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Information on EC 4.2.1.84 - nitrile hydratase and Organism(s) Pseudonocardia thermophila and UniProt Accession Q7SID2
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4.2.1.84 nitrile hydrataseIUBMB Comments
Acts on short-chain aliphatic nitriles, converting them into the corresponding amides. Does not act on these amides or on aromatic nitriles. cf. EC 3.5.5.1 nitrilase.
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Word Map
- 4.2.1.84
- rhodococcus
- amidase
- acrylamide
- rhodochrous
- erythropolis
- synthesis
-
feiii
-
low-spin
-
fe-type
-
non-heme
-
sulfenic
- benzonitrile
- pseudonocardia
-
sulfinate
- propionamide
-
cysteine-sulfinic
-
neonicotinoid
- ruber
- propionitrile
-
cgmcc
- thiacloprid
-
carboxamido
- aldoxime
- indole-3-acetonitrile
- chlororaphis
-
metallochaperone
- industry
- pharmacology
- degradation
- environmental protection
- analysis
The taxonomic range for the selected organisms is: Pseudonocardia thermophila
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
nhase, nitrile hydratase, nilco, l-nhase, h-nhase, co-type nhase, cobalt-containing nitrile hydratase, fe-nhase, ctnhase, anhase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3-cyanopyridine hydratase
-
-
-
-
acrylonitrile hydratase
-
-
-
-
aliphatic nitrile hydratase
-
-
-
-
H-NHase
-
-
-
-
H-nitrilase
-
-
-
-
hydratase, nitrile
-
-
-
-
L-Nhase
-
-
-
-
L-nitrilase
-
-
-
-
NHase
NI1 NHase
-
-
-
-
nitrilase
-
-
-
-
NHase
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
an aliphatic amide = a nitrile + H2O
modeling of the catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation using the enzyme crystal structure, PDB code 1IRE, overview. Active site activation is the first step of NHase catalysis, in which the Co2+ coordinated to a water molecule forms a Co-OH complex mediated by the oxidized alpha-CEA113. Then the oxygen atom in the Co-OH attacks the C atom in the -CN triple bond of acrylonitrile, forming a precursor of acrylamide, proton rearrangement happens transforming the precursor into the final product of acrylamide, under the assistance of the hydrogen atom in the -OH group of alpha-Ser112
an aliphatic amide = a nitrile + H2O
thermal-stable mechanism of thermophilic nitrile hydratases, molecular dynamic simulation, overview
an aliphatic amide = a nitrile + H2O
mechanism of action for the hydration of nitriles by NHase, overview. The cysteine-sulfenic acid ligand acts as the catalytic nucleophile. The first step in catalysis involves the direct ligation of the nitrile to the active site lowspin, trivalent metal ion. One proton transfer occurs between the alphaCys113-OH ligand and the nitrile N-atom, while the second transfer occurs between the water molecule that reforms alphaCys113-OH and the newly forming imidate N-atom
an aliphatic amide = a nitrile + H2O
substrate binding occurs via breathing and flip-flop mechanisms
-
an aliphatic amide = a nitrile + H2O
possible role of water and active center residues in reaction mechanism is shown
-
an aliphatic amide = a nitrile + H2O
reaction mechanism, overview
-
an aliphatic amide = a nitrile + H2O
reaction mechanism, first-shell mechanism of CoIII-NHase involving Tyr68 as catalytic base, deprotonated Tyr68 is proposed to abstract a proton from the nucleophilic water molecule, thus activating it for attack on the metal-bound substrate, modelling, detailed overview
-
an aliphatic amide = a nitrile + H2O
mechanism of action for the hydration of nitriles by NHase, overview. The cysteine-sulfenic acid ligand acts as the catalytic nucleophile. The first step in catalysis involves the direct ligation of the nitrile to the active site lowspin, trivalent metal ion. One proton transfer occurs between the alphaCys113-OH ligand and the nitrile N-atom, while the second transfer occurs between the water molecule that reforms alphaCys113-OH and the newly forming imidate N-atom
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
C-O bond cleavage by elimination of water
-
-
-
-
PATHWAY SOURCE
PATHWAYS
KEGG
-
-, -, -, -
SYSTEMATIC NAME
IUBMB Comments
aliphatic-amide hydro-lyase (nitrile-forming)
Acts on short-chain aliphatic nitriles, converting them into the corresponding amides. Does not act on these amides or on aromatic nitriles. cf. EC 3.5.5.1 nitrilase.
