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Enzyme Nomenclature
Information on EC 1.3.1.14 - dihydroorotate dehydrogenase (NAD+)
Word Map on EC 1.3.1.14
- 1.3.1.14
- pyrimidine
- flavin
- lactis
- medicine
- l-dihydroorotate
- brequinar
-
lactococcus
- pharmacology
- fmn
-
enterococcus
- nutrition
- faecalis
- ubiquinone
- berghei
-
carbamyl
-
1.3.3.1
-
half-reaction
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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota
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EC NUMBER 
COMMENTARY 
1.3.1.14
-
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RECOMMENDED NAME
GeneOntology No.
dihydroorotate dehydrogenase (NAD+)
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
trans-dehydrogenation mechanism
-
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
ping-pong steady-state kinetic mechanism
-
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
ping-pong steady-state kinetic mechanism
-
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
electron transfer mechanism
-
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
PyrDI contains the dihydroorotate-binding site, but PyrDII is required for full activity in vivo. Holoenzyme joins a NAD+-reductase activity
-
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
detailed thermodynamic analysis, midpoint reduction potential of 2Fe-2S center -212 mV, midpoint reduction potential of FMN -298 mV
-
(S)-dihydroorotate + NAD+ = orotate + NADH + H+
-
-
-
-
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
dehydrogenation
-
-
-
-
oxidation
-
-
-
-
redox reaction
-
-
-
-
reduction
-
-
-
-
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
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SYSTEMATIC NAME
IUBMB Comments
(S)-dihydroorotate:NAD+ oxidoreductase
Binds FMN, FAD and a [2Fe-2S] cluster. The enzyme consists of two subunits, an FMN binding catalytic subunit and a FAD and iron-sulfur binding electron transfer subunit [4]. The reaction, which takes place in the cytosol, is the only redox reaction in the de-novo biosynthesis of pyrimidine nucleotides. Other class 1 dihydroorotate dehydrogenases use either fumarate (EC 1.3.98.1) or NADP+ (EC 1.3.1.15) as electron acceptor. The membrane bound class 2 dihydroorotate dehydrogenase (EC 1.3.5.2) uses quinone as electron acceptor.
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CAS REGISTRY NUMBER
COMMENTARY
37255-26-8
-
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ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
subunit PyrDb; bifunctional orotate reductase and H2O2-forming NADH oxidase
UniProt
family IB enzyme, also contains family IA enzyme, milk fermenting bacterium
-
-
family IB enzyme, also contains family IA enzyme; milk-fermenting bacterium
-
-
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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
(S)-dihydroorotate + 2,6-dichlorophenolindophenol
orotate + reduced 2,6-dichlorophenolindophenol
-
-
-
?
5-fluorodihydroorotate + NAD+
5-fluoroorotate + NADH + H+
-
more active substrate for reverse reaction than orotate
-
-
r
(S)-dihydroorotate + acceptor
orotate + reduced acceptor
-
different specific activities with potassium ferricyanide, O2, fumarate and NAD+ as electron acceptors for PyrDI and the holoenzyme
-
?
(S)-dihydroorotate + acceptor
orotate + reduced acceptor
-
fourth step in UMP-biosynthesis
-
?
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
-
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
?
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
anti-elimination of hydrogen from (S)-dihydroorotate
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
equilibrium favours direction of orotate reduction
-
?
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
equilibrium favours direction of orotate reduction
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
equilibrium favours direction of orotate reduction
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
equilibrium favours direction of orotate reduction
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
equilibrium favours direction of orotate reduction
orotate is identical with 4-carboxyuracil
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
?, r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
substrate is oxidized by NAD+ and oxygen
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
substrate is oxidized by NAD+ and oxygen
lipoic acid is no substitute for orotate
?
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
-
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
?
