Summary: Nitrile hydratase, alpha chain
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Nitrile hydratase Edit Wikipedia article
|PDB structures||RCSB PDB PDBe PDBsum|
|Gene Ontology||AmiGO / EGO|
R-C≡N + H2O → R-C(O)NH2
In biochemistry, cobalt is in general found in a corrin ring, such as in vitamin B12. Nitrile hydratase is one of the rare enzyme types that use cobalt in a non-corrinoid manner. 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.
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. 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.
NHases have been efficiently used for the industrial production of acrylamide from acrylonitrile 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.
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.
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) or as a nucleophile. Subsequently, the functional role of the SOH center as nucleophile has obtained experimental support.
- Foerstner KU, Doerks T, Muller J, Raes J, Bork P (2008). "A nitrile hydratase in the eukaryote Monosiga brevicollis". In Hannenhalli, Sridhar. PLoS ONE 3 (12): e3976. doi:10.1371/journal.pone.0003976. PMC 2603476. PMID 19096720.
- Marron AO, Akam M, Walker G (2012). "Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups". In Stiller, John. PLoS ONE 7 (4): e32867. doi:10.1371/journal.pone.0032867.
- 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.
- Hopmann, KH; Guo JD, Himo F (2007). "Theoretical Investigation of the First-Shell Mechanism of Nitrile Hydratase". Inorg. Chem. 46 (12). doi:10.1021/ic061894c.
- Hopmann, KH; Himo F (March 2008). "Theoretical Investigation of the Second-Shell Mechanism of Nitrile Hydratase". European Journal of Inorganic Chemistry 2008 (9). doi:10.1002/ejic.200701137.
- 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". JACS. doi:10.1021/ja410462j.
- Prasad, S; Bhalla, TC (May 2010). "Nitrile hydratases (NHases): At the interface of academia and industry .". Biotechnology Advances 28 (6): 725. doi:10.1016/j.biotechadv.2010.05.020. PMID 20685247.
- Rzeznicka, K; Schätzle, S; Böttcher, D; Klein, J; Bornscheuer, UT (Aug 2009). "Cloning and functional expression of a nitrile hydratase (NHase) from Rhodococcus equi TG328-2 in Escherichia coli, its purification and biochemical characterisation.". Appl Microbiol Biotechnol 85 (5): 1417–25. doi:10.1007/s00253-009-2153-y. PMID 19662400.
- Song, L; Wang, M; Yang, X; Qian, S (Jun 2007). "Purification and characterization of the enantioselective nitrile hydratase from Rhodococcus sp. AJ270.". Biotechnol J 2 (6): 717–24. doi:10.1002/biot.200600215. PMID 17330219.
- Miyanaga, A; Fushinobu, S; Ito, K; Shoun, H; Wakagi, T (Jan 2004). "Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding.". Eur J Biochem 271 (2): 429–38. doi:10.1046/j.1432-1033.2003.03943.x. PMID 14717710.
- DiCosimo, R; Eisenberg, A; Fager, SK; Perkins, NE; Gallagher, FG; Cooper, SM; Gavagan, JE; Stieglitz, B et al. (Oct 1999). "5-Cyanovaleramide production using immobilized Pseudomonas chlororaphis B23.". Bioorg Med Chem 7 (10): 2239–45. doi:10.1016/S0968-0896(99)00157-1. PMID 10579532. More than one of
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No Pfam abstract.
Nagashima S, Nakasako M, Dohmae N, Tsujimura M, Takio K, Odaka M, Yohda M, Kamiya N, Endo I; , Nat Struct Biol 1998;5:347-351.: Novel non-heme iron center of nitrile hydratase with a claw setting of oxygen atoms. PUBMED:9586994 EPMC:9586994
Internal database links
|Similarity to PfamA using HHSearch:||Frankia_peptide|
External database links
This tab holds annotation information from the InterPro database.
InterPro entry IPR004232
Nitrile hydratases (EC) are bacterial enzymes that catalyse the hydration of nitrile compounds to the corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and are normally active as a tetramer, alpha(2)beta(2). Nitrile hydratases contain either a non-haem iron or a non-corrinoid cobalt centre, both types sharing a highly conserved peptide sequence in the alpha subunit (CXLCSC) that provides all the residues involved in coordinating the metal ion. Each type of nitrile hydratase specifically incorporated its metal with the help of activator proteins encoded by flanking regions of the nitrile hydratase genes that are necessary for metal insertion. The Fe-containing enzyme is photo-regulated: in the dark the enzyme is inactivated due to the association of nitric oxide (NO) to the iron, while in the light the enzyme is active by photo-dissociation of NO. The NO is held in place by a claw setting formed through specific oxygen atoms in two modified cysteines and a serine residue in the active site [PUBMED:9586994, PUBMED:9195885]. The cobalt-containing enzyme is unaffected by NO, but was shown to undergo a similar effect with carbon monoxide [PUBMED:17267045, PUBMED:14717710]. Fe- and cobalt-containing enzymes also display different inhibition patterns with nitrophenols.
Thiocyanate hydrolase (SCNase) is a cobalt-containing metalloenzyme with a cysteine-sulphinic acid ligand that hydrolyses thiocyanate to carbonyl sulphide and ammonia [PUBMED:16417356].
The two enzymes, nitrile hydratase and SCNase, are homologous over regions corresponding to almost the entire coding regions of the genes: the beta and alpha subunits of thiocyanate hydrolase were homologous to the amino- and carboxyl-terminal halves of the beta subunit of nitrile hydratase, and the gamma subunit of thiocyanate hydrolase was homologous to the alpha subunit of nitrile hydratase [PUBMED:9573140].
This entry represents the structural domain of the alpha subunit of both iron- and cobalt-containing nitrile hydratases; the alpha subunit is a duplication of two structural repeats, each consisting of 4 layers, alpha/beta/beta/alpha [PUBMED:9195885]. This structure is also found in the related protein, the gamma subunit of thiocyanate hydrolase (SCNase).
The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.
|Molecular function||transition metal ion binding (GO:0046914)|
|catalytic activity (GO:0003824)|
|Biological process||nitrogen compound metabolic process (GO:0006807)|
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|Seed source:||Structural domain|
|Number in seed:||37|
|Number in full:||386|
|Average length of the domain:||157.00 aa|
|Average identity of full alignment:||41 %|
|Average coverage of the sequence by the domain:||86.98 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||11|
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the NHase_alpha domain has been found. There are 57 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.
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