CAS REGISTRY NUMBER
COMMENTARY
82391-37-5
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3-cyanopyridine + H2O
nicotinamide
substrate of recombinant wild-type enzyme, not of mutant enzymes
-
-
?
4-cyanopyridine + H2O
isonicotinamide
substrate of recombinant wild-type enzyme, not of mutant enzymes
-
-
?
benzonitrile + H2O
benzamide
substrate of recombinant wild-type and mutant enzymes
-
-
?
methacrylonitrile + H2O
methacrylamide
substrate of recombinant wild-type and mutant enzymes
-
-
?
3-cyanopyridine + H2O
nicotinamide
substrate of recombinant wild-type enzyme, not of mutant enzymes
-
-
?
4-cyanopyridine + H2O
isonicotinamide
substrate of recombinant wild-type enzyme, not of mutant enzymes
-
-
?
methacrylonitrile + H2O
methacrylamide
substrate of recombinant wild-type and mutant enzymes
-
-
?
acrylonitrile + H2O
acrylamide
analysis of the structure model of the enzyme-substrate complex and catalytic mechanism, overview
-
-
?
acrylonitrile + H2O
acrylamide
substrate of recombinant wild-type and mutant enzymes
-
-
?
acrylonitrile + H2O
acrylamide
substrate of recombinant wild-type and mutant enzymes
-
-
?
an aliphatic amide
a nitrile + H2O
-
ligand exchange reactions, overview
-
-
?
benzonitrile + H2O
benzamide
substrate of recombinant wild-type and mutant enzymes
-
-
?
additional information
?
-
substrate specificity, overview
-
-
?
additional information
?
-
molecular modeling study of enzyme-substrate binding modes in the bi-enzyme pathway for degradation of nitrile to acid, specific residues within the enzyme's binding pockets formed diverse contacts with the substrate, molecular docking, overview. Top substrate having favorable interactions with nitrile hydratase is 3-cyanopyridine
-
-
?
additional information
?
-
the enzyme shows a preference for aromatic nitriles as substrates rather than aliphatic ones. Tryptophan residue betaTrp72 may be involved in substrate binding
-
-
?
additional information
?
-
the enzyme shows a preference for aromatic nitriles as substrates rather than aliphatic ones. Tryptophan residue betaTrp72 may be involved in substrate binding
-
-
?
additional information
?
-
-
computational molecular dynamics modelling of ligand docking and substrate transport and binding, overview
-
-
?
additional information
?
-
-
NHase hydrates a nitrile to provide the corresponding amide product via an addition reaction of one water molecule, active site structure involving amidate nitrogen donors from the peptide backbone, overview
-
-
?
additional information
?
-
the enzyme shows a preference for aromatic nitriles as substrates rather than aliphatic ones. Tryptophan residue betaTrp72 may be involved in substrate binding
-
-
?
additional information
?
-
the enzyme shows a preference for aromatic nitriles as substrates rather than aliphatic ones. Tryptophan residue betaTrp72 may be involved in substrate binding
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
additional information
?
-
molecular modeling study of enzyme-substrate binding modes in the bi-enzyme pathway for degradation of nitrile to acid, specific residues within the enzyme's binding pockets formed diverse contacts with the substrate, molecular docking, overview. Top substrate having favorable interactions with nitrile hydratase is 3-cyanopyridine
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Co2+
Co3+
a Co-type NHase, Co3+ coordinated to a water molecule forms a Co-OH complex mediated by the oxidized alpha-CEA113
Fe2+
with cobalt substitution for iron, the enzyme activity becomes weak
Co2+
Co3+
Fe2+
with cobalt substitution for iron, the enzyme activity becomes weak
Fe3+
-
the unique active site structure of metalloenzyme nitrile hydratase includes a central metal ion, Co3+ or Fe3+, coordinated octahedrally by two amide nitrogens from the peptide backbone, one cysteine sulfur and two oxidized cysteine sulfurs, Cys-SO and Cys-SO2
additional information
Co2+
cobalt-containing nitrile hydratase, noncorrin cobalt at the catalytic center, structure, overview. Two cysteine residues (alphaCys111 and alphaCys113) coordinated to the cobalt are posttranslationally modified to cysteine-sulfinic acid and to cysteine-sulfenic acid, respectively
Co2+
cobalt-containing nitrile hydratase, noncorrin cobalt at the catalytic center, structure, overview. Two cysteine residues (alphaCys111 and alphaCys113) coordinated to the cobalt are posttranslationally modified to cysteine-sulfinic acid and to cysteine-sulfenic acid, respectively
Co3+
-
the enzyme belongs to the CoIII-NHase group of enzymes, octahedrally coordinated metal ion with two deprotonated backbone amides as ligands as well as three cysteine residues, two of which are posttranslationally oxidized to cysteine-sulfenic and cysteine-sulfinic acids
Co3+
-
the unique active site structure of metalloenzyme nitrile hydratase includes a central metal ion, Co3+ or Fe3+, coordinated octahedrally by two amide nitrogens from the peptide backbone, one cysteine sulfur and two oxidized cysteine sulfurs, Cys-SO and Cys-SO2
additional information
structure comparison with the Fe-type NHase, overview. In cobalt-containing nitrile hydratase, a tryptophan residue betaTrp72, which may be involved in substrate binding, replaces the tyrosine residue of iron-containing nitrile hydratase
additional information
