Information on EC 4.1.1.18 - lysine decarboxylase

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

EC NUMBER
COMMENTARY hide
4.1.1.18
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RECOMMENDED NAME
GeneOntology No.
lysine decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
L-lysine = cadaverine + CO2
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decarboxylation
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PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
aminopropylcadaverine biosynthesis
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Biosynthesis of secondary metabolites
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bisucaberin biosynthesis
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desferrioxamine B biosynthesis
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desferrioxamine E biosynthesis
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L-lysine degradation I
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L-lysine degradation X
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lupanine biosynthesis
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Lysine degradation
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Metabolic pathways
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Tropane, piperidine and pyridine alkaloid biosynthesis
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lysine metabolism
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SYSTEMATIC NAME
IUBMB Comments
L-lysine carboxy-lyase (cadaverine-forming)
A pyridoxal-phosphate protein. Also acts on 5-hydroxy-L-lysine.
CAS REGISTRY NUMBER
COMMENTARY hide
9024-76-4
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
Bacterium cadaveris
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Manually annotated by BRENDA team
wild indigo
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Manually annotated by BRENDA team
bifunctional L-lysine oxidase/decarboxylase
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Manually annotated by BRENDA team
bifunctional L-lysine oxidase/decarboxylase
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
Cytisus beanii
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Manually annotated by BRENDA team
Cytisus canariensis
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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-
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
all of the detectable lysine decarboxylase activity is due to the action of ornithine decarboxylase
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
no activity in Loktanella hongkongensis
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Manually annotated by BRENDA team
no activity in Marinovum algicola
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Manually annotated by BRENDA team
no activity in Marinovum algicola ATCC 51442
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Manually annotated by BRENDA team
no activity in Phaeobacter gallaeciensis BS107
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Manually annotated by BRENDA team
no activity in Rattus norvegicus
all of the detectable lysine decarboxylase activity is due to the action of ornithine decarboxylase
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Manually annotated by BRENDA team
no activity in Thalassobius mediterraneus
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Manually annotated by BRENDA team
no activity in Thalassobius mediterraneus XSM19
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Manually annotated by BRENDA team
no activity in Thalassococcus halodurans
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Manually annotated by BRENDA team
no activity in Thalassococcus halodurans UST050418-052
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
winter triticale, cultivars Witon and Tornado
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
Senecio fuchsii
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
JC2049
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Manually annotated by BRENDA team
strain HB8, isozymes TT1887, TT1465
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
strain AQ 3627
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Manually annotated by BRENDA team
gene cadA
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
delta-Hydroxylysine
1,5-Diamino-2-hydroxypentane + CO2
show the reaction diagram
L-2,4-diaminobutanoate
1,3-diaminopropane + CO2
show the reaction diagram
L-Lys
?
show the reaction diagram
L-Lys
Cadaverine + CO2
show the reaction diagram
L-lysine
1,5-diaminopentane + CO2
show the reaction diagram
L-lysine
cadaverine + CO2
show the reaction diagram
L-Orn
Putrescine + CO2
show the reaction diagram
L-ornithine
1,4-diaminobutane + CO2
show the reaction diagram
S-Aminoethyl-L-Cys
1-Amino-2-(S-aminoethyl)mercaptoethane + CO2
show the reaction diagram
additional information
?
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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
L-Lys
?
