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Information on EC 4.1.1.18 - lysine decarboxylase and Organism(s) Selenomonas ruminantium and UniProt Accession O50657
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4.1.1.18 lysine decarboxylaseIUBMB Comments
A pyridoxal-phosphate protein. Also acts on 5-hydroxy-L-lysine.
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Word Map
- 4.1.1.18
- ornithine
- urease
- aeromonas
-
dihydrolase
- decarboxylases
-
voges-proskauer
-
dna-dna
- esculin
-
non-motile
-
cadba
- salicin
- 1,5-diaminopentane
- d-mannitol
- melibiose
- dulcitol
- ruminantium
- adonitol
-
selenomonas
- sobria
-
enteroinvasive
- d-sorbitol
- carbenicillin
- cephalothin
- corrodens
-
simmons
- alvei
-
macconkey
-
quinolizidine
-
hafnia
- eikenella
- huperzia
- d-arabitol
-
4.1.1.17
- synthesis
- medicine
The taxonomic range for the selected organisms is: Selenomonas ruminantium
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
The expected taxonomic range for this enzyme is: Bacteria, Eukaryota, Archaea
Synonyms
lysine decarboxylase, l-lysine decarboxylase, inducible lysine decarboxylase, srldc, ecldcc, maldc, constitutive lysine decarboxylase, ldci/cada, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
LDC
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
decarboxylation
-
-
-
-
PATHWAY SOURCE
PATHWAYS
BRENDA
KEGG
-
-, -, -, -, -, -, -, -
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
9024-76-4
-
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
L-Orn
Putrescine + CO2
-
the ratio of activity with L-Orn to activity with L-Lys is 0.69 in wild type enzyme, 1.0 in mutant enzyme A44V/G45T/V46P, 4.o in mutant enzyme M50V/A52C/P54D/T55S, 0.64 in mutant enzyme M50V, 1.2 in mutant enzyme A52C, 1.8 in mutant enzyme P54D, 0.66 in mutant enzyme T55S, 1.9 in mutant enzyme M50V/A52C, 1.8 in mutant enzyme P54D/T55S, 2.6 in mutant enzyme A52C/P54D, 2.4 in mutant enzyme M50V/A52C/P54D and 2.7 in mutant enzyme A52C/P54D/T55S
-
-
?
L-Lys
Cadaverine + CO2
constitutive enzyme is involved in synthesis of cadaverine, which is an essential constituent of the peptidoglycan for normal cell growth
-
-
?
L-Lys
Cadaverine + CO2
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 0.83 for the wild-type enzyme
-
-
?
L-Lys
Cadaverine + CO2
-
the ratio of activity with L-Orn to activity with L-Lys is 0.69 in wild type enzyme, 1.0 in mutant enzyme A44V/G45T/V46P, 4.0 in mutant enzyme M50V/A52C/P54D/T55S, 0.64 in mutant enzyme M50V, 1.2 in mutant enzyme A52C, 1.8 in mutant enzyme P54D, 0.66 in mutant enzyme T55S, 1.9 in mutant enzyme M50V/A52C, 1.8 in mutant enzyme P54D/T55S, 2.6 in mutant enzyme A52C/P54D, 2.4 in mutant enzyme M50V/A52C/P54D and 2.7 in mutant enzyme A52C/P54D/T55S
-
-
?
additional information
?
-
substrate and product binding structure and binding mode, overview. A shallow substrate-binding hole is formed at the interface between the sheet domains of two monomers. The epsilon-amino group of the cadaverine product seems to be stabilized by hydroxyl groups of residues Tyr290 and Ser356. Hydrophobic residues such as Tyr298 and Phe360 provide hydrophobicity for the stabilization of five methylene groups of cadaverine. Asp299 also aids the stabilization of hydrophobic parts of cadaverine. Residues Asp324 and Tyr352 are located in the vicinity of the epsilon-amino group of cadaverine
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-
?
additional information
?
-
-
substrate and product binding structure and binding mode, overview. A shallow substrate-binding hole is formed at the interface between the sheet domains of two monomers. The epsilon-amino group of the cadaverine product seems to be stabilized by hydroxyl groups of residues Tyr290 and Ser356. Hydrophobic residues such as Tyr298 and Phe360 provide hydrophobicity for the stabilization of five methylene groups of cadaverine. Asp299 also aids the stabilization of hydrophobic parts of cadaverine. Residues Asp324 and Tyr352 are located in the vicinity of the epsilon-amino group of cadaverine
-
-
?
