Summary: Nitrile hydratase beta subunit

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Wikipedia: Nitrile hydratase
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Nitrile hydratase Edit Wikipedia article

nitrile hydratase

Identifiers

Databases

PDB structures

AmiGO / EGO

Search
PMC	articles
PubMed	articles
NCBI Protein	search

In enzymology, 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

R-C≡N + H₂O → R-C(O)NH₂

[edit] Metal cofactor

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.

[edit] 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.^[1] 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.^[2]

[edit] Industrial applications

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.

[edit] Structure

Structure of nitrile hydratase.^[3]

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

Symbol

NHase_alpha

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

Nitrile hydratase beta subunit

Identifiers

Symbol

NHase_beta

Available protein structures:
Pfam	structures
PDB	RCSB PDB; PDBe
PDBsum	structure summary

[edit] Enzymatic 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.

[edit] References

^ Foerstner KU, Doerks T, Muller J, Raes J, Bork P (2008). Hannenhalli, Sridhar. ed. "A nitrile hydratase in the eukaryote Monosiga brevicollis". PLoS ONE 3 (12): e3976. doi:10.1371/journal.pone.0003976. PMC 2603476. PMID 19096720. //www.ncbi.nlm.nih.gov/pmc/articles/PMC2603476/.
^ Marron AO, Akam M, Walker G (2012). Stiller, John. ed. "Nitrile Hydratase Genes Are Present in Multiple Eukaryotic Supergroups". 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.

[edit] Further reading

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.

Carbon-oxygen lyases (EC 4.2) (primarily dehydratases)

4.2.1: Hydro-Lyases

Carbonic anhydrase
Fumarase
Aconitase
Enolase
- Alpha
- Enolase 2
Enoyl-CoA hydratase/3-Hydroxyacyl ACP dehydrase
Methylglutaconyl-CoA hydratase
Tryptophan synthase
Cystathionine beta synthase
Porphobilinogen synthase
3-isopropylmalate dehydratase
Urocanate hydratase
Uroporphyrinogen III synthase
Nitrile hydratase

4.2.2: Acting on polysaccharides

Hyaluronate lyase

4.2.3: Acting on phosphates

Threonine synthase

4.2.99: Other

Carboxymethyloxysuccinate lyase

B
enzm
1.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
- 10
- 11
- 13
- 14
- 15-18
2.1
- 2
- 3
- 4
- 5
- 6
- 7
- 8
2.7.10
2.7.11-12
3.1
- - 3.1.3.48
- 2
- 3
- 4
  - 3.4.21
- 5
- 6
- 7
- 22
- 23
- 24
4.1
- 2
- 3
- 4
- 5
- 6
5.1
- 2
- 3
- 4
- 99
6.1-3
- 4
- 5-6

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Nitrile hydratase beta subunit Provide feedback

Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their 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 they contain one iron atom per alpha beta unit [1].

Literature references

Huang W, Jia J, Cummings J, Nelson M, Schneider G, Lindqvist Y; , Structure 1997;5:691-699.: Crystal structure of nitrile hydratase reveals a novel iron centre in a novel fold. PUBMED:9195885 EPMC:9195885

External database links

PANDIT:	PF02211
Pseudofam:	PF02211
SCOP:	2ahj
SYSTERS:	NHase_beta

This tab holds annotation information from the InterPro database.

InterPro entry IPR024690

Nitrile hydratases (EC:4.2.1.84) are unusual metalloenzymes that catalyse the hydration of nitriles to their 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 they contain one iron atom per alpha beta unit [PUBMED:9195885].

This entry represents the structural domain of nitrile hydratase beta subunit which contains irregular array of helices in the N-terminal extension.

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

Molecular function

nitrile hydratase activity (GO:0018822)

Domain organisation

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	Seed (33)	Full (440)	Representative proteomes				NCBI (463)	Meta (350)
	Seed (33)	Full (440)	RP15 (31)	RP35 (80)	RP55 (108)	RP75 (156)	NCBI (463)	Meta (350)
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¹Cannot generate PP/Heatmap alignments for seeds; no PP data available

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	Seed (33)	Full (440)	Representative proteomes				NCBI (463)	Meta (350)
	Seed (33)	Full (440)	RP15 (31)	RP35 (80)	RP55 (108)	RP75 (156)	NCBI (463)	Meta (350)
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	Seed (33)	Full (440)	Representative proteomes				NCBI (463)	Meta (350)
	Seed (33)	Full (440)	RP15 (31)	RP35 (80)	RP55 (108)	RP75 (156)	NCBI (463)	Meta (350)
Raw Stockholm	Download	Download	Download	Download	Download	Download	Download	Download
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Curation and family details

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Curation

Seed source:

Pfam-B_5347 (release 5.2)

Previous IDs:

none

Type:

Domain

Author:

Bateman A

Number in seed:

33

Number in full:

440

Average length of the domain:

165.30 aa

Average identity of full alignment:

25 %

Average coverage of the sequence by the domain:

93.48 %

HMM information

HMM build commands:

build method: hmmbuild -o /dev/null HMM SEED

search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq

Model details:

Parameter	Sequence	Domain
Gathering cut-off	21.3	21.3
Trusted cut-off	21.7	21.7
Noise cut-off	19.8	21.0

Model length:

222

Family (HMM) version:

10

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Species distribution

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Interactions

There are 2 interactions for this family. More...

NHase_beta NHase_alpha

Structures

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_beta domain has been found. There are 80 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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Archea	Eukaryota
Bacteria	Other sequences
Viruses	Unclassified
Viroids	Unclassified sequence

Family: NHase_beta (PF02211)

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Summary: Nitrile hydratase beta subunit

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Nitrile hydratase Edit Wikipedia article

Contents

[edit] Metal cofactor

[edit] Metabolic pathway

[edit] Industrial applications

[edit] Structure

[edit] Enzymatic mechanism

[edit] References

[edit] Further reading

Nitrile hydratase beta subunit Provide feedback

Literature references

External database links

InterPro entry IPR024690

Gene Ontology

Domain organisation

Alignments

Alignment types

Viewing

Reformatting

Downloading

View options

Format an alignment

Download options

External links

HMM logo

Trees

Curation and family details

Curation

HMM information

Species distribution

Sunburst controls

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Change the size of the sunburst

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Selections

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How the sunburst is generated

Colouring and labels

Anomalies in the taxonomy tree

Missing taxonomic levels

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Sub-species

Too many species/sequences

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Annotation

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Selected sequences

Species trees

Interactive tree

Interactions

Structures