structure comparison with the Fe-type NHase, overview. In cobalt-containing nitrile hydratase, a tryptophan residue betaTrp72, which may be involved in substrate binding, replaces the tyrosine residue of iron-containing nitrile hydratase
additional information
-
the apoenzyme shows no detectable activity, a disulfide bond between highly conserved Co-binding residues alphaCys108 and alphaCys113 is formed in the apoenzyme structure
additional information
the apoenzyme shows no detectable activity, a disulfide bond between highly conserved Co-binding residues alphaCys108 and alphaCys113 is formed in the apoenzyme structure
additional information
the apoenzyme shows no detectable activity, a disulfide bond between highly conserved Co-binding residues alphaCys108 and alphaCys113 is formed in the apoenzyme structure
additional information
-
redox potentials and structures of metal ion-enzyme complexes, overview
additional information
structure comparison with the Fe-type NHase, overview. In cobalt-containing nitrile hydratase, a tryptophan residue betaTrp72, which may be involved in substrate binding, replaces the tyrosine residue of iron-containing nitrile hydratase
additional information
structure comparison with the Fe-type NHase, overview. In cobalt-containing nitrile hydratase, a tryptophan residue betaTrp72, which may be involved in substrate binding, replaces the tyrosine residue of iron-containing nitrile hydratase
additional information
-
the apoenzyme shows no detectable activity, a disulfide bond between highly conserved Co-binding residues alphaCys108 and alphaCys113 is formed in the apoenzyme structure
additional information
the apoenzyme shows no detectable activity, a disulfide bond between highly conserved Co-binding residues alphaCys108 and alphaCys113 is formed in the apoenzyme structure
additional information
the apoenzyme shows no detectable activity, a disulfide bond between highly conserved Co-binding residues alphaCys108 and alphaCys113 is formed in the apoenzyme structure
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1-butaneboronic acid
competitive inhibitor, binds directly to the low-spin Co(III) ion in the active site of PtNHase
n-butyric acid
competitive inhibitor, the hydroxyl group of enzyme residue betaTyr68 forms hydrogen bonds with both n-butyric acid and residue alphaSer112, which is located in the active center. Butyric acid acts as a stabilizer of Fe-type NHase, Co-type NHase is more stable
phenylboronic acid
competitive inhibitor, binds to the enzyme active site
1-butaneboronic acid
competitive inhibitor, binds directly to the low-spin Co(III) ion in the active site of PtNHase
phenylboronic acid
competitive inhibitor, binds to the enzyme active site
n-butyric acid
competitive inhibitor, the hydroxyl group of enzyme residue betaTyr68 forms hydrogen bonds with both n-butyric acid and residue alphaSer112, which is located in the active center. Butyric acid acts as a stabilizer of Fe-type NHase, Co-type NHase is more stable
additional information
enzyme-boronic acid complexes represent a snapshot of reaction intermediates
-
additional information
enzyme-boronic acid complexes represent a snapshot of reaction intermediates
-
additional information
the enzyme shows a high tolerance against acrylamide
-
additional information
the enzyme shows a high tolerance against acrylamide
-
additional information
enzyme-boronic acid complexes represent a snapshot of reaction intermediates
-
additional information
enzyme-boronic acid complexes represent a snapshot of reaction intermediates
-
additional information
the enzyme shows a high tolerance against acrylamide
-
additional information
the enzyme shows a high tolerance against acrylamide
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
nitrile hydratase activator protein
residue aTyr114 may be involved in the interaction with the nitrile hydratase activator protein of Pseudomonas thermophila
-
nitrile hydratase activator protein
residue aTyr114 may be involved in the interaction with the nitrile hydratase activator protein of Pseudomonas thermophila
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.12
3-Cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
0.079
4-cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
0.12
3-Cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
0.079
4-cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
3.6
acrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
9.9
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
58
acrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
107
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
0.02
Benzonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
0.025
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
0.11
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
0.23
Benzonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
0.49
Methacrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
2.3
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
2.6
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
4.7
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
3.6
acrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
9.9
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
58
acrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
107
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
0.02
Benzonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