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
L-Lys
Cadaverine + CO2
constitutive enzyme is involved in synthesis of cadaverine, which is an essential constituent of the peptidoglycan for normal cell growth
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
pyridoxal 5'-phosphate
PLP, binding structure and binding mode, overview. The highly flexible active site contributes to the low affinity for pyridoxal 5'-phosphate in SrLDC. The cofactor affinity is increased in enzyme mutant A225C/T302C due to introduction of an artificial disulfide bond
pyridoxal 5'-phosphate
PLP, binding structure and binding mode, overview. The PLP cofactor binds mainly to the pocket formed at the barrel domain, and the catalytic residue Lys51 interacts with the aldehyde group of the pyridoxal ring. The pyridine ring is stabilized by hydrogen bond between N1 of the ring and the acidic residue Glu255. The phosphate moiety of PLP is mainly stabilized by strong hydrogen bonds with the side-chains of His179, Ser182, and Tyr352, and the main chains of Gly219, Gly257, and Arg258 are also involved in the stabilization of the moiety
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
22
L-Lys
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322T/I326L
270
L-Lys
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322A
3.3
L-Orn
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322T/I326L
additional information
additional information
kinetic analysis of wild-type and mutant enzymes
-
additional information
additional information
-
kinetic analysis of wild-type and mutant enzymes
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
5.5
L-Lys
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322A
19
L-Lys
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322T/I326L
3 - 6
L-Orn
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322T/I326L
4.8
L-Orn
pH 6.0, 30°C, mutant enzyme A44V/G45T/V46P/P54D/S322A
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0175
DL-alpha-Difluoromethyllysine
pH 6.0, 40°C, reaction with L-Lys
0.028
DL-alpha-Difluoromethyllysine
pH 6.0, 40°C, reaction with L-Orn
0.00525
DL-alpha-difluoromethylornithine
pH 6.0, 40°C, reaction with L-Lys
0.0082
DL-alpha-difluoromethylornithine
pH 6.0, 40°C, reaction with L-Orn
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 8
-
pH 7.0: about 70% of maximal activity, pH 9.0: about 25% of maximal activity
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
30 - 41
-
30°C: 38% of maximal activity, 37°C: 71% of maximal activity, 41°C: optimum
pI VALUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
drastic descent of enzyme activity owing to degradation of LDC at entry into the stationary phase of cell growth
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
evolution
Selenomonas ruminantium SrLDC shows much lower pyridoxal 5'-phosphate affinity than other pyridoxal 5'-phosphate-dependent enzymes. The highly flexible active site contributes to the low affinity for pyridoxal 5'-phosphate in SrLDC
physiological function
lysine decarboxylase (LDC) is an important enzyme for maintenance of pH homeostasis and the biosynthesis of cadaverine. Most of bacteria utilize acid stress-induced lysine decarboxylase in the response to the environmental acid stress
additional information
additional information
due to the flexible pyridoxal 5'-phosphate binding site, the protein undergoes an open/closed conformational change at the PLP binding site depending on the pyridoxal 5'-phosphate binding. Especially, two loops located in the vicinity of the pyridoxal 5'-phosphate binding site, the pyridoxal 5'-phosphate stabilization loop (PS-loop) and the regulatory loop (R-loop), undergo a significant structural movement depending on the pyridoxal 5'-phosphate binding
additional information
-
due to the flexible pyridoxal 5'-phosphate binding site, the protein undergoes an open/closed conformational change at the PLP binding site depending on the pyridoxal 5'-phosphate binding. Especially, two loops located in the vicinity of the pyridoxal 5'-phosphate binding site, the pyridoxal 5'-phosphate stabilization loop (PS-loop) and the regulatory loop (R-loop), undergo a significant structural movement depending on the pyridoxal 5'-phosphate binding
additional information
structure of enzyme SrLDC in complex with pyridoxal 5'-phosphate and cadaverine and binding mode of cofactor and substrate, overview
additional information
-
structure of enzyme SrLDC in complex with pyridoxal 5'-phosphate and cadaverine and binding mode of cofactor and substrate, 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