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
mechanism and pH-dependence of reaction
-
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
mechanism of dehydrogenation, mechanism of electron transfer: L-dihydroorotate transfers a pair of electrons to FMN via iron-sulfur cluster via FAD to NAD+
-
?, r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
mechanism of dehydrogenation, mechanism of electron transfer: L-dihydroorotate transfers a pair of electrons to FMN via iron-sulfur cluster via FAD to NAD+
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
?, r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
NAD+ as ultimate electron acceptor
-
r
(S)-dihydroorotate + NAD+
orotate + NADH + H+
-
at higher pH values reaction favours direction of dihydroorotate oxidation, whereas at lower pH values direction of orotate reduction is favoured
-
r
dihydroorotate + acceptor
orotate + reduced acceptor
-
acceptor: NAD+
-
-
?
dihydroorotate + acceptor
orotate + reduced acceptor
-
acceptor: menadione
-
-
?
dihydroorotate + acceptor
orotate + reduced acceptor
acceptor: NAD+ for pyrDa gene product, fumarate for pyrDb gene product
-
-
-
dihydroorotate + acceptor
orotate + reduced acceptor
-
activity measurement in permeabilized Ehrlich ascites tumor cells, acceptor: nitroblue tetrazolium
-
-
?
dihydroorotate + NAD+
orotate + NADH + H+
-
-
breakdown of orotate
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
biosynthesis of pyrimidines
-
?
dihydroorotate + NAD+
orotate + NADH + H+
-
enzyme presumably functions mainly in the metabolic synthesis of pyrimidines
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
additional information
?
-
-
not: uracil, cytosine, 5-methylcytosine, thymine as substrates
-
-
-
additional information
?
-
-
not: uracil, cytosine, 5-methylcytosine, thymine as substrates
-
-
-
additional information
?
-
-
3-acetylpyridine-NAD+ is a more effective oxidant for dihydroorotate than NAD+, methylene blue can serve as oxidant, but not cytochrome c
-
-
-
additional information
?
-
-
NAD+ binding domain in the beta subunit of enzyme, Cys-135 plays a catalytic role and Lys-48 is important for orienting the substrate in the active site and is able to interact with FMN
-
-
-
additional information
?
-
O2, fumarate, and NADP+ do not serve as electron acceptors
-
-
-
additional information
?
-
-
O2, fumarate, and NADP+ do not serve as electron acceptors
-
-
-
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NATURAL SUBSTRATES
NATURAL PRODUCTS
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
(S)-dihydroorotate + acceptor
orotate + reduced acceptor
-
fourth step in UMP-biosynthesis
-
?
dihydroorotate + NAD+
orotate + NADH + H+
-
-
breakdown of orotate
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
biosynthesis of pyrimidines
-
?
dihydroorotate + NAD+
orotate + NADH + H+
-
enzyme presumably functions mainly in the metabolic synthesis of pyrimidines
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
dihydroorotate + NAD+
orotate + NADH + H+
-
fourth step and sole redox reaction in the pyrimidine de novo biosynthetic pathway
-
r
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COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
4Fe-4S-center
-
cofactor content: 4 non-heme iron and 4 labile sulfur atoms per heterotetramer
4Fe-4S-center
-
cofactor content: 4 non-heme iron and 4 labile sulfur atoms per heterotetramer
4Fe-4S-center
-
cofactor content: 4 non-heme iron and 4 labile sulfur atoms per heterotetramer
4Fe-4S-center
-
cofactor content: 4 non-heme iron and 4 labile sulfur atoms per heterotetramer; iron-sulfur cluster resides on the beta subunit
4Fe-4S-center
-
two [2Fe-2S] clusters as cofactors, tightly bound to the beta subunit and located in the interface of the two dimers centered between the FMN and FAD group, Cys-226, Cys-231, Cys-234 and Cys-249 binds the iron-sulfur cluster
FAD
-
flavoprotein, ratio FAD to FMN 1:1; one molecule FAD and one molecule FMN per enzyme molecule
FAD
-
