Nitrite reductase refers to any of several classes of

enzyme An enzyme () is a protein that acts as a biological catalyst by accelerating chemical reactions. The molecules upon which enzymes may act are called substrate (chemistry), substrates, and the enzyme converts the substrates into different mol ...

s that catalyze the reduction of

nitrite The nitrite polyatomic ion, ion has the chemical formula . Nitrite (mostly sodium nitrite) is widely used throughout chemical and pharmaceutical industries. The nitrite anion is a pervasive intermediate in the nitrogen cycle in nature. The name ...

. There are two classes of NIR's. A multi haem enzyme reduces NO₂⁻ to a variety of products.

Copper Copper is a chemical element; it has symbol Cu (from Latin ) and atomic number 29. It is a soft, malleable, and ductile metal with very high thermal and electrical conductivity. A freshly exposed surface of pure copper has a pinkish-orang ...

containing enzymes carry out a single electron transfer to produce

nitric oxide Nitric oxide (nitrogen oxide, nitrogen monooxide, or nitrogen monoxide) is a colorless gas with the formula . It is one of the principal oxides of nitrogen. Nitric oxide is a free radical: it has an unpaired electron, which is sometimes den ...

Iron based

There are several types of iron based enzymes. Cytochrome cd₁, or ''Pseudomonas'' cytochrome oxidase contains two c and two d type

heme Heme (American English), or haem (Commonwealth English, both pronounced /Help:IPA/English, hi:m/ ), is a ring-shaped iron-containing molecule that commonly serves as a Ligand (biochemistry), ligand of various proteins, more notably as a Prostheti ...

s with two

polypeptide Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty ...

chains. Different forms of this reductase catalyze the formation of

nitrous oxide Nitrous oxide (dinitrogen oxide or dinitrogen monoxide), commonly known as laughing gas, nitrous, or factitious air, among others, is a chemical compound, an Nitrogen oxide, oxide of nitrogen with the Chemical formula, formula . At room te ...

. A version of this compound was originally called errocytochrome c-551: oxidoreductase">errocytochrome c-551:oxidoreductase It was initially considered an oxidase. It catalyzes the reduction of NO₂⁻ to NO. This tetraheme enzyme has two Protein subunit">subunits, each containing a c-type and a d-type heme. The reduced d hemes bind nitrite and convert it to product. Cytochrome c nitrite reductase (ccNIR) is a multiheme enzyme that converts nitrite to ammonia on each active site. The active site iron is bound to a protoporphyrin IX ring that is covalently linked to the enzyme's proteins.

Proposed mechanism

The ccNIR protein uses six electrons and seven hydrogens to reduce nitrite to ammonia. The active site of the enzyme contains an iron in a +2

oxidation state In chemistry, the oxidation state, or oxidation number, is the hypothetical Electrical charge, charge of an atom if all of its Chemical bond, bonds to other atoms are fully Ionic bond, ionic. It describes the degree of oxidation (loss of electrons ...

. The oxidation level allows nitrite to bond more strongly than to the +3 state due to increased

pi backbonding In chemistry, pi backbonding or π backbonding is a π-bonding interaction between a filled (or half filled) orbital of a transition metal atom and a vacant orbital on an adjacent ion or molecule. In this type of interaction, electrons from the ...

. This electronic effect transfers

electron density Electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typical ...

into the nitrite antibonding orbital between

nitrogen Nitrogen is a chemical element; it has Symbol (chemistry), symbol N and atomic number 7. Nitrogen is a Nonmetal (chemistry), nonmetal and the lightest member of pnictogen, group 15 of the periodic table, often called the Pnictogen, pnictogens. ...

and

oxygen Oxygen is a chemical element; it has chemical symbol, symbol O and atomic number 8. It is a member of the chalcogen group (periodic table), group in the periodic table, a highly reactivity (chemistry), reactive nonmetal (chemistry), non ...

