation statements)

References 31 publications

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“…1 and 2), most notably the structures of the constituent metalloclusters and the nucleotide-binding site, have been defined by high-resolution x-ray crystal structures of the component proteins (7)(8)(9)(10)(11)(12)(13)(14)(15). In addition to the individual proteins, structures of complexes between Fe protein and MoFe protein have also been obtained at moderate resolutions (16)(17)(18)(19)) that correspond to several of the putative intermediates indicated in Scheme 1.…”

Section: Intermolecular Electron Transfer and The Role Of Atp Hydrolymentioning

confidence: 99%

How many metals does it take to fix N ₂ ? A mechanistic overview of biological nitrogen fixation

Howard

Rees

2006

Proc. Natl. Acad. Sci. U.S.A.

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During the process of biological nitrogen fixation, the enzyme nitrogenase catalyzes the ATP-dependent reduction of dinitrogen to ammonia. Nitrogenase consists of two component metalloproteins, the iron (Fe) protein and the molybdenum-iron (MoFe) protein; the Fe protein mediates the coupling of ATP hydrolysis to interprotein electron transfer, whereas the active site of the MoFe protein contains the polynuclear FeMo cofactor, a species composed of seven iron atoms, one molybdenum atom, nine sulfur atoms, an interstitial light atom, and one homocitrate molecule. This Perspective provides an overview of biological nitrogen fixation and introduces three contributions to this special feature that address central aspects of the mechanism and assembly of nitrogenase. Biological nitrogen fixation, as defined by the reduction of dinitrogen to ammonia under physiological conditions, is thermodynamically favorable (1). Even at low intracellular dissolved gas pressure, the reaction has a large negative free energy when reduced ferredoxin (Fd red ) serves as the electron donor. Nevertheless, the enzymatic reaction, as catalyzed by the complex metalloclustercontaining nitrogenase system, does not proceed without the additional input of substantial quantities of energy in the specific form of ATP hydrolysis. These requirements may be summarized by the following equation:where n is the ratio of ATP hydrolyzed per electron transferred. This expression encompasses three central questions relevant to the mechanism of nitrogenase:What is the role of nucleotide hydrolysis in electron transfer and substrate reduction? How are substrates bound and reduced at the active site? How are the nitrogenase metalloclusters assembled and inserted?These issues are addressed in the contributions to this Nitrogen Fixation Special Feature by the groups of Watt (2); Seefeldt, Dean, and Hoffman (3); and Ribbe, Hodgson, and Hedman (4). The purpose of this Perspective is to provide both a background for these contributions and a summary of our views on the progress made in deciphering the molecular mechanisms of this fascinating process. Intermolecular Electron Transfer and the Role of ATP Hydrolysis in NitrogenaseThe overall reaction mechanism of biological nitrogen fixation (Eq. 1) may be divided into two parts (5, 6): (i) the control or regulation of electron transfer to the substrate reduction site and (ii) the substrate reduction process itself. What sets nitrogenase apart from essentially all other enzymatically catalyzed redox processes is the number of electrons (eight) that must ultimately be delivered to the substrates each turnover cycle, with the consequent demand for precise timing of the underlying electron transfer events. The first part of this mechanism consists of a cycle involving the ATP-dependent electron transfer between the two protein components of nitrogenase, named Fe protein and MoFe protein, as diagrammatically shown in Scheme 1. The second part of the process, discussed subsequently, involves substrate reduction on the MoF...

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Section: Intermolecular Electron Transfer and The Role Of Atp Hydrolymentioning

confidence: 99%

How many metals does it take to fix N ₂ ? A mechanistic overview of biological nitrogen fixation

Howard

Rees

2006

Proc. Natl. Acad. Sci. U.S.A.