show the reaction diagram
L-Lys
Cadaverine + CO2
show the reaction diagram
L-lysine
cadaverine + CO2
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
1,5-pentanediamine
Bacterium cadaveris
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6-aminohexanoate
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alpha-difluoromethyl-lysine
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LCD suicide inhibitor, 74% inhibition at 1 mM
alpha-Difluoromethylcadaverine
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alpha-Monofluoromethylcadaverine
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alpha-Trifluoromethylcadaverine
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alpha-Vinyllysine
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Br-
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CaCl2
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cadaverine
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Cl-
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diethyldithiocarbamic acid
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DL-alpha-Difluoromethyllysine
DL-alpha-difluoromethylornithine
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competitive and irreversible
FeCl2
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H2PO4-
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HgCl2
Bacterium cadaveris
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HPO42-
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hydroxylamine
Bacterium cadaveris
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iodoacetamide
Bacterium cadaveris
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KCl
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L-Arg
Bacterium cadaveris
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LiCl
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MnCl2
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PCMB
Bacterium cadaveris
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inhibition is eliminated by addition of 2-mercaptoethanol or glutathione, and pyridoxal 5'-phosphate
ppGpp
pppGpp
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inhibits LdcI only at pH values higher than 6.5
Semicarbazide
Bacterium cadaveris
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SO42-
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additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
sulfhydryl groups
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the enzyme contains six sulfhydryl groups
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7
delta-hydroxylysine
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1.3
L-2,4-diaminobutanoate
pH 7.5, 30C
0.37 - 270
L-Lys
0.058 - 12.7
L-lysine
0.96 - 4.5
L-Orn
3.4 - 4.5
S-aminoethyl-L-Cys
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.052
L-2,4-diaminobutanoate
Streptomyces coelicolor
Q9L072
pH 7.5, 30C
2.6 - 636
L-Lys
1.68 - 30
L-lysine
3 - 289.8
L-Orn
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
40
L-2,4-diaminobutanoate
Streptomyces coelicolor
Q9L072
pH 7.5, 30C
2561
0.13 - 690
L-lysine
134
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0175 - 0.028
DL-alpha-Difluoromethyllysine
0.00525 - 0.0082
DL-alpha-difluoromethylornithine
0.0002377 - 0.002791
ppGpp
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
600
L-Arg
Bacterium cadaveris
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at 37C, pH not specified in the publication
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
17.8
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85.7
Bacterium cadaveris
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-
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 7.5
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assay at, transcription of cadBA in a pH-dependent manner, overview
5.8
Bacterium cadaveris
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6.2 - 8
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7.5
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additional information
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5 - 8
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pH 4.5: about 30% of maximal activity, pH 8: about 35% of maximal activity
4.5 - 7
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pH 4.5: about 35% of maximal activity, pH 7.0: about 60% of maximal activity
4.7 - 6.6
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50% of maximal activity at pH 4.7 and 6.6
5.2 - 8.8
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pH 5.2: 40% of maximal activity, pH 8.8: 30% of maximal activity
7 - 8
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pH 7.0: about 70% of maximal activity, pH 9.0: about 25% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
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assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 80
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20C: about 25% of maximal activity, 80C: about 95% of maximal activity
30 - 41
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30C: 38% of maximal activity, 37C: 71% of maximal activity, 41C: optimum
40 - 70
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40C: about 40% of maximal activity, 70C: about 90% of maximal activity
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
4.5
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isoelectric focusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
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Manually annotated by BRENDA team
additional information
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no appreciable activity is detected in cotyledons and shoots
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
42000
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2 * 42000, SDS-PAGE
44000
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2 * 44000, SDS-PAGE
76500
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2 * 76500, SDS-PAGE
79000
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7 * 79000, SDS-PAGE
81000
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10 * 81000, X-ray crystallography
82000
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SDS-PAGE
85000
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x * 85000, SDS-PAGE
88000
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gel filtration
95000
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gel filtration
150000
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gel filtration
154000
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dimeric enzyme form, sedimentation data
422000
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pentameric enzyme form, native PAGE
531000
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gel filtration
545000
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heptameric enzyme form, gel filtration
730000
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decameric enzyme form, sedimentation data
761000
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decameric enzyme form, analytical ultracentrifugation at 6800 rpm
795700
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decameric enzyme form, analytical ultracentrifugation at 3600 rpm
800000
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gel filtration
1000000
Bacterium cadaveris
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equilibrium sedimentation
1174000
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pentadecameric enzyme form, analytical ultracentrifugation at 2600 rpm
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
decamer
heptamer
hexamer
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isozyme TT1465, crystallization data
homodecamer
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10 * 81000, X-ray crystallography
