![FeMoco cluster](https://upload.wikimedia.org/wikipedia/commons/6/60/FeMoco_cluster.svg)
FeMoco ( cofactor) is the primary
cofactor of
nitrogenase
Nitrogenases are enzymes () that are produced by certain bacteria, such as cyanobacteria (blue-green bacteria) and rhizobacteria. These enzymes are responsible for the Organic redox reaction, reduction of nitrogen (N2) to ammonia (NH3). Nitrog ...
. Nitrogenase is the enzyme that catalyzes the conversion of atmospheric nitrogen molecules N
2 into
ammonia
Ammonia is an inorganic compound of nitrogen and hydrogen with the formula . A stable binary hydride, and the simplest pnictogen hydride, ammonia is a colourless gas with a distinct pungent smell. Biologically, it is a common nitrogenous was ...
(NH
3) through the process known as
nitrogen fixation
Nitrogen fixation is a chemical process by which molecular nitrogen (), with a strong triple covalent bond, in the air is converted into ammonia () or related nitrogenous compounds, typically in soil or aquatic systems but also in industry. Atmo ...
. Containing
iron
Iron () is a chemical element with symbol Fe (from la, ferrum) and atomic number 26. It is a metal that belongs to the first transition series and group 8 of the periodic table. It is, by mass, the most common element on Earth, right in f ...
and
molybdenum
Molybdenum is a chemical element with the symbol Mo and atomic number 42 which is located in period 5 and group 6. The name is from Neo-Latin ''molybdaenum'', which is based on Ancient Greek ', meaning lead, since its ores were confused with lea ...
, the cofactor is called FeMoco. Its
stoichiometry
Stoichiometry refers to the relationship between the quantities of reactants and products before, during, and following chemical reactions.
Stoichiometry is founded on the law of conservation of mass where the total mass of the reactants equal ...
is Fe
7MoS
9C.
Structure
The FeMo cofactor is a
cluster
may refer to:
Science and technology Astronomy
* Cluster (spacecraft), constellation of four European Space Agency spacecraft
* Asteroid cluster, a small asteroid family
* Cluster II (spacecraft), a European Space Agency mission to study t ...
with composition Fe
7MoS
9C. Fe is the
chemical symbol
Chemical symbols are the abbreviations used in chemistry for chemical elements, functional groups and chemical compounds. Element symbols for chemical elements normally consist of one or two letters from the Latin alphabet and are written with th ...
for the element
iron
Iron () is a chemical element with symbol Fe (from la, ferrum) and atomic number 26. It is a metal that belongs to the first transition series and group 8 of the periodic table. It is, by mass, the most common element on Earth, right in f ...
(ferrum), and Mo is the symbol for
molybdenum
Molybdenum is a chemical element with the symbol Mo and atomic number 42 which is located in period 5 and group 6. The name is from Neo-Latin ''molybdaenum'', which is based on Ancient Greek ', meaning lead, since its ores were confused with lea ...
. This large cluster can be viewed as two subunits composed of one Fe
4S
3 (
iron(III) sulfide
Iron(III) sulfide, also known as ferric sulfide or sesquisulfide (), is one of the several binary iron sulfides. It is a solid, black powder that degrades at ambient temperature.
Reactions
() decays at a temperature over 20 °C into iron ...
) cluster and one MoFe
3S
3 cluster. The two clusters are linked by three
sulfide
Sulfide (British English also sulphide) is an inorganic anion of sulfur with the chemical formula S2− or a compound containing one or more S2− ions. Solutions of sulfide salts are corrosive. ''Sulfide'' also refers to chemical compounds lar ...
ligands. The unique iron (Fe) is anchored to the
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, respo ...
by a
cysteine
Cysteine (symbol Cys or C; ) is a semiessential proteinogenic amino acid with the formula . The thiol side chain in cysteine often participates in enzymatic reactions as a nucleophile.
When present as a deprotonated catalytic residue, sometime ...
. It is also bound to three sulfides, resulting in
tetrahedral molecular geometry
In a tetrahedral molecular geometry, a central atom is located at the center with four substituents that are located at the corners of a tetrahedron. The bond angles are cos−1(−) = 109.4712206...° ≈ 109.5° when all four substituents are ...
. The additional six Fe centers in the cluster are each bonded to three sulfides. These six internal Fe centers define a trigonal prismatic arrangement around a central carbide center. The molybdenum is attached to three sulfides and is anchored to the protein by the imidazole group of a histidine residue. Also bound to Mo is a bidentate
homocitrate cofactor, leading to octahedral geometry.
Crystallographic analysis of the MoFe protein initially proposed the
geometry
Geometry (; ) is, with arithmetic, one of the oldest branches of mathematics. It is concerned with properties of space such as the distance, shape, size, and relative position of figures. A mathematician who works in the field of geometry is c ...
of FeMoco, which was confirmed by extended
X-ray absorption fine-structure (EXAFS) studies.
[Roat-Malone, R.M. Ch.6 MoFe Protein Structure. Bioinorganic Chemistry. John Wiley & Sons, Inc., Hoboken, New Jersey, 2002. 253-254. .] The Fe-S, Fe-Fe and Fe-Mo distances were determined to be 2.32, 2.64, and 2.73 Å respectively.
Electronic properties of FeMoco
According to the analysis by
electron paramagnetic resonance spectroscopy
Electron paramagnetic resonance (EPR) or electron spin resonance (ESR) spectroscopy is a method for studying materials that have unpaired electrons. The basic concepts of EPR are analogous to those of nuclear magnetic resonance (NMR), but the spin ...