flavoprotein, ratio FAD to FMN 1:1; two molecules FAD per heterotetramer
FAD
-
FAD is located on the beta subunit; two molecules FAD per heterotetramer
FAD
-
FAD is located on the beta subunit; two tightly bound FAD per heterotetrameric enzyme, FAD is necessary for ability to use NAD+ as electron acceptor, detailed way of binding
FAD
-
1 mol/mol of subunit PyrDII; 1 mol PyrDII binds 1 mol FAD and 1 mol [2Fe-2S]
flavin
-
flavoprotein with two different flavins, probably FAD and FMN; interaction of flavin and dihydroorotate is completely dependent on cysteine
flavin
-
flavin coenzyme; flavoprotein with two different flavins, probably FAD and FMN
flavin
-
flavoprotein with two different flavins, probably FAD and FMN; NAD+-linked flavoprotein
flavin
-
1 mol of flavin per 31 g of protein; flavoprotein with two different flavins, probably FAD and FMN
flavin
-
flavoprotein with two different flavins, probably FAD and FMN; metalloflavoprotein
FMN
-
flavoprotein, ratio FAD to FMN 1:1; one molecule FAD and one molecule FMN per enzyme molecule
FMN
-
flavoprotein, ratio FAD to FMN 1:1; two molecules of FMN per heterotetramer
FMN
-
FMN is located on the alpha subunit; two molecules of FMN per heterotetramer
FMN
-
FMN is located on the alpha subunit; two tightly bound FMN per heterotetrameric enzyme, detailed way of binding
FMN
-
PyrDI is an FMN-containing iron-sulfur flavoprotein, 1 FMN molecule per PyrDI molecule
FMN
-
key charge-stabilizing role for Lys-48 of subunit D during reduction of FMN by dihydroorotate or by electron transfer from the 2Fe-2S center
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INHIBITORS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
(S,S)-N-(1-carboxyethyl)-N'-(1-carboxy-2-phenylethyl)urea
-
4 mM, 20% inhibition
5-Benzyl-3-(1-carboxy-2-phenylethyl)hydantoin
-
time-dependent irreversible inhibition at the active site, mechanism
Hg2+
complete inhibition of both orotate reductase and NADH oxidase reaction
hydantoin
-
derived from alpha-amino acids, weak competitive inhibitors, compounds with a benzyl goup are better inhibitors
p-chloromercuribenzoate
complete inhibition of both orotate reductase and NADH oxidase reaction
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
-
not activated by L-serine or L-alanine; thiol activation involves reduction of side chain of a cysteine residue corresponding to Cys-130, which functions as a general base
-
cysteine
-
essential for assay, interaction of enzyme with orotate or dihydroorotate is dependent on cysteine, whereas NADH oxidase activity is not
cysteine
-
reaction rate increases 2fold in the presence of 2-7 mM cysteine
cysteine
-
essential for assay, interaction of enzyme with orotate or dihydroorotate is dependent on cysteine, whereas NADH oxidase activity is not; required for activation of purified enzyme, but not if crude extract is used for assay
cysteine
-
L-cysteine activates strongly, D-cysteine is also an activator, 1.8 mM L-cysteine is required at pH 8 for half-maximal activity, 10 mM for near-maximal activity
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
22
L-dihydroorotate
Clostridium oroticum
-
formation of orotate, in absence of NAD+ or NADH, pH 8, 10 mM cysteine
3.97
Orotate
Clostridium oroticum
-
formation of L-dihydroorotate, in absence of NAD+ or NADH, pH 8, 10 mM cysteine
additional information
additional information
Clostridium oroticum
-
values not per enzyme molecule, but per mol of flavin
-
additional information
additional information
Clostridium oroticum
-
values not per enzyme molecule, but per mol of flavin
-
additional information
additional information
Clostridium oroticum
-
values not per enzyme molecule, but per mol of flavin
-
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Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.06
native wild type enzyme, using 2,6-dichlorophenolindophenol as acceptor, at 30°C
5.9
recombinant wild type enzyme, using 2,6-dichlorophenolindophenol as acceptor, at 37°C
additional information
