Information on EC 1.7.2.5 - nitric oxide reductase (cytochrome c)

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea

EC NUMBER
COMMENTARY hide
1.7.2.5
-
RECOMMENDED NAME
GeneOntology No.
nitric oxide reductase (cytochrome c)
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
nitrous oxide + 2 ferricytochrome c + H2O = 2 nitric oxide + 2 ferrocytochrome c + 2 H+
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
oxidation
-
-
-
-
redox reaction
reduction
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
nitrate reduction I (denitrification)
-
-
nitrifier denitrification
-
-
denitrification
-
-
Nitrogen metabolism
-
-
Microbial metabolism in diverse environments
-
-
SYSTEMATIC NAME
IUBMB Comments
nitrous oxide:ferricytochrome-c oxidoreductase
The enzyme from Pseudomonas aeruginosa contains a dinuclear centre comprising a non-heme iron centre and heme b3, plus heme c, heme b and calcium; the acceptor is cytochrome c551
CAS REGISTRY NUMBER
COMMENTARY hide
37256-43-2
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
Agrobacterium tumefaciens C58 / ATCC 33970
-
-
-
Manually annotated by BRENDA team
strain ATCC12472
-
-
Manually annotated by BRENDA team
strain ATCC12472
-
-
Manually annotated by BRENDA team
Cupriavidus necator H16 / ATCC 23440 / NCIB 10442 / S-10-1
-
-
-
Manually annotated by BRENDA team
strain JCM2391, dependent on O2 supply
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Geobacter metallireducens GS-15 / ATCC 53774 / DSM 7210
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
Magnetococcus sp.
-
-
-
Manually annotated by BRENDA team
nitric oxide reductase subunit C
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
genes norC and norB encoding the two enzyme subunits
D5GU62 AND D5GU63
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
recombinant truncated NOR exhibits the same spectroscopic properties and reactivity to NO and O2 as wil-type NOR, although its enzymatic activity toward NO is considerably decreased
metabolism
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 nitric oxide + 2 ferrocytochrome c + 2 H+
nitrous oxide + 2 ferricytochrome c + H2O
show the reaction diagram
2 nitric oxide + reduced acceptor
nitrous oxide + acceptor + H2O
show the reaction diagram
N2O + acceptor + H2O
NO + reduced acceptor
show the reaction diagram
-
-
-
-
r
N2O + phenazine methosulfate + H2O
NO + reduced phenazine methosulfate
show the reaction diagram
nitric oxide + ferrocytochrome c552
nitrous oxide + ferricytochrome c552 + H2O
show the reaction diagram
-
-
-
-
?
nitric oxide + NAD(P)H + H+
nitrous oxide + NAD(P)+ + H2O
show the reaction diagram
cytochrome P450nor is a nitric oxide reductase involved in fungal denitrification
-
-
?
nitric oxide + NADH
nitrous oxide + NAD+ + H2O
show the reaction diagram
-
-
-
-
?
nitric oxide + NADH + H+
nitrous oxide + NAD+
show the reaction diagram
cytochrome P450nor is a nitric oxide reductase involved in fungal denitrification
-
-
?
nitric oxide + NADH + H+
nitrous oxide + NAD+ + H2O
show the reaction diagram
nitric oxide + oxidized acceptor + H+
nitrous oxide + reduced acceptor + H2O
show the reaction diagram
-
-
-
-
?
nitric oxide + reduced acceptor
nitrous oxide + oxidized acceptor + H2O
show the reaction diagram
nitric oxide + reduced ascorbate
nitrous oxide + oxidized ascorbate + H2O
show the reaction diagram
-
-
-
-
?
nitric oxide + reduced cytochrome c
nitrous oxide + cytochrome c + H2O
show the reaction diagram
nitric oxide + reduced N,N,N',N'-tetramethyl-p-phenylenediamine
nitrous oxide + oxidized N,N,N',N'-tetramethyl-p-phenylenediamine + H2O
show the reaction diagram
nitric oxide + reduced phenazine methosulfate
nitrous oxide + oxidized phenazine methosulfate + H2O
show the reaction diagram
nitric oxide + reduced pseudoazurin
nitrous oxide + oxidized pseudoazurin + H2O
show the reaction diagram
nitric oxide + reduced pseudoazurin
nitrous oxide + pseudoazurin + H2O
show the reaction diagram
-
-
-
-
?
nitrous oxide + 2 ferricytochrome c + H2O
2 nitric oxide + 2 ferrocytochrome c + 2 H+
show the reaction diagram
Q59647 AND Q59646
-
-
-
?
NO + 5-hydroxy-1,4-naphthoquinol
N2O + H2O + 5-hydroxy-1,4-naphthoquinone
show the reaction diagram
-
-
-
-
?
