Nitrile hydratase

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nitrile hydratase
Identifiers
EC no. 4.2.1.84
CAS no. 82391-37-5
Databases
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BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum
Gene Ontology AmiGO / QuickGO
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PMC articles
PubMed articles
NCBI proteins

Nitrile hydratases (NHases; EC 4.2.1.84) are mononuclear iron or non-corrinoid cobalt enzymes that catalyse the hydration of diverse nitriles to their corresponding amides:

Contents

R-C≡N + H
2
O
R-C(O)NH
2

Metal cofactor

Nitrile hydratases use Fe(III) or Co(III) at their active sites. These ions are low-spin. [1]

The cobalt-based nitrile hydratases are rare examples of enzymes that use cobalt. Cobalt, when it occurs in enzymes, is usually bound to a corrin ring, as in vitamin B12.

The mechanism by which the cobalt is transported to NHase without causing toxicity is unclear, although a cobalt permease has been identified, which transports cobalt across the cell membrane. The identity of the metal in the active site of a nitrile hydratase can be predicted by analysis of the sequence data of the alpha subunit in the region where the metal is bound. The presence of the amino acid sequence VCTLC indicates a Co-centred NHase and the presence of VCSLC indicates Fe-centred NHase.

Metabolic pathway

Nitrile hydratase and amidase are two hydrating and hydrolytic enzymes responsible for the sequential metabolism of nitriles in bacteria that are capable of utilising nitriles as their sole source of nitrogen and carbon, and in concert act as an alternative to nitrilase activity, which performs nitrile hydrolysis without formation of an intermediate primary amide. A sequence in genome of the choanoflagellate Monosiga brevicollis was suggested to encode for a nitrile hydratase. [2] The M. brevicollis gene consisted of both the alpha and beta subunits fused into a single gene. Similar nitrile hydratase genes consisting of a fusion of the beta and alpha subunits have since been identified in several eukaryotic supergroups, suggesting that such nitrile hydratases were present in the last common ancestor of all eukaryotes. [3]

Industrial applications

NHases have been efficiently used for the industrial production of acrylamide from acrylonitrile [4] on a scale of 600 000 tons per annum, [5] and for removal of nitriles from wastewater. Photosensitive NHases intrinsically possess nitric oxide (NO) bound to the iron centre, and its photodissociation activates the enzyme. Nicotinamide is produced industrially [4] by the hydrolysis of 3-cyanopyridine catalysed by the nitrile hydratase from Rhodococcus rhodochrous J1, [6] [7] producing 3500 tons per annum of nicotinamide for use in animal feed. [5]

Structure

Structure of nitrile hydratase. PDB 2ahj EBI.jpg
Structure of nitrile hydratase.

NHases are composed of two types of subunits, α and β, which are not related in amino acid sequence. NHases exist as αβ dimers or α2β2 tetramers and bind one metal atom per αβ unit. The 3-D structures of a number of NHases have been determined. The α subunit consists of a long extended N-terminal "arm", containing two α-helices, and a C-terminal domain with an unusual four-layered structure (α-β-β-α). The β subunit consists of a long N-terminal loop that wraps around the α subunit, a helical domain that packs with N-terminal domain of the α subunit, and a C-terminal domain consisting of a β-roll and one short helix.

Nitrile hydratase, alpha chain
Identifiers
SymbolNHase_alpha
Pfam PF02979
InterPro IPR004232
SCOP2 2ahj / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 1ahj , 1ire , 1ugp , 1ugq , 1ugr , 1ugs , 1v29 , 2ahj , 2cyz , 2cz0 , 2cz1 , 2cz6 , 2cz7 , 2d0q , 2qdy
Nitrile hydratase beta subunit
Identifiers
SymbolNHase_beta
Pfam PF02211
InterPro IPR003168
SCOP2 2ahj / SCOPe / SUPFAM
Available protein structures:
Pfam   structures / ECOD  
PDB RCSB PDB; PDBe; PDBj
PDBsum structure summary
PDB 1ahj , 1ire , 1ugp , 1ugq , 1ugr , 1ugs , 2ahj , 2cyz , 2cz0 , 2cz1 , 2cz6 , 2cz7 , 2d0q , 2dpp , 2qdy , 2zcf , 2zpb , 2zpe , 2zpf , 2zpg , 2zph , 2zpi

Assembly

An assembly pathway for nitrile hydratase was first proposed when gel filtration experiments found that the complex exists in both αβ and α2β2 forms. [9] In vitro experiments using mass spectrometry further revealed that the α and β subunits first assemble to form the αβ dimer. The dimers can then subsequently interact to form a tetramer. [10]