0.025
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
0.11
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
0.23
Benzonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
0.49
Methacrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
2.3
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
2.6
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
4.7
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
additional information
additional information
-
the wild-type enzyme shows significantly lower Km values for aromatic substrates than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Km values for aromatic substrates than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Km values for aromatic substrates than for aliphatic ones
-
additional information
additional information
-
enzyme-ligand complex kinetic constants, overview
-
additional information
additional information
-
the wild-type enzyme shows significantly lower Km values for aromatic substrates than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Km values for aromatic substrates than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Km values for aromatic substrates than for aliphatic ones
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
131
3-Cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
90
4-cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
131
3-Cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
90
4-cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
15.2
acrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
33.9
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
621
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
1910
acrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
4.9
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
7.4
Benzonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
123
Benzonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
132
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
14.1
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
34.6
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
482
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
1000
Methacrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
15.2
acrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
33.9
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
621
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
1910
acrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
4.9
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
7.4
Benzonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
123
Benzonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
132
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
14.1
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
34.6
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
482
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
1000
Methacrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1090
3-Cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
1140
4-cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
1090
3-Cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
1140
4-cyanopyridine
pH 7.6, 25°C, recombinant wild-type enzyme
0.26
acrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
3.4
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
5.8
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
537
acrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
32
Benzonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
45
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
5290
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
6150
Benzonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
5.4
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
15
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
103
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
2040
Methacrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
0.26
acrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
3.4
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
5.8
acrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
537
acrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
32
Benzonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
45
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
5290
Benzonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
6150
Benzonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
5.4
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant betaY68F
15
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaY114T
103
Methacrylonitrile
pH 7.6, 25°C, recombinant mutant alphaT109S
2040
Methacrylonitrile
pH 7.6, 25°C, recombinant wild-type enzyme
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.033
benzoic acid
pH 7.6, 25°C, recombinant wild-type enzyme
1.3
n-butyric acid
pH 7.6, 25°C, recombinant wild-type enzyme
9.9
propionic acid
pH 7.6, 25°C, recombinant wild-type enzyme
0.033
benzoic acid
pH 7.6, 25°C, recombinant wild-type enzyme
1.3
n-butyric acid
pH 7.6, 25°C, recombinant wild-type enzyme
9.9
propionic acid
pH 7.6, 25°C, recombinant wild-type enzyme
additional information
additional information
-
the wild-type enzyme shows significantly lower Ki values for aromatic inhibitors than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Ki values for aromatic inhibitors than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Ki values for aromatic inhibitors than for aliphatic ones