NO + 5-hydroxy-2-methyl-1,4-naphthoquinol
N2O + H2O + 5-hydroxy-2-methyl-1,4-naphthoquinone
show the reaction diagram
-
-
-
-
?
NO + menaquinol
N2O + H2O + menaquinone
show the reaction diagram
-
-
-
-
?
NO + NADH
N2O + H2O + NAD+
show the reaction diagram
NO + NADPH
N2O + H2O + NADP+
show the reaction diagram
NO + reduced acceptor
N2O + H2O + acceptor
show the reaction diagram
NO + reduced cytochrome c551
N2O + H2O + oxidized cytochrome c551
show the reaction diagram
-
-
-
-
?
O2 + reduced acceptor + H+
H2O + oxidized acceptor
show the reaction diagram
-
-
-
-
?
O2 + reduced cytochrome c
H2O + cytochrome c
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2 nitric oxide + 2 ferrocytochrome c + 2 H+
nitrous oxide + 2 ferricytochrome c + H2O
show the reaction diagram
2 nitric oxide + reduced acceptor
nitrous oxide + acceptor + H2O
show the reaction diagram
N2O + acceptor + H2O
NO + reduced acceptor
show the reaction diagram
-
-
-
-
r
nitric oxide + NAD(P)H + H+
nitrous oxide + NAD(P)+ + H2O
show the reaction diagram
Q96WS9
cytochrome P450nor is a nitric oxide reductase involved in fungal denitrification
-
-
?
nitric oxide + NADH + H+
nitrous oxide + NAD+
show the reaction diagram
P23295
cytochrome P450nor is a nitric oxide reductase involved in fungal denitrification
-
-
?
nitric oxide + NADH + H+
nitrous oxide + NAD+ + H2O
show the reaction diagram
nitric oxide + reduced pseudoazurin
nitrous oxide + pseudoazurin + H2O
show the reaction diagram
-
-
-
-
?
nitrous oxide + 2 ferricytochrome c + H2O
2 nitric oxide + 2 ferrocytochrome c + 2 H+
show the reaction diagram
Q59647 AND Q59646
-
-
-
?
NO + NADH
N2O + H2O + NAD+
show the reaction diagram
NO + NADPH
N2O + H2O + NADP+
show the reaction diagram
NO + reduced acceptor
N2O + H2O + acceptor
show the reaction diagram
additional information
?
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cytochrome
-
cytochrome c
NADPH
phenazine methosulfate
-
with NADH
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
copper
-
contains CuA in the small subunit
Cu2+
-
protein contains heme c, heme b, and copper in a 1:2:1 stoichiometry
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-heptyl-3-hydroxy-4-quinolone
-
i.e. Pseudomonas quinolone signal or PQS, a cell-to-cell communication signal, PQS represses denitrification in vivo and regulates denitrification primarily through iron chelation, PQS signaling under anaerobic conditions, detailed overview
Antimycin
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100% inhibition at 0.005 mg per mg vesicle protein, no inhibition with isoascorbate plus 2,3,5,6-tetramethyl-1,4-benzendiamine as electron donors
antimycin A
-
100% inhibition at 0.0075 mg per ml, no inhibition with ascorbate plus 2,3,5,6-tetramethyl-1,4-benzendiamine as electron donors
CN-
-
10 mM, 50% inhibition
cytochrome c
-
-
elaidic acid
-
-
linoleic acid
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-
linolenic acid
-
-
Myxothiazol
NH2OH
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at 5 mM 58% inhibition
NO2
-
1 mM, 20% inhibition of activity
o-phenanthroline
-
at 1 mM 60% inhibition
oleic acid
-
-
p-chloromercuribenzoate
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at 1 mM 85% inhibition
palmitoleic acid
-
-
Triton X-100
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
cardiolipin
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-
n-octyl-beta-D-glucopyranoside
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340% activity
n-octyl-beta-D-thioglucopyranoside
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340% activity
phosphatidylglycerol
-
-
Soybean phospholipids
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340% activity
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.14
5-hydroxy-1,4-naphthoquinone
-
-
0.26
5-hydroxy-2-methyl-1,4-naphthoquinol
-
-
0.22 - 0.8
NADH
0.32 - 0.93
NADPH
0.019
nitric oxide
-
in 50 mM MOPS, pH 7.0
0.00025 - 0.2
NO
0.002
phenazine methosulfate
-
-
0.027 - 0.035
pseudoazurin
-
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
12 - 40
nitric oxide
14.9 - 667
NO
0.88 - 70.38
pseudoazurin
-
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.005
cytochrome c
-
-
0.0235
elaidic acid
-
-
0.0125
linoleic acid
-
-
0.014
linolenic acid
-
-
0.0065
oleic acid
-
-
0.0098
palmitoleic acid
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0021
-
with ascorbate and 2,3,5,6-tetramethyl-1,4-benzoquinone as electron donors
0.0028
-
with ascorbate and 2,3,5,6-tetramethyl-1,4-benzoquinone as electron donors
0.0033
-
with ascorbate and 2,3,5,6-tetramethyl-1,4-benzoquinone as electron donors
0.004
-
with ascorbate and 2,3,5,6-tetramethyl-1,4-benzoquinone as electron donors
0.101
-
with reduced menadione as electron donor
0.16
-