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224

226

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“…Subsequently, the reduced Fe protein binds two MgATP molecules and undergoes a conformational change, which allows it to complex with the MoFe protein (i.e., stage (i) in Scheme 1). (iv) addition of MgADP [37,62,63] (Table 1). These structural insights highlight the role of the Fe protein in energetically coupling different nucleotide-binding states to nitrogenase catalysis, which may have some general relevance to other nucleotide-dependent molecular motor systems [63].…”

Section: The Fe Protein Cyclementioning

confidence: 99%

Cleaving the N,N Triple Bond: The Transformation of Dinitrogen to Ammonia by Nitrogenases

Lee

Ribbe

2014

The Metal-Driven Biogeochemistry of Gaseous Compounds in the Environment

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Biological nitrogen fixation is a natural process that converts atmospheric nitrogen (N2) to bioavailable ammonia (NH3). This reaction not only plays a key role in supplying bio-accessible nitrogen to all life forms on Earth, but also embodies the powerful chemistry of cleaving the inert N,N triple bond under ambient conditions. The group of enzymes that carry out this reaction are called nitrogenases and typically consist of two redox active protein components, each containing metal cluster(s) that are crucial for catalysis. In the past decade, a number of crystal structures, including several at high resolutions, have been solved. However, the catalytic mechanism of nitrogenase, namely, how the N,N triple bond is cleaved by this enzyme under ambient conditions, has remained elusive. Nevertheless, recent biochemical and spectroscopic studies have led to a better understanding of the potential intermediates of N2 reduction by the molybdenum (Mo)-nitrogenase. In addition, it has been demonstrated that carbon monoxide (CO), which was thought to be an inhibitor of N2 reduction, could also be reduced by the vanadium (V)-nitrogenase to small alkanes and alkenes. This chapter will begin with an introduction to biological nitrogen fixation and Mo-nitrogenase, continue with a discussion of the catalytic mechanism of N2 reduction by Mo-nitrogenase, and conclude with a survey of the current knowledge of N2- and CO-reduction by V-nitrogenase and how V-nitrogenase compares to its Mo-counterpart in these catalytic activities.

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“…32 The first water molecule from the FeMoco side is linked to the homocitrate molecule by hydrogen bond. All the four water molecules in the chain are at hydrogen bond distances from one another.…”

Section: His β192mentioning

confidence: 99%

“…We analyzed the structure of the nitrogenase complex Av1•(Av2) 2 reported previously. 32 A fragment of the structure (Fig. 3) was obtained using a database.…”

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The role of a P-cluster in the nitrogenase atpase reaction

et al. 2006

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Structural data on the nitrogenase complex of Azotobacter vinelandii, Av1•(Av2) 2 , stabi lized by MgADP•AlF 4 -and, in particular, the structure and properties of a P cluster involved in the nitrogenase ATPase reaction, were analyzed. The ATP binding site and all nitrogenase metal clusters are arranged in one plane, the distances between the closest partners being 14-15 Å. The ATP binding site in the Fe protein, which decreases the half reduction poten tial (E m ) of the [4Fe-4S] cluster in Av2 to -0.43 V, does not affect the potentials of the P cluster and Fe-Mo cofactor (FeMoco). Amino acids 74-95 in the β subunit of Av1 "en velop" the P cluster in Av1; therefore, the phosphate intermediate of the ATPase reaction of nitrogenase occurs apparently in the direct contact with the P cluster. By increasing the acceptor properties of the P cluster, this intermediate may favor the electron transfer from the Fe protein to the P cluster, thus bringing it into the super reduced state.

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Biochemical and Structural Characterization of the Cross-Linked Complex of Nitrogenase: Comparison to the ADP-AlF₄^--Stabilized Structure^,

Cited by 92 publications

References 31 publications

How many metals does it take to fix N ₂ ? A mechanistic overview of biological nitrogen fixation

How many metals does it take to fix N ₂ ? A mechanistic overview of biological nitrogen fixation

Cleaving the N,N Triple Bond: The Transformation of Dinitrogen to Ammonia by Nitrogenases

The role of a P-cluster in the nitrogenase atpase reaction

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Biochemical and Structural Characterization of the Cross-Linked Complex of Nitrogenase: Comparison to the ADP-AlF4--Stabilized Structure,

Cited by 92 publications

References 31 publications

How many metals does it take to fix N 2 ? A mechanistic overview of biological nitrogen fixation

How many metals does it take to fix N 2 ? A mechanistic overview of biological nitrogen fixation

Cleaving the N,N Triple Bond: The Transformation of Dinitrogen to Ammonia by Nitrogenases

The role of a P-cluster in the nitrogenase atpase reaction

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Product

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Biochemical and Structural Characterization of the Cross-Linked Complex of Nitrogenase: Comparison to the ADP-AlF₄^--Stabilized Structure^,

How many metals does it take to fix N ₂ ? A mechanistic overview of biological nitrogen fixation

How many metals does it take to fix N ₂ ? A mechanistic overview of biological nitrogen fixation