-
additional information
additional information
-
the wild-type enzyme shows significantly lower Ki values for aromatic inhibitors than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Ki values for aromatic inhibitors than for aliphatic ones
-
additional information
additional information
the wild-type enzyme shows significantly lower Ki values for aromatic inhibitors than for aliphatic ones
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7.5
7.5
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
25
25
50
chimeric nitrile hydratases (SBpNHase) from the thermal sensitive nitrile hydratasese from Bordetella petrii and the relatively thermal-stable nitrile hydratases from Pseudonocardia thermophila (constructed by swapping the corresponding C-domains) retains 50% residual activity
additional information
additional information
the enzyme exhibits a high optimum temperature
additional information
the enzyme exhibits a high optimum temperature
additional information
the enzyme exhibits a high optimum temperature
additional information
the enzyme exhibits a high optimum temperature
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
metabolism
hydrolysis mediated by nitrilase, NHase, and amidase is the most common way for nitrile degradation
additional information
additional information
-
in Co-type NHase, the side-chain of alphaThr109, located iin the cysteine cluster region, undergoes a hydrophobic interaction with the side-chain of alphaVal136. The hydroxyl group of residue alphaTyr114, located near the cysteine cluster region, forms hydrogen bonds with the main-chain oxygen atoms of alphaLeu119 and alphaLeu121, via a water molecule
additional information
in Co-type NHase, the side-chain of alphaThr109, located iin the cysteine cluster region, undergoes a hydrophobic interaction with the side-chain of alphaVal136. The hydroxyl group of residue alphaTyr114, located near the cysteine cluster region, forms hydrogen bonds with the main-chain oxygen atoms of alphaLeu119 and alphaLeu121, via a water molecule
additional information
in Co-type NHase, the side-chain of alphaThr109, located iin the cysteine cluster region, undergoes a hydrophobic interaction with the side-chain of alphaVal136. The hydroxyl group of residue alphaTyr114, located near the cysteine cluster region, forms hydrogen bonds with the main-chain oxygen atoms of alphaLeu119 and alphaLeu121, via a water molecule
additional information
the recombinant enzyme shows almost the same specific activity and other properties as the native enzyme. Structure of the active center of the recombinant enzyme, overview
additional information
the recombinant enzyme shows almost the same specific activity and other properties as the native enzyme. Structure of the active center of the recombinant enzyme, overview
additional information
-
in Co-type NHase, the side-chain of alphaThr109, located iin the cysteine cluster region, undergoes a hydrophobic interaction with the side-chain of alphaVal136. The hydroxyl group of residue alphaTyr114, located near the cysteine cluster region, forms hydrogen bonds with the main-chain oxygen atoms of alphaLeu119 and alphaLeu121, via a water molecule
additional information
in Co-type NHase, the side-chain of alphaThr109, located iin the cysteine cluster region, undergoes a hydrophobic interaction with the side-chain of alphaVal136. The hydroxyl group of residue alphaTyr114, located near the cysteine cluster region, forms hydrogen bonds with the main-chain oxygen atoms of alphaLeu119 and alphaLeu121, via a water molecule
additional information
in Co-type NHase, the side-chain of alphaThr109, located iin the cysteine cluster region, undergoes a hydrophobic interaction with the side-chain of alphaVal136. The hydroxyl group of residue alphaTyr114, located near the cysteine cluster region, forms hydrogen bonds with the main-chain oxygen atoms of alphaLeu119 and alphaLeu121, via a water molecule
additional information
the recombinant enzyme shows almost the same specific activity and other properties as the native enzyme. Structure of the active center of the recombinant enzyme, overview
additional information
the recombinant enzyme shows almost the same specific activity and other properties as the native enzyme. Structure of the active center of the recombinant enzyme, overview
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable).
The reliability class of the localization prediction ranges from 1 (very reliable) to 5 (not reliable). PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant apoenzyme and mutant enzymes, sitting drop vapor diffusion method, 8 mg/ml protein, with a reservoir solution containing 1.4 M tri-sodium citrate, and 0.1 M HEPES-NaOH, pH 7.5, 5°C, crystals of a complex with n-butyric acid are prepared by soaking a native crystal in a reservoir solution containing 15 mM n-butyric acid for 3 h, X-ray diffraction structure determination and analysis at 1.63-2.0 A resolution, molecular replacement and modeling
purified recombinant enzyme, free or in complex with inhibitors 1-butaneboronic acid and phenylboronic acid, X-ray diffraction structure determination and analysis at 1.2-1.9 A resolution