Mechanism

The metal centre is located in the central cavity at the interface between two subunits. All protein ligands to the metal atom are provided by the α subunit. The protein ligands to the iron are the sidechains of the three cysteine (Cys) residues and two mainchain amide nitrogens. The metal ion is octahedrally coordinated, with the protein ligands at the five vertices of an octahedron. The sixth position, accessible to the active site cleft, is occupied either by NO or by a solvent-exchangeable ligand (hydroxide or water). The two Cys residues coordinated to the metal are post-translationally modified to Cys-sulfinic (Cys-SO2H) and -sulfenic (Cys-SOH) acids.

Quantum chemical studies predicted that the Cys-SOH residue might play a role as either a base (activating a nucleophilic water molecule) [11] or as a nucleophile. [12] Subsequently, the functional role of the SOH center as nucleophile has obtained experimental support. [13]

Related Research Articles

<span class="mw-page-title-main">Nicotinamide</span> Dietary supplement and medication

Niacinamide or nicotinamide is a form of vitamin B3 found in food and used as a dietary supplement and medication. As a supplement, it is used orally (swallowed by mouth) to prevent and treat pellagra (niacin deficiency). While nicotinic acid (niacin) may be used for this purpose, niacinamide has the benefit of not causing skin flushing. As a cream, it is used to treat acne, and has been observed in clinical studies to improve the appearance of aging skin by reducing hyperpigmentation and redness. It is a water-soluble vitamin. Niacinamide is the supplement name, while nicotinamide is the scientific name.

<span class="mw-page-title-main">Tryptophan synthase</span>

Tryptophan synthase or tryptophan synthetase is an enzyme that catalyses the final two steps in the biosynthesis of tryptophan. It is commonly found in Eubacteria, Archaebacteria, Protista, Fungi, and Plantae. However, it is absent from Animalia. It is typically found as an α2β2 tetramer. The α subunits catalyze the reversible formation of indole and glyceraldehyde-3-phosphate (G3P) from indole-3-glycerol phosphate (IGP). The β subunits catalyze the irreversible condensation of indole and serine to form tryptophan in a pyridoxal phosphate (PLP) dependent reaction. Each α active site is connected to a β active site by a 25 angstrom long hydrophobic channel contained within the enzyme. This facilitates the diffusion of indole formed at α active sites directly to β active sites in a process known as substrate channeling. The active sites of tryptophan synthase are allosterically coupled.

<span class="mw-page-title-main">Michael addition reaction</span> Reaction in organic chemistry

In organic chemistry, the Michael reaction or Michael 1,4 addition is a reaction between a Michael donor and a Michael acceptor to produce a Michael adduct by creating a carbon-carbon bond at the acceptor's β-carbon. It belongs to the larger class of conjugate additions and is widely used for the mild formation of carbon-carbon bonds.

<span class="mw-page-title-main">Nitrilase</span> Class of enzymes

Nitrilase enzymes catalyse the hydrolysis of nitriles to carboxylic acids and ammonia, without the formation of "free" amide intermediates. Nitrilases are involved in natural product biosynthesis and post translational modifications in plants, animals, fungi and certain prokaryotes. Nitrilases can also be used as catalysts in preparative organic chemistry. Among others, nitrilases have been used for the resolution of racemic mixtures. Nitrilase should not be confused with nitrile hydratase which hydrolyses nitriles to amides. Nitrile hydratases are almost invariably co-expressed with an amidase, which converts the amide to the carboxylic acid. Consequently, it can sometimes be difficult to distinguish nitrilase activity from nitrile hydratase plus amidase activity.

Aromatic-ring-hydroxylating dioxygenases (ARHD) incorporate two atoms of dioxygen (O2) into their substrates in the dihydroxylation reaction. The product is (substituted) cis-1,2-dihydroxycyclohexadiene, which is subsequently converted to (substituted) benzene glycol by a cis-diol dehydrogenase.

<span class="mw-page-title-main">Catalytic triad</span> Set of three coordinated amino acids

A catalytic triad is a set of three coordinated amino acids that can be found in the active site of some enzymes. Catalytic triads are most commonly found in hydrolase and transferase enzymes. An acid-base-nucleophile triad is a common motif for generating a nucleophilic residue for covalent catalysis. The residues form a charge-relay network to polarise and activate the nucleophile, which attacks the substrate, forming a covalent intermediate which is then hydrolysed to release the product and regenerate free enzyme. The nucleophile is most commonly a serine or cysteine amino acid, but occasionally threonine or even selenocysteine. The 3D structure of the enzyme brings together the triad residues in a precise orientation, even though they may be far apart in the sequence.