monomer
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1 * 95000, SDS-PAGE
tetramer
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isozyme TT1887, crystallization data
additional information
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enzyme interacts strongly with regulatory ATPase variant A, RavA, forming a cage-like structure consisting of two enzyme decamers linked by up to five RavA oligomers. Enzyme activity is not affected by binding to RavA, but complex formation results in stimulation of RavA ATPase activity
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cage-like complex of about 3.3 MDa consisting of two LdcI (81 kDa) decamers and up to five RavA (56 kDa) hexamers, hanging drop vapor diffusion method, using
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hanging drop vapour diffusion method, with 18-28% (w/v) PEG 1000, 100 mM NaCl, 100 mM Tris-HCl pH 8.5, 15% (v/v) glycerol, 5 mM tris(2-carboxyethyl)phospine hydrochloride
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both isozymes TT1465 and TT1887
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pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5.3
Bacterium cadaveris
-
crystalline enzyme is stable
37294
5.5 - 8
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stable
654982
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
35
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30 min, 50% loss of activity without pyridoxal-5'-phosphate
65
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no activity detected after 10 min
80
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pH 5.5, 10 min, 35% loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
calcium alginate can completely entrap the enzyme while retaining activity and improving stability during operation and storage
Bacterium cadaveris
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dithiothreitol is required for stabilization during purification and storage
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pyridoxal 5'-phosphate is indispensable for stability
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, crude extract, stable for months
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-80C, stable for one month in presence of 20% glycerol, loss of activity within 2 weeks without glycerol
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0-4C,50% loss of activity within 24 h
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4C, 0.01 M potassium phosphate buffer, pH 6.2, 0.01 mM pyridoxal 5'-phosphate, stable for several weeks
Bacterium cadaveris
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
enzyme form ldc
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Mono Q column chromatography and Superdex 200 gel filtration
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Corynebacterium glutamicum ATCC 13032
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expressed in Escherichia coli BL21 (DE3) pLysS cells
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expression in Escherichia coli
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gene cadA from strain V02-64, DNA and amino acid sequence, and gene cluster and intergenic region determination and analysis, subcloning in Escherichia coli, quantitative analysis of lysine decarboxylase expression levels dependent on acid conditions at pH 4.0-7.5, primer extension analysis, the gene encoding the enzyme is located in an acid-induced operon, overview, cadA mRNA exhibited about 40fold greater expression at pH 5.0 than at pH 5.5, in cells exposed to pH 7.5, the cadA transcript shows the largest quantity under all conditions, the amount of cadA single transcript is nearly 100fold higher than the polycistronic cadBA transcript for each pH condition
gene cadA, encoded in the cadBA operon, also coding for a lysine-cadaverine antiporter, CadB, expression of cadA in Escherichia coli strain S17-1 and S17-1lambdapir, transcription of cadBA in a pH-dependent manner, overview
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EXPRESSION
ORGANISM
UNIPROT
LITERATURE
cadA (encoding the lysine decarboxylase) shows higher relative expression level in acid adapted cells than non-acid adapted cells
the Sitobion avenae feeding on triticale cultivar Tornado causes a decrease in the LCD activity with exception of root tissue after two weeks of feeding. In case of cultivar Witon reduction of LCD activity is observed only durig initial period of Sitobion avenae feeding
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
L89R
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the mutant elutes at the expected position for an LdcI dimer (about 150000 Da), the mutant shows about 5fold lower level of activity than wild type and this activity is not inhibited by ppGpp
R206S
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the ppGpp-binding site mutant shows wild type oligomerisation profile, the mutant is insensitive to the addition of ppGpp and has activity comparable to wild type LdcI in the absence of ppGpp
R97A
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the ppGpp-binding site mutant shows wild type oligomerisation profile, the mutant is insensitive to the addition of ppGpp and has activity comparable to wild type LdcI in the absence of ppGpp
A44V/G45T/V46P
A44V/G45T/V46P/P54D
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the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 3.8, compared to 0.83 for the wild-type enzyme
A44V/G45T/V46P/P54D/S322A
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the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 58, compared to 0.83 for the wild-type enzyme
A44V/G45T/V46P/P54D/S322T/I326L
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the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 13, compared to 0.83 for the wild-type enzyme
A52C/P54D
A52C/P54D/T55S
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the ratio of activity with L-Orn to activity with L-Lys is 2.7, compared to 0.69 for the wild-type enzyme
G319W
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the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 3.9, compared to 0.83 for the wild-type enzyme
M50V
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the ratio of activity with L-Orn to activity with L-Lys is 0.64, compared to 0.69 for the wild-type enzyme
M50V/A52C
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the ratio of activity with L-Orn to activity with L-Lys is 1.9, compared to 0.69 for the wild-type enzyme
M50V/A52C/P54D
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the ratio of activity with L-Orn to activity with L-Lys is 2.4, compared to 0.69 for the wild-type enzyme
M50V/A52C/P54D/T55S
P54D/T55S
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the ratio of activity with L-Orn to activity with L-Lys is 1.8, compared to 0.69 for the wild-type enzyme
S322A
-
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 24, compared to 0.83 for the wild-type enzyme
S322T/I326L
-
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 13, compared to 0.83 for the wild-type enzyme
T55S
-
the ratio of activity with L-Orn to activity with L-Lys is 0.66, compared to 0.69 for the wild-type enzyme
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
medicine
lysine appears important for dental biofilm accumulation and the epithelial barrier to bacterial proinflammatory agents. After oral hygiene restriction, lysine decarboxylase activity seems to determine dental biofilm lysine content and biofilm accumulation. When biofilm lysine exceeds minimal blood plasma content after oral hygiene restriction, less gingival crevicular fluid appears despite more biofilm
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