purified recombinant enzyme, sitting drop vapor diffusion method, 8 mg/ml protein, with a reservoir solution containing 1.4 M tri-sodium citrate, and 0.1 M HEPES-NaOH, pH 7.5, 5°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement and modeling
dockings and interactions of a series of aliphatic and aromatic nitriles are modelled and the differences are reported
-
dockings of the substrates and products to the crystal structure 1IRE, overview
-
purified recombinant apoenzyme and mutant enzymes, sitting drop vapor diffusion method, 8 mg/ml protein, with a reservoir solution containing 1.4 M tri-sodium citrate, and 0.1 M HEPES-NaOH, pH 7.5, 5°C, crystals of a complex with n-butyric acid are prepared by soaking a native crystal in a reservoir solution containing 15 mM n-butyric acid for 3 h, X-ray diffraction structure determination and analysis at 1.63-2.0 A resolution, molecular replacement and modeling
purified recombinant enzyme, free or in complex with inhibitors 1-butaneboronic acid and phenylboronic acid, X-ray diffraction structure determination and analysis at 1.2-1.9 A resolution
purified recombinant enzyme, sitting drop vapor diffusion method, 8 mg/ml protein, with a reservoir solution containing 1.4 M tri-sodium citrate, and 0.1 M HEPES-NaOH, pH 7.5, 5°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement and modeling
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
alphaT109S
site-directed mutagenesis, the mutant shows similar characteristics compared to the wild-type enzyme
alphaY114T
site-directed mutagenesis, the mutant shows a very low cobalt content and catalytic activity compared to the wild-type enzyme, and oxidative modifications of aCys111 and aCys113 residues are not observed
betaY68F
site-directed mutagenesis, the mutant shows an elevated Km value and a significantly decreased kcat value compared to the wild-type enzyme
alphaT109S
site-directed mutagenesis, the mutant shows similar characteristics compared to the wild-type enzyme
alphaY114T
site-directed mutagenesis, the mutant shows a very low cobalt content and catalytic activity compared to the wild-type enzyme, and oxidative modifications of aCys111 and aCys113 residues are not observed
betaY68F
site-directed mutagenesis, the mutant shows an elevated Km value and a significantly decreased kcat value compared to the wild-type enzyme
T109S
similar characteristics to the wild-type enzyme
Y114T
very low cobalt content and catalytic activity compared to the wild-type enzyme
additional information
additional information
improvement of thermal stability of the industrialized mesophilic NHase by introducing stable salt-bridge interactions into its thermal sensitive regions
additional information
homologous protein fragment swapping method is used for the improvement of the stability of NHase from Pseudomonas putida NRRL-18668, site targeted amino recombination software and molecular dynamics are used for determination of the crossover sites for fragment recombination, overview. One thermophilic NHase fragment M1 to G98 from Comamonas testosteroni 5-MGAM-4D and two fragments K165-V196 and K165-D209 from Pseudonocardia thermophila JCM3095 are selected to swap the corresponding fragments of Pseudomonas putida NHase. The chimeric NHases show 1.4 to 3.5fold enhancement in thermostability, some show reduced activity and product inhibition compared to wild-type Pseudomonas putida NHase. But mutants 3AB and 3ABC show increased activity due to altered secondary structure compared to the Pseudomonas putida wild-type
additional information
homologous protein fragment swapping method is used for the improvement of the stability of NHase from Pseudomonas putida NRRL-18668, site targeted amino recombination software and molecular dynamics are used for determination of the crossover sites for fragment recombination, overview. One thermophilic NHase fragment M1 to G98 from Comamonas testosteroni 5-MGAM-4D and two fragments K165-V196 and K165-D209 from Pseudonocardia thermophila JCM3095 are selected to swap the corresponding fragments of Pseudomonas putida NHase. The chimeric NHases show 1.4 to 3.5fold enhancement in thermostability, some show reduced activity and product inhibition compared to wild-type Pseudomonas putida NHase. But mutants 3AB and 3ABC show increased activity due to altered secondary structure compared to the Pseudomonas putida wild-type
additional information
homologous protein fragment swapping method is used for the improvement of the stability of NHase from Pseudomonas putida NRRL-18668, site targeted amino recombination software and molecular dynamics are used for determination of the crossover sites for fragment recombination, overview. One thermophilic NHase fragment M1 to G98 from Comamonas testosteroni 5-MGAM-4D and two fragments K165-V196 and K165-D209 from Pseudonocardia thermophila JCM3095 are selected to swap the corresponding fragments of Pseudomonas putida NHase. The chimeric NHases show 1.4 to 3.5fold enhancement in thermostability, some show reduced activity and product inhibition compared to wild-type Pseudomonas putida NHase. But mutants 3AB and 3ABC show increased activity due to altered secondary structure compared to the Pseudomonas putida wild-type
additional information