The Reformatsky reaction is an organic reaction which condenses aldehydes or ketones with α-halo esters using metallic zinc to form β-hydroxy-esters:

<span class="mw-page-title-main">Nucleophilic conjugate addition</span> Organic reaction

Nucleophilic conjugate addition is a type of organic reaction. Ordinary nucleophilic additions or 1,2-nucleophilic additions deal mostly with additions to carbonyl compounds. Simple alkene compounds do not show 1,2 reactivity due to lack of polarity, unless the alkene is activated with special substituents. With α,β-unsaturated carbonyl compounds such as cyclohexenone it can be deduced from resonance structures that the β position is an electrophilic site which can react with a nucleophile. The negative charge in these structures is stored as an alkoxide anion. Such a nucleophilic addition is called a nucleophilic conjugate addition or 1,4-nucleophilic addition. The most important active alkenes are the aforementioned conjugated carbonyls and acrylonitriles.

<span class="mw-page-title-main">Succinyl coenzyme A synthetase</span> Class of enzymes

Succinyl coenzyme A synthetase is an enzyme that catalyzes the reversible reaction of succinyl-CoA to succinate. The enzyme facilitates the coupling of this reaction to the formation of a nucleoside triphosphate molecule from an inorganic phosphate molecule and a nucleoside diphosphate molecule. It plays a key role as one of the catalysts involved in the citric acid cycle, a central pathway in cellular metabolism, and it is located within the mitochondrial matrix of a cell.

<span class="mw-page-title-main">Cyclic nucleotide phosphodiesterase</span> Class of enzymes

3′,5′-cyclic-nucleotide phosphodiesterases (EC 3.1.4.17) are a family of phosphodiesterases. Generally, these enzymes hydrolyze a nucleoside 3′,5′-cyclic phosphate to a nucleoside 5′-phosphate:

<span class="mw-page-title-main">Hexosaminidase</span> Class of enzymes

Hexosaminidase is an enzyme involved in the hydrolysis of terminal N-acetyl-D-hexosamine residues in N-acetyl-β-D-hexosaminides.

<span class="mw-page-title-main">UDP-glucose 4-epimerase</span> Class of enzymes

The enzyme UDP-glucose 4-epimerase, also known as UDP-galactose 4-epimerase or GALE, is a homodimeric epimerase found in bacterial, fungal, plant, and mammalian cells. This enzyme performs the final step in the Leloir pathway of galactose metabolism, catalyzing the reversible conversion of UDP-galactose to UDP-glucose. GALE tightly binds nicotinamide adenine dinucleotide (NAD+), a co-factor required for catalytic activity.

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<span class="mw-page-title-main">Anthranilate synthase</span>

The enzyme anthranilate synthase catalyzes the chemical reaction

<span class="mw-page-title-main">Fatty-acyl-CoA synthase</span>

Fatty-acyl-CoA Synthase, or more commonly known as yeast fatty acid synthase, is an enzyme complex responsible for fatty acid biosynthesis, and is of Type I Fatty Acid Synthesis (FAS). Yeast fatty acid synthase plays a pivotal role in fatty acid synthesis. It is a 2.6 MDa barrel shaped complex and is composed of two, unique multi-functional subunits: alpha and beta. Together, the alpha and beta units are arranged in an α6β6 structure. The catalytic activities of this enzyme complex involves a coordination system of enzymatic reactions between the alpha and beta subunits. The enzyme complex therefore consists of six functional centers for fatty acid synthesis.

<span class="mw-page-title-main">Ferredoxin-thioredoxin reductase</span>

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<span class="mw-page-title-main">Transition metal nitrile complexes</span> Class of coordination compounds containing nitrile ligands (coordinating via N)

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<span class="mw-page-title-main">Nicotinonitrile</span> Chemical compound

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Heterobimetallic catalysis is an approach to catalysis that employs two different metals to promote a chemical reaction. Included in this definition are cases where: 1) each metal activates a different substrate, 2) both metals interact with the same substrate, and 3) only one metal directly interacts with the substrate(s), while the second metal interacts with the first.