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pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
6.5
7.5
and 6.5, NADH oxidase reaction and dihydrorotate oxidase reaction
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
5.5 - 7.8
-
pH 5.5: 13% of the activity at pH 6.5; pH 7.8: 65% of the activity at pH 6.5
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
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PDB
SCOP
CATH
ORGANISM
UNIPROT
Lactococcus lactis subsp. cremoris (strain MG1363)
Lactococcus lactis subsp. cremoris (strain MG1363)
Lactococcus lactis subsp. cremoris (strain MG1363)
Lactococcus lactis subsp. lactis (strain IL1403)
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MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
28000
28099
-
heterotetramer 2 * 33094 and 2 * 28099 predicted from seqeuence, 2 * 38000 and 2 * 31000, SDS-PAGE
31000
-
heterotetramer 2 * 33094 and 2 * 28099 predicted from seqeuence, 2 * 38000 and 2 * 31000, SDS-PAGE
33000
33094
-
heterotetramer 2 * 33094 and 2 * 28099 predicted from seqeuence, 2 * 38000 and 2 * 31000, SDS-PAGE
38000
-
heterotetramer 2 * 33094 and 2 * 28099 predicted from seqeuence, 2 * 38000 and 2 * 31000, SDS-PAGE
114000
-
gel filtration; molecular mass of the holoenzyme, calculated mass 122400 Da
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SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
heterotetramer
tetramer
heterotetramer
-
alpha2,beta2; alpha subunit is named PyrDB, beta subunit is named PyrK
heterotetramer
-
alpha2,beta2, family IB enzyme; alpha subunit is named PyrDB, beta subunit is named PyrK
heterotetramer
-
alpha2,beta2, alpha subunit with 331 amino acid residues, beta subunit with 262 amino acid residues, two closely interacting PyrDB-PyrK dimers; alpha subunit is named PyrDB, beta subunit is named PyrK
tetramer
-
2 * 33000 + 2 * 28000; heterotetramer 2 * 33094 and 2 * 28099 predicted from seqeuence, 2 * 38000 and 2 * 31000, SDS-PAGE
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Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-18°C, prepared enzyme, that is a yellow powder, several weeks, stable
-
-20°C, 0.27 M sodium phosphate, pH 6.3, over 6 months, less than 15% loss of activity
-
on ice at room temperature, PyrDI, gradually loses activity over a period of hours
-
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
; expression in Escherichia coliBL21 DE3, expression of pyrDI alone and coexpression with pyrDII
-
genes encoding the two alpha and beta polypeptides, expression in Escherichia coli
genes encoding the two alpha and beta polypeptides, expression in Escherichia coli
-
genes encoding the two alpha and beta polypeptides, expression in Escherichia coli
-
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
K48A
-
KM-value for dihydroorotate is 2.2fold higher than wild-type value, kcat is 411fold lower than wild-type value
K48E
-
KM-value for dihydroorotate is 4.1fold higher than wild-type value, kcat is 67.5fold lower than wild-type value
K48Q
-
KM-value for dihydroorotate is 1.5fold higher than wild-type value, kcat is 448fold lower than wild-type value
K48R
-
KM-value for dihydroorotate is 2fold lower than wild-type value, kcat is 117fold lower than wild-type value
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Renatured/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
activity can be recovered by mixing the purified subunits; PyrDII-containing inclusion bodies are denatured and refolded through dialysis into buffer
-
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APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
medicine
nutrition
pharmacology
-
drug design based upon selective enzyme inhibition
medicine
-
enzyme is a part of the pyrimidine biosynthesis pathway and plays a role as target for the chemotherapy of parasitic and neoplastic diseases
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LINKS TO OTHER DATABASES (specific for EC-Number 1.3.1.14)
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