homologous protein fragment swapping method is used for the improvement of the stability of NHase from Pseudomonas putida NRRL-18668, site targeted amino recombination software and molecular dynamics are used for determination of the crossover sites for fragment recombination, overview. One thermophilic NHase fragment M1 to G98 from Comamonas testosteroni 5-MGAM-4D and two fragments K165-V196 and K165-D209 from Pseudonocardia thermophila JCM3095 are selected to swap the corresponding fragments of Pseudomonas putida NHase. The chimeric NHases show 1.4 to 3.5fold enhancement in thermostability, some show reduced activity and product inhibition compared to wild-type Pseudomonas putida NHase. But mutants 3AB and 3ABC show increased activity due to altered secondary structure compared to the Pseudomonas putida wild-type
additional information
-
transfer of stabilized salt-bridge interactions from three deformation-prone thermal-sensitive regions (A1, A2 and A3 in beta-subunit) of the thermophilic NHase 1V29 from Bacillus SC-105-1 and 1UGQ from Pseudonocardia thermophila JCM3095 into industrialized mesophilic NHase-TH from Rhodococcus ruber TH
additional information
the chimeric NHase (SBpNHase) from the thermal sensitive nitrile hydratasese from Bordetella petrii and the relatively thermal-stable nitrile hydratases from Pseudonocardia thermophila is constructed by swapping the corresponding C-domains
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
determination of thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation using crystal structures with PDB ID 1UGQ. In 1UGQ, the absence of a charged residue decreases the thermal sensitivity of region B1, and the formation of a small beta-sheet containing a stable salt-bridge in C-beta-terminal significantly enhances the thermal stability
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
4°C, purified recombinant wild-type enzyme, retains complete activity for 1 year, and the catalytic center does not change as confimed by analysis of the crystal structure
4°C, purified recombinant wild-type enzyme, retains complete activity for 1 year, and the catalytic center does not change as confimed by analysis of the crystal structure
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant enzyme from Escherichia coli strain HB101 by heat treatment at 55°C for 30 min, ammonium sulfate precipitation, anion exchange chromatography, hydrophobic interaction chromatography, and a another differentstep of anion exchange chromatography
recombinant soluble wild-type and mutant enzymes from Escherichia coli strain JM109 by ammonium sulfate fractionation and two different steps of anion echange chromatography
recombinant enzyme from Escherichia coli strain HB101 by heat treatment at 55°C for 30 min, ammonium sulfate precipitation, anion exchange chromatography, hydrophobic interaction chromatography, and a another differentstep of anion exchange chromatography
recombinant soluble wild-type and mutant enzymes from Escherichia coli strain JM109 by ammonium sulfate fractionation and two different steps of anion echange chromatography
the chimeric NHase (SBpNHase) from the thermal sensitive nitrile hydratasese from Bordetella petrii and the relatively thermal-stable nitrile hydratases from Pseudonocardia thermophila is constructed by swapping the corresponding C-domains
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expression of wild-type and mutant enzymes in Escherichia coli strain JM109
genetic organization of wild-type and chimeric mutant enzymes, expression of wild-type and recombinant chimeric mutants in Escherichia coli strain JM109
recombinant expression in Escherichia coli strain HB101 from vector pUC18. The recombinant enzyme shows almost the same specific activity and other properties as the native enzyme
expression of wild-type and mutant enzymes in Escherichia coli strain JM109
genetic organization of wild-type and chimeric mutant enzymes, expression of wild-type and recombinant chimeric mutants in Escherichia coli strain JM109
recombinant expression in Escherichia coli strain HB101 from vector pUC18. The recombinant enzyme shows almost the same specific activity and other properties as the native enzyme
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
-
nitrile hydratase is used for large scale industrial production of important commodities such as acrylamide and nicotinamide
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Miyanaga, A.; Fushinobu, S.; Ito, K.; Shoun, H.; Wakagi, T.
Mutational and structural analysis of cobalt-containing nitrile hydratase on substrate and metal binding
Eur. J. Biochem.
271
429-438
2004
Pseudonocardia thermophila, Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila (Q7SID3), Pseudonocardia thermophila JCM 3095, Pseudonocardia thermophila JCM 3095 (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID3)
Tastan Bishop, A.O.; Sewell, T.
A new approach to possible substrate binding mechanisms for nitrile hydratase
Biochem. Biophys. Res. Commun.
343
319-325
2006
Pseudonocardia thermophila
Peplowski, L.; Kubiak, K.; Nowak, W.
Insights into catalytic activity of industrial enzyme Co-nitrile hydratase. Docking studies of nitriles and amides
J. Mol. Model.
13
725-730
2007
Pseudonocardia thermophila, Pseudonocardia thermophila JCM 3095
Yano, T.; Ozawa, T.; Masuda, H.
Structural and functional model systems for analysis of the active center of nitrile hydratase
Chem. Lett.
37
672-677
2008
Pseudonocardia thermophila, Pseudonocardia thermophila JCM 3095
-
Peplowski, L.; Kubiak, K.; Nowak, W.