<span class="mw-page-title-main">Cobalt in biology</span> Use of Cobalt by organisms

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References

  1. Karunagala Pathiranage, Wasantha Lankathilaka; Gumataotao, Natalie; Fiedler, Adam T.; Holz, Richard C.; Bennett, Brian (2021). "Identification of an Intermediate Species along the Nitrile Hydratase Reaction Pathway by EPR Spectroscopy". Biochemistry. 60 (49): 3771–3782. doi:10.1021/acs.biochem.1c00574. PMID   34843221.
  2. Foerstner KU, Doerks T, Muller J, Raes J, Bork P (2008). Hannenhalli S (ed.). "A nitrile hydratase in the eukaryote Monosiga brevicollis". PLOS ONE. 3 (12): e3976. Bibcode:2008PLoSO...3.3976F. doi: 10.1371/journal.pone.0003976 . PMC   2603476 . PMID   19096720.
  3. Marron AO, Akam M, Walker G (2012). Stiller J (ed.). "Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups". PLOS ONE. 7 (4): e32867. Bibcode:2012PLoSO...732867M. doi: 10.1371/journal.pone.0032867 . PMC   3323583 . PMID   22505998.
  4. 1 2 Schmidberger, J. W.; Hepworth, L. J.; Green, A. P.; Flitsch, S. L. (2015). "Enzymatic Synthesis of Amides". In Faber, Kurt; Fessner, Wolf-Dieter; Turner, Nicholas J. (eds.). Biocatalysis in Organic Synthesis 1. Science of Synthesis. Georg Thieme Verlag. pp. 329–372. ISBN   9783131766113.
  5. 1 2 Asano, Y. (2015). "Hydrolysis of Nitriles to Amides". In Faber, Kurt; Fessner, Wolf-Dieter; Turner, Nicholas J. (eds.). Biocatalysis in Organic Synthesis 1. Science of Synthesis. Georg Thieme Verlag. pp. 255–276. ISBN   9783131766113.
  6. Nagasawa, Toru; Mathew, Caluwadewa Deepal; Mauger, Jacques; Yamada, Hideaki (1988). "Nitrile Hydratase-Catalyzed Production of Nicotinamide from 3-Cyanopyridine in Rhodococcus rhodochrous J1". Appl. Environ. Microbiol. 54 (7): 1766–1769. Bibcode:1988ApEnM..54.1766N. doi:10.1128/AEM.54.7.1766-1769.1988. PMC   202743 . PMID   16347686.
  7. Hilterhaus, L.; Liese, A. (2007). "Building Blocks". In Ulber, Roland; Sell, Dieter (eds.). White Biotechnology. Advances in Biochemical Engineering / Biotechnology. Vol. 105. Springer Science & Business Media. pp. 133–173. doi:10.1007/10_033. ISBN   9783540456957. PMID   17408083.{{cite book}}: |journal= ignored (help)
  8. Nagashima S, Nakasako M, Dohmae N, et al. (May 1998). "Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms". Nat. Struct. Biol. 5 (5): 347–51. doi:10.1038/nsb0598-347. PMID   9586994. S2CID   20435546.
  9. Payne, MS; Wu, S; Fallon, RD; Tudor, G; Stieglitz, B; Turner, IM; Nelson, MJ (May 1997). "A stereoselective cobalt-containing nitrile hydratase". Biochemistry. 36 (18): 5447–54. doi:10.1021/bi962794t. PMID   9154927.
  10. Marsh JA, Hernández H, Hall Z, Ahnert SE, Perica T, Robinson CV, Teichmann SA (Apr 2013). "Protein complexes are under evolutionary selection to assemble via ordered pathways". Cell. 153 (2): 461–470. doi:10.1016/j.cell.2013.02.044. PMC   4009401 . PMID   23582331.
  11. Hopmann, KH; Guo JD, Himo F (2007). "Theoretical Investigation of the First-Shell Mechanism of Nitrile Hydratase". Inorg. Chem. 46 (12): 4850–4856. doi:10.1021/ic061894c. PMID   17497847.
  12. Hopmann, KH; Himo F (March 2008). "Theoretical Investigation of the Second-Shell Mechanism of Nitrile Hydratase". European Journal of Inorganic Chemistry. 2008 (9): 1406–1412. doi:10.1002/ejic.200701137.
  13. Salette, M; Wu R, Sanishvili R, Liu D, Holz RC (2014). "The Active Site Sulfenic Acid Ligand in Nitrile Hydratases can Function as a Nucleophile". Journal of the American Chemical Society. 136 (4): 1186–1189. doi:10.1021/ja410462j. PMC   3968781 . PMID   24383915.{{cite journal}}: CS1 maint: multiple names: authors list (link)

Further reading