with NADH and 2,3-dimethoxy-5-methyl-1,4-benzoquinone as electron donors
0.22
-
with N,N,N',N'-tetramethyl-1,4-benzendiamine and ascorbate as electron donors
0.78
-
with NADH and duroquinone as electron donors
1.53
-
with NADH as electron donor
2.27
-
with NADH and menadione as electron donors
2.79
-
with ascorbate and phenazine methosulfate as electron donors
7.3
-
last purification step
25.8
-
with ascorbate, phenazine methosulfate and cytochrome c as electron donors
60
-
ascorbate and phenazine methosulfate as electron donors
245
-
with NADPH as electron donor
295
-
with NADH as electron donor
additional information
-
NO reductase activity is measured under anaerobic conditions using a NO-selective Clark-type electrode. Spectroscopic measurements using a stopped-flow thermostated instrument
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.2
-
membrane-bound activity
6
-
in 20 mM bis-Tris propane buffer 8-fold more activity than at pH 8.5
7.7
D5GU62 AND D5GU63
assay at
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.8 - 6
-
at pH 6.0 half of the activity of pH 4.8
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
42 - 60
D5GU62 AND D5GU63
assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
additional information
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
NorB is themembrane-spanning subunit
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Neisseria meningitidis (strain alpha14)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Pseudomonas aeruginosa (strain ATCC 15692 / DSM 22644 / CIP 104116 / JCM 14847 / LMG 12228 / 1C / PRS 101 / PAO1)
Roseobacter denitrificans (strain ATCC 33942 / OCh 114)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
15000
-
1 * 34000 + 1 * 15000, SDS-PAGE
18000
-
composed of two subunits with molecular weights on SDS-PAGE of 1 * 37000 and 1 * 18000
20000
-
1 * 20000 + 1 * 42000, SDS-PAGE
34000
-
1 * 34000 + 1 * 15000, SDS-PAGE
42000
-
1 * 20000 + 1 * 42000, SDS-PAGE
45689
-
x * 45689, deduced from nucleotide sequence
46000
-
1 * 46000
49000
-
calculated, large subunit
54400
-
subunit NorB, calculated from amino acid sequence
56000
-
1 * 56000 + 1 * 17000
69500
-
DNA sequence
71800
-
NOR enzyme complex, calculated from amino acid sequence
75000
-
SDS-PAGE
84500
-
amino acid composition
90160
-
calculated from amino acid sequence
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
heterodimer
homodimer
-
2 * 45000, SDS-PAGE
monomer
additional information
Q59647 AND Q59646
structure analysis of Pseudomonas aeruginosa cNOR shows that three conserved glutamate residues locate at the close proximity to the active site and forms a small hydrophilic cavity
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
lipoprotein
-
contains cardiolipin, phosphatidylglycerol and phosphatidylethanolamine
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
at cryogenic temperature -173°C wild-type, S286V- and S286T-mutant
-
in the ferric resting and in the ferrous carbonmonoxy states, at 1.0 and 1.05 A resolution, respectively
-
sitting drop vapour diffusion, crystals diffract to less than 2.0 A
-
in complex with variable heavy chain domain of camel heavy chain antibody, sitting drop vapor diffusion method, using 100 mM potassium phosphate pH 7.0, 0.01% (v/v) phenyl ethanol, 0.005% (v/v) n-dodecyl-beta-D-maltopyranoside
-
oxidized S-NOR at 3 A resolution, reduced S-NOR at 2.8 A resolution, NO-reacted S-NOR at 2.8 A resolution
-
all-atom molecular dynamics simulations within an explicit membrane/solvent environment reveal two possible proton transfer pathways leading from the periplasm to the active site, while no pathways from the cytoplasmic side are found, consistently with the experimental observations that the enzyme is not a proton pump. One of the pathways is blocked in the crystal structure and requires small structural rearrangements to allow for water channel formation. That pathway is equivalent to the functional periplasmic cavity postulated in cbb3 oxidase
crystal structure analysis, PDB ID 3O0R
Q59647 AND Q59646
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5
-
inactivation after 1 h at room temperature
395132
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
0.8% octyl glucoside is needed for solubilzation
-
a phospholipid is required for high catalytic activity
-
active under aerobic conditions
-
after one cycle of freezing to -20°C and thawing stable, after more cycles activity is lost
-
solubilized in dodecyl maltoside
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, stable
-
-20°C, stable for 2 months
-
17°C, 0.1% laurylpropanediol-3-phosphorylcholine ether or 0.1% dodecylmaltoside, 8 days, 100% activity
-
17°C, Triton X-100, 2 days, 100% activity
-
4°C, 2 d, 50% activity, the inclusion of 0.01% 2-phenylethanol, 1 mM benzamidine and 100 nM pepstatin stabilizes