, the resting state of the FeMo cofactor has a spin state of S=3/2. Upon one-electron reduction, the cofactor becomes EPR silent. Understanding the process in which an electron is transferred in the protein adduct shows a more precise kinetic model of the FeMo cofactor. Density functional theory calculations have suggested that the formal oxidation state is Mo
IV-2Fe
II-5Fe
III-C
4−-H
+, but the "true" oxidation states have not been confirmed experimentally.
Biosynthesis
Biosynthesis
Biosynthesis is a multi-step, enzyme-catalyzed process where substrates are converted into more complex products in living organisms. In biosynthesis, simple compounds are modified, converted into other compounds, or joined to form macromolecules. ...
of FeMoco is a complicated process that requires several
Nif gene
The ''nif'' genes are genes encoding enzymes involved in the fixation of atmospheric nitrogen into a form of nitrogen available to living organisms. The primary enzyme encoded by the ''nif'' genes is the nitrogenase complex which is in charge of ...
products, specifically those of nifS, nifQ, nifB, nifE, nifN, nifV, nifH, nifD, and nifK (expressed as the proteins NifS, NifU, etc.). FeMoco assembly is proposed to be initiated by NifS and NifU which mobilize Fe and sulfide into small Fe-S fragments. These fragments are transferred to the NifB scaffold and arranged into a Fe
7MoS
9C cluster before transfer to the NifEN protein (encoded by nifE and nifN) and rearranged before delivery to the MoFe protein. Several other factors participate in the biosynthesis. For example, NifV is the
homocitrate synthase
In enzymology, a homocitrate synthase () is an enzyme that catalysis, catalyzes the chemical reaction
:acetyl-CoA + H2O + 2-oxoglutarate \rightleftharpoons (R)-2-hydroxybutane-1,2,4-tricarboxylate + CoA
The 3 substrate (biochemistry), substrates ...
that supplies
homocitrate to FeMoco. NifV, a protein factor, is proposed to be involved in the storage and/or mobilization of Mo. Fe protein is the electron donor for MoFe protein
6. These biosynthetic factors have been elucidated and characterized with the exact functions and sequence confirmed by biochemical, spectroscopic, and structural analyses.
Isolation
Isolation of the FeMo cofactor from nitrogenase is done through centrifugal sedimentation of nitrogenase into the MoFe protein and the Fe protein. The FeMo cofactor is extracted by treating the MoFe protein with acids. The first extraction is done with
N,N-dimethylformamide
Dimethylformamide is an organic compound with the formula ( CH3)2NC(O)H. Commonly abbreviated as DMF (although this initialism is sometimes used for dimethylfuran, or dimethyl fumarate), this colourless liquid is miscible with water and the major ...
and the second by a mixture of
N-methylformamide
''N''-Methylformamide (NMF) is a colorless, nearly odorless, organic compound and secondary amide with molecular formula CH3NHCHO, which is a liquid at room temperature. NMF is mainly used as a reagent in various organic syntheses with limited a ...
and Na
2HPO
4 before final sedimentation by centrifugation.
Identity of the core atom in the cofactor
The three proteins that play a direct role in the M-cluster synthesis are NifH, NifEN, and NifB. The NifB protein is responsible for the assembly of the Fe-S core of the cofactor; a process that involves stitching together two
Fe-4Sclusters. NifB belongs to the SAM (S-adenosyl-L-methionine) enzyme superfamily. During the biosynthesis of the FeMo cofactor, NifB and its SAM cofactor are directly involved in the insertion of a carbon atom at the center of the Fe-S complex. An equivalent of SAM donates a methyl group, which becomes the interstitial carbide of the M-cluster. The methyl group of SAM is mobilized by radical removal of an H by a 5’-deoxyadenosine radical (5’-dA·). Presumably, a transient –CH2· radical is formed that is subsequently incorporated into the metal cluster forming a Fe
6-carbide species. The interstitial carbon remains associated with the FeMo cofactor after insertion into the nitrogenase, The central carbon atom has been confirmed by
13C labeling with detection by pulsed EPR spectroscopy. In addition to EPR spectroscopy, X-ray
diffractometry
A diffractometer is a measuring instrument for analyzing the structure of a material from the scattering pattern produced when a beam of radiation or particles (such as X-rays or neutrons) interacts with it.
Principle
Because it is relatively e ...
was used to verify that there was a central atom in the middle of the FeMo cofactor and x-ray emission spectroscopic studies showed that central atom was carbon due to the 2p→1s carbon-iron transition. The use of X-ray crystallography showed that while the FeMo cofactor is not in its catalytic form, the carbon keeps the structure rigid which helps describe the reactivity of nitrogenase.
Binding of substrates
The location of substrate attachment to the complex has yet to be elucidated. It is believed that the Fe atoms closest to the interstitial carbon participate in substrate activation, but the terminal molybdenum is also a candidate for nitrogen fixation.
[Hallmen, P. P.; Kästner, J. "N2 Binding to the FeMo-Cofactor of Nitrogenase. ''Z. Anorg. Allg. Chem.'' 2014. {{doi, 10.1002/zaac.201400114]
References
Cluster chemistry
Iron–sulfur proteins
Iron(III) compounds
Sulfur compounds
Metalloproteins
Molybdenum(IV) compounds
Cofactors
Molybdenum enzymes