. The occupation of the

LUMO In chemistry, HOMO and LUMO are types of molecular orbitals. The acronyms stand for ''highest occupied molecular orbital'' and ''lowest unoccupied molecular orbital'', respectively. HOMO and LUMO are sometimes collectively called the ''frontie ...

decreases the strength of the N-O bond. A second electronic effect is the

hydrogen bonding In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently b ...

of both oxygens to nearby

amino acids Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although over 500 amino acids exist in nature, by far the most important are the Proteinogenic amino acid, 22 α-amino acids incorporated into p ...

. These acids are often

arginine Arginine is the amino acid with the formula (H2N)(HN)CN(H)(CH2)3CH(NH2)CO2H. The molecule features a guanidinium, guanidino group appended to a standard amino acid framework. At physiological pH, the carboxylic acid is deprotonated (−CO2−) a ...

and

Histidine Histidine (symbol His or H) is an essential amino acid that is used in the biosynthesis of proteins. It contains an Amine, α-amino group (which is in the protonated –NH3+ form under Physiological condition, biological conditions), a carboxylic ...

. The interactions lengthen the N-O bonds and facilitate cleavage of an oxygen from nitrogen. The Fe-NO bond is linear and has six shared valence electrons. This is not a stable state for an Fe-NO bond. However, a bent seven electron configuration is too stable to undergo further reaction without considerable energy input. To compensate for this barrier, two rapid, consecutive, single electron reductions form an eight electron complex. The electron transfer occurs before a shift in geometry from a linear to bent geometry. Two

protonation In chemistry, protonation (or hydronation) is the adding of a proton (or hydron, or hydrogen cation), usually denoted by H+, to an atom, molecule, or ion, forming a conjugate acid. (The complementary process, when a proton is removed from a Brø ...

s of the nitrogen lead to an increased N-O bond distance. The resulting intermediate is a hydroxylamine. further protonation of the hydroxylamine leads to the breakage of the N-O bond to form water. The oxidation of iron from Fe^(II) to Fe^(III), coupled with a further protonation of nitrogen leads to the release of ammonia.

Copper based

To date, there have been several types of Copper Nitrite Reductases discovered. These CuNIR are found in many different fungi and bacteria; for example, the bacterial genera ''

Pseudomonas ''Pseudomonas'' is a genus of Gram-negative bacteria belonging to the family Pseudomonadaceae in the class Gammaproteobacteria. The 348 members of the genus demonstrate a great deal of metabolic diversity and consequently are able to colonize a ...

'', ''

Bordetella ''Bordetella'' () is a genus of small (0.2 – 0.7 μm), Gram-negative, coccobacilli bacteria of the phylum Pseudomonadota. ''Bordetella'' species, with the exception of ''Bordetella petrii, B. petrii'', are obligate aerobes, as well as hig ...

'', '' Alcaligenes'', and '' Achromobacter'' all contain CuNIR. What is common to all CuNIR is the presence of at least one type 1 copper center in the protein. These centers are similar to Azurin in their bonding structure. Each type 1 Cu is strongly bonded to a

thiolate In organic chemistry, a thiol (; ), or thiol derivative, is any organosulfur compound of the form , where R represents an alkyl or other organic substituent. The functional group itself is referred to as either a thiol group or a sulfhydryl grou ...

sulfur from a

cysteine Cysteine (; symbol Cys or C) is a semiessential proteinogenic amino acid with the chemical formula, formula . The thiol side chain in cysteine enables the formation of Disulfide, disulfide bonds, and often participates in enzymatic reactions as ...

, two

imidazole Imidazole (ImH) is an organic compound with the formula . It is a white or colourless solid that is soluble in water, producing a mildly alkaline solution. It can be classified as a heterocycle, specifically as a diazole. Many natural products, ...

nitrogens from different Histidine residues, and a sulfur atom of an axial

Methionine Methionine (symbol Met or M) () is an essential amino acid in humans. As the precursor of other non-essential amino acids such as cysteine and taurine, versatile compounds such as SAM-e, and the important antioxidant glutathione, methionine play ...

ligand. This induces a distorted

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 arccos(−) = 109.4712206...° ≈ 109.5° when all four substituents are ...