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate, Resource Q, Resource PHE, Superdex 200
-
DEAE column chromatography and hydroxyapatite column chromatography
-
DEAE-Sepharose CL-6B anion-exchange chromatography, Sephacryl S-300 gel filtration, and Mono Q anion-exchange chromatography. Enzyme is solubilized with sucrose monodecanoate from the membranes of Roseobacter denitrificans grown aerobically under light conditions, and purified to electrophoretic homogeneity
-
Q-Sepharose anion exchange chromatography
-
Q-Sepharose column chromatography and HiTrap chelating Sepharose column chromatography
-
recombinant enzyme from Escherichia coli by solubilization with 1% w/v n-dodecyl-beta-D-maltoside, ultracentrifugation, and anion exchange chromatography
recombinant FlRd
-
recombinant His-tagged NorH, wild-type cNOR, and mutant cNOR lacking norH by nickel affinity chromatography from Escherichia coli
D5GU62 AND D5GU63
recombinant wild-type and mutant NorC subunits from Escherichia coli strain BL21(DE3) by anion exchange chromatography, gel filtration, and again ion exchange chromatography
T7 tag affinity chromatography and Superdex75 gel filtration
-
using detergent lauryl maltoside
-
water-soluble NorC domain expressed in Escherichia coli
-
with n-dodecyl-beta-D-maltoside
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cycA-promoter induced aerobic expression of the protein dimer in Paracoccus denitrificans, expression in Escherichia coli
-
expressed in Escherichia coli
expressed in Escherichia coli JM109 cells
-
expressed in the soluble fraction of Escherichia coli JM109, modified N-terminus, 92% activity of wild-type
-
expression in Escherichia coli
gene norB and norC, recombinant expression in Escherichia coli strain JM109
gene norC, recombinant expression of wild-type and mutant NorC subunits in Escherichia coli strain BL21(DE3)
genes norC and norB encoding the two enzyme subunits of enzyme cNor, and gene norH, a third gene enclosed into the gene cluster that is cotranscribed in a single mRNA from an inducible promoter. NorH constitutes a third subunit of the cNor, recombinant expression of His-tagged isolated NorH, of His-tagged wild-type enzyme cNOR, and of His-tagged NorH-deficient cNOR in Escherichia coli
D5GU62 AND D5GU63
overexpression in Aspergillus oryzae
-
the water-soluble domain of NorC, cytochrome c type, expressed in Escherichia coli
-
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
induction of norB gene expression occurs in the presence of exogenously added NO, Fur regulates norB by a novel indirect activation method by preventing the binding of a gonococcal ArsR homologue
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
A239K
-
6% activity of modified soluble wild-type enzyme
A242K
-
42% activity of modified soluble wild-type enzyme
G240K
-
63% activity of modified soluble wild-type enzyme
M244K
-
60% activity of modified soluble wild-type enzyme
M247K
-
130% activity of modified soluble wild-type enzyme
N241K
-
38% activity of modified soluble wild-type enzyme
N246K
-
45% activity of modified soluble wild-type enzyme
S286T
-
7% activity of wild-type
S286V
-
1% activity of wild-type
T243H
-
8% activity of modified soluble wild-type enzyme
T243K
-
12% activity of modified soluble wild-type enzyme
T243R
-
17% activity of modified soluble wild-type enzyme
H25F
-
3% of wild-type kcat
H25F/Y195F
-
strong decrease in NOR activity
Y195F
-
15% of wild-type kcat
D185A
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
D185E
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
D185N
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
E122A
-
substitution leads to an almost complete loss of NOR activity
E122D
-
substitution mutant retains 83.2% of the activity of the wild-type enzyme
E122Q
-
substitution mutant retains 1.3% of the activity of the wild-type enzyme
E125A
-
substitution leads to an almost complete loss of NOR activity
E125D
-
substitution leads to an almost complete loss of NOR activity
E125Q
-
substitution mutant retains 13.4% of the activity of the wild-type enzyme
E58Q
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
E78F
site-directed mutagenesis, the mutant does not express
K54A
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
N47F
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
N47L
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
Q394M
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
Q398L
site-directed mutagenesis, mutation of a conserved residue involved in the proton transfer, kinetics compared to the wild-type
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
environmental protection
Show AA Sequence (802 entries)
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