Mechanical aspects of nitrile hydratase enzymatic activity. Steered molecular dynamics simulations of Pseudonocardia thermophila JCM 3095
Chem. Phys. Lett.
467
144-149
2008
Pseudonocardia thermophila, Pseudonocardia thermophila JCM 3095
-
Hopmann, K.H.; Himo, F.
On the role of tyrosine as catalytic base in nitrile hydratase
Eur. J. Inorg. Chem.
2008
3452-3459
2008
Pseudonocardia thermophila, Rhodococcus erythropolis, Rhodococcus erythropolis N-771, Pseudonocardia thermophila JCM 3095
-
Yu, H.; Liu, J.; Shen, Z.
Modeling catalytic mechanism of nitrile hydratase by semi-empirical quantum mechanical calculation
J. Mol. Graph. Model.
27
522-528
2008
Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID2)
Liu, J.; Yu, H.; Shen, Z.
Insights into thermal stability of thermophilic nitrile hydratases by molecular dynamics simulation
J. Mol. Graph. Model.
27
529-535
2008
Bacillus sp. (in: Bacteria), Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID2), Bacillus sp. (in: Bacteria) SC-105-1
Zhang, Y.; Zeng, Z.; Zeng, G.; Liu, X.; Chen, M.; Liu, L.; Liu, Z.; Xie, G.
Enzyme-substrate binding landscapes in the process of nitrile biodegradation mediated by nitrile hydratase and amidase
Appl. Biochem. Biotechnol.
170
1614-1623
2013
Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID2), Rhodococcus erythropolis (P13448), Rhodococcus erythropolis AJ270 (P13448), Rhodococcus erythropolis AJ270
Miyanaga, A.; Fushinobu,S.; Ito, K.; Wakagi, T.
Crystal structure of cobalt-containing nitrile hydratase
Biochem. Biophys. Res. Commun.
288
1169-1174
2001
Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila (Q7SID3), Pseudonocardia thermophila JCM 3095 (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID3)
Cui, Y.; Cui, W.; Liu, Z.; Zhou, L.; Kobayashi, M.; Zhou, Z.
Improvement of stability of nitrile hydratase via protein fragment swapping
Biochem. Biophys. Res. Commun.
450
401-408
2014
Comamonas testosteroni (Q5XPL4), Comamonas testosteroni (Q5XPL5), Comamonas testosteroni 5-MGAM-4D (Q5XPL4), Comamonas testosteroni 5-MGAM-4D (Q5XPL5), Comamonas testosteroni 5-MGAM-4D, Pseudomonas putida, Pseudomonas putida NRRL-18668, Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila (Q7SID3), Pseudonocardia thermophila JCM 3095 (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID3)
Martinez, S.; Wu, R.; Sanishvili, R.; Liu, D.; Holz, R.
The active site sulfenic acid ligand in nitrile hydratases can function as a nucleophile
J. Am. Chem. Soc.
136
1186-1189
2014
Pseudonocardia thermophila (Q7SID2), Pseudonocardia thermophila (Q7SID3), Pseudonocardia thermophila JCM 3095 (Q7SID2), Pseudonocardia thermophila JCM 3095 (Q7SID3)
Chen, J.; Yu, H.; Liu, C.; Liu, J.; Shen, Z.
Improving stability of nitrile hydratase by bridging the salt-bridges in specific thermal-sensitive regions
J. Biotechnol.
164
354-362
2012
Rhodococcus ruber, Pseudonocardia thermophila, Bacillus sp. (in: Bacteria) (Q7SID2), Bacillus sp. (in: Bacteria) (Q7SID3), Rhodococcus ruber TH, Pseudonocardia thermophila JCM 3095, Bacillus sp. (in: Bacteria) SC-105-1 (Q7SID2), Bacillus sp. (in: Bacteria) SC-105-1 (Q7SID3)
Sun, W.; Zhu, L.; Chen, X.; Wu, L.; Zhou, Z.; Liu, Y.
The stability enhancement of nitrile hydratase from Bordetella petrii by swapping the C-terminal domain of beta subunit
Appl. Biochem. Biotechnol.
178
1481-1487
2016
Bordetella petrii (A9IEH0 AND A9IEH2), Bordetella petrii, Pseudonocardia thermophila (Q7SID3 AND Q7SID2), Bordetella petrii DSM 128043 (A9IEH0 AND A9IEH2)
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