Information on EC 4.3.1.28 - L-lysine cyclodeaminase

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The expected taxonomic range for this enzyme is: Streptomyces

EC NUMBER
COMMENTARY
4.3.1.28
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RECOMMENDED NAME
GeneOntology No.
L-lysine cyclodeaminase
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REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
L-lysine = L-pipecolate + NH3
show the reaction diagram
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-
-
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SYSTEMATIC NAME
IUBMB Comments
L-lysine ammonia-lyase (cyclizing; ammonia-forming)
Requires bound NAD+. The enzyme produces the non-proteinogenic amino acid L-pipecolate, which is incorporated into multiple secondary metabolite products, including rapamycin, tobulysin, virginiamycin and pristinamycin.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
fkbL
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gene name
-
lysine cyclodeaminase
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lysine cyclodeaminase
Streptomyces hygroscopicus NRRL 5491
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lysine cyclodeaminase
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rapL
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gene name
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rapL
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; gene name
rapL
Streptomyces hygroscopicus NRRL 5491
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; gene name
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tubZ
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-
gene name
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visC
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gene name
-
visC
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gene name
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
; variant Streptomyces hygroscopicus ascomyceticus
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Manually annotated by BRENDA team
Streptomyces hygroscopicus NRRL 5491
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-
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
malfunction
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introduction of a frameshift mutation into rapL gene gives rise to a mutant which does not produce significant amounts of rapamycin. Growth of this rapL mutant on media containing added L-pipecolate restores wild-type levels of rapamycin production
malfunction
Streptomyces hygroscopicus NRRL 5491
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introduction of a frameshift mutation into rapL gene gives rise to a mutant which does not produce significant amounts of rapamycin. Growth of this rapL mutant on media containing added L-pipecolate restores wild-type levels of rapamycin production
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SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
5-hydroxylysine
?
show the reaction diagram
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-
-
-
?
L-4-thialysine
?
show the reaction diagram
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-
-
-
?
L-lysine
L-pipecolate + NH3
show the reaction diagram
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-
-
-
?
L-lysine
L-pipecolate + NH3
show the reaction diagram
-
-
-
-
?
L-lysine
L-pipecolate + NH3
show the reaction diagram
-
-
-
-
?
L-lysine
L-pipecolate + NH3
show the reaction diagram
Streptomyces hygroscopicus NRRL 5491
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-
-
-
?
L-ornithine
?
show the reaction diagram
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-
-
-
?
L-ornithine
?
show the reaction diagram
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the enzyme also accepts L-ornithine as a substrate, albeit with a significantly reduced catalytic efficiency
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?
additional information
?
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4-azalysine, L-2,4-diaminobutyric acid, 1,5-diaminopentane, N3-trifluoroacetyl-L-lysine, N3-Boc-L-lysine and N3-methyl-L-lysine compete against L-lysine turnover without being converted by the enzyme
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COFACTOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
NAD+
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there is no requirement for an external cofactor for full activity, although sequence data indicate NAD+ as cofactor. NAD+ binds very tightly to the enzyme
NAD+
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the enzyme has about 0.17 equivalents of tightly bound NAD+. In the presence of exogenous NAD+, the initial rate is elevated 8fold with a Km of 0.0023 mM for the cofactor
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Al3+
-
151% relative activity at 3 mM
Fe2+
-
1308% relative activity at 3 mM
Mg2+
-
227% relative activity at 3 mM
additional information
-
activity is not enhanced in the presence of Na+, Ca2+, Mn2+, and Zn2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
(R)-(-)-nipecotic acid
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-
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thiazolidine-2-carboxylic acid
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(S)-(+)-nipecotic acid
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-
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additional information
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no inhibition by the substrate L-lysine up to 2.0 M, by the product L-pipecolate at concentrations up to 1.0 M or by NADH up to 1.1 mM
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ACTIVATING COMPOUND
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
dithiothreitol
-
increase in enzyme activity between 2.1 and 2.5fold in the presence of dithiothreitol at 1-3 mM
glycerol
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enzyme activity increases progressively up to at least 30% (v/v) glycerol. Activity is enhanced 4.6fold at 30% (v/v) glyerol
additional information
-
activity is not enhanced in the presence of ammonium sulfate
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KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.046
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L-lysine
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0.1 mM NAD+, in 100 mM HEPES (pH 8.0), at 30C
1.39
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L-lysine
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in 100 mM potassium phosphate buffer, pH 8.0 containing 10% (v/v) glycerol, at 37C
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.61
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L-lysine
-
0.1 mM NAD+, in 100 mM HEPES (pH 8.0), at 30C
kcat/KM VALUE [1/mMs-1]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
13
-
L-lysine
-
0.1 mM NAD+, in 100 mM HEPES (pH 8.0), at 30C
12307
0.14
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L-ornithine
-
0.1 mM NAD+, in 100 mM HEPES (pH 8.0), at 30C
12348
IC50 VALUE [mM]
IC50 VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
4.8
-
(R)-(-)-nipecotic acid
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in 100 mM HEPES (pH 8.0), at 30C
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0.68
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(S)-(+)-nipecotic acid
-
in 100 mM HEPES (pH 8.0), at 30C
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0.096
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thiazolidine-2-carboxylic acid
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in 100 mM HEPES (pH 8.0), at 30C
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5.4
9
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about 50% activity at pH 6.0 and 7.5. The enzyme activity is minimal at pH values below 5.4 and above 9.0
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
40
70
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the initial rate of L-lysine cyclodeamination is very low at or below room temperature, but it increases significantly from 23C to 61C and drops again suddenly at 66C, about 50% activity at 50C
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
?
-
x * 37100, SDS-PAGE
?
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x * about 40000, SDS-PAGE
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4
37
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enzyme stability does not change significantly between 4C and 37C, while there is clear loss of enzyme stability at temperatures greater than 37C
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
Ni-NTA column chromatography
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Q-Sepharose column chromatography and ammonium sulfate precipitation
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Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Escherichia coli BL21(DE3) cells
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expressed in Escherichia coli DH10B cells
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expressed in Escherichia coli M15[pREP4] cells
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