. The cysteine ligated to the type 1 Cu center is located directly next to a Histidine in the

primary structure Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the primary structure of a protein is reported starting from the amino-terminal (N) end to the carboxyl-terminal (C) end. Protein biosynthe ...

of the amino acids. This Histidine is bound to the Type 2 Cu center responsible for binding and reducing nitrite. This Cys-His bridge plays an important role in facilitating rapid electron transfer from the type 1 center to the type 2.

Proposed mechanism

The type 2 copper center of a copper nitrite reductase is the

active site In biology and biochemistry, the active site is the region of an enzyme where substrate molecules bind and undergo a chemical reaction. The active site consists of amino acid residues that form temporary bonds with the substrate, the ''binding s ...

of the enzyme. The Cu is bound by nitrogens of two Histidines from one

monomer A monomer ( ; ''mono-'', "one" + '' -mer'', "part") is a molecule that can react together with other monomer molecules to form a larger polymer chain or two- or three-dimensional network in a process called polymerization. Classification Chemis ...

, and bound by one Histidine from another monomer; the Cys-His bridge to the type 1 Cu. This gives the molecule a distorted tetrahedral geometry. In the resting state, the Cu is also binding a water molecule that is displaced by nitrite. As nitrite displaces water, Cu is bound by both oxygens in a bidentate fashion. A nearby

Aspartic acid Aspartic acid (symbol Asp or D; the ionic form is known as aspartate), is an α-amino acid that is used in the biosynthesis of proteins. The L-isomer of aspartic acid is one of the 22 proteinogenic amino acids, i.e., the building blocks of protei ...

residue hydrogen bonds to one of the newly formed oxygen

ligand In coordination chemistry, a ligand is an ion or molecule with a functional group that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's el ...

s. An incoming electron reduces the Cu from

(II) to (I). This change facilitates a shift in nitrite binding so that the nitrogen is bound to Cu, and one oxygen has an extended bond length due to hydrogen bonding. A second hydrogen bond forms from Histidine or a nearby water molecule and leads to the cleavage of the N-O bond. The Cu is now five

coordinate In geometry, a coordinate system is a system that uses one or more numbers, or coordinates, to uniquely determine and standardize the position of the points or other geometric elements on a manifold such as Euclidean space. The coordinates are ...

bonded to

and water. Nitric oxide is released as Cu is oxidized to state (II) and returns to the resting configuration.

Assimilatory

Assimilatory nitrate reductase is an enzyme of the assimilative

metabolism Metabolism (, from ''metabolē'', "change") is the set of life-sustaining chemical reactions in organisms. The three main functions of metabolism are: the conversion of the energy in food to energy available to run cellular processes; the co ...

involved in reduction of

nitrate Nitrate is a polyatomic ion with the chemical formula . salt (chemistry), Salts containing this ion are called nitrates. Nitrates are common components of fertilizers and explosives. Almost all inorganic nitrates are solubility, soluble in wa ...

. The nitrite is immediately reduced to

ammonia Ammonia is an inorganic chemical compound of nitrogen and hydrogen with the chemical formula, formula . A Binary compounds of hydrogen, stable binary hydride and the simplest pnictogen hydride, ammonia is a colourless gas with a distinctive pu ...

(probably via hydroxylamine) by the activity of nitrite reductase. The term assimilatory refers to the fact that the product of the enzymatic activity remains in the organism. In this case, the product is ammonia which has an inhibitive effect on assimilatory nitrate reductase, thus ensuring that the organism produces the ammonia according to its requirements.

Iron based

Proposed mechanism

Copper based

Proposed mechanism

Assimilatory

See also

References

Further reading