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
homodimer
additional information
homodimer
2 * 44000, recombinant His-tagged enzyme, SDS-PAGE
additional information
SrLDC functions as a dimer and each monomer consists of two distinct domains, a pyridoxal 5'-phosphate-binding-barrel domain and a sheet domain. A shallow substrate-binding hole is formed at the interface between the sheet domains of two monomers
additional information
-
SrLDC functions as a dimer and each monomer consists of two distinct domains, a pyridoxal 5'-phosphate-binding-barrel domain and a sheet domain. A shallow substrate-binding hole is formed at the interface between the sheet domains of two monomers
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant His6-tagged enzyme, mixing 0.001 ml of 65 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution, containing 28% w/v PEG 400, 0.1 M sodium citrate tribasic-citric acid, pH 6.0, and 0.2 M MgCl2, and equilibration against 0.5 ml of reservoir solution, 20°C, the apo-form II crystals of SrLDC are crystallized using a reservoir solution containing 1.15 M sodium citrate and 0.1 M sodium cacodylate, pH 5.0. The crystals of SrLDC complexed with PLP/cadaverine are crystallized using 50% PEG 200, 0.1 M sodium phosphate, pH 4.2, 0.2 M sodium chloride, and 5 mM PLP, followed by soaking in 10 mM L-lysine solution for 30 min, X-ray diffraction structure determination and analysis at 2.0-2.9 A resolution, molecular replacement with the structure of L/ODC from Vibrio vulnificus (VvL/ODC, PDB ID 2PLK) as search model, model building
purified SrLDCA225C/T302C mutant, hanging drop vapour diffusion method, mixing of 0.001 ml of 65 mg/ml protein in 40 mM Tris-HCl, pH 8.0, with 0.001 ml of reservoir solution containing 1.4 M ammonium sulfate, 0.1 M sodium cacodylate, pH 6.5, and 0.2 M sodium chloride, and equilibration against 0.5 ml of reservoir solution, 20°C, X-ray diffraction structure determination and analysis at 1.8 A resolution, molecular replacement using the structure of refined SrLDC as a model, model building
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
A225C/T302C
site-directed mutagenesis, due to high flexibility at the pyridoxal 5'-phosphate (PLP) binding site, use of the enzyme for cadaverine production requires continuous supplement of large amounts of PLP. In order to develop an LDC enzyme from Selenomonas ruminantium (SrLDC) with an enhanced affinity for PLP, an internal disulfide bond between Ala225 and Thr302 residues is introduced with a desire to retain the PLP binding site in a closed conformation. The SrLDCA225C/T302C mutant shows bound PLP, and exhibits 3fold enhanced PLP affinity compared with the wild-type SrLDC. The mutant also exhibits a dramatically enhanced LDC activity and cadaverine conversion particularly under no or low PLP concentrations. Introduction of the disulfide bond renders mutant SrLDC more resistant to high pH and temperature. The formation of the introduced disulfide bond and the maintenance of the PLP binding site in the closed conformation are confirmed by determination of the crystal structure of the mutant. Mutant structure determination and analysis, overview. The mutant shows increased affinity for pyridoxal 5'-phosphate and increased activity compared to wild-type
A44V/G45T/V46P
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 2.0, compared to 0.83 for the wild-type enzyme
A44V/G45T/V46P/P54D
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
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
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
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 1.0, compared to 0.83 for the wild-type enzyme
A52C/P54D
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 1.6, compared to 0.83 for the wild-type enzyme
G319W
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
K2C/G227C
site-directed mutagenesis, the mutant shows reduced affinity for pyridoxal 5'-phosphate and reduced activity compared to wild-type
M50V/A52C/P54D/T55S
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 1.5, compared to 0.83 for the wild-type enzyme
P54D
the ratio of turnover number to Km-value obtained with L-Orn relative to that obtained with L-Lys as substrate is 2.2, compared to 0.83 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
A44V/G45T/V46P
-
the ratio of activity with L-Orn to activity with L-Lys is 1.0, compared to 0.69 for the wild-type enzyme
A52C
-
the ratio of activity with L-Orn to activity with L-Lys is 1.2, compared to 0.69 for the wild-type enzyme
A52C/P54D
-
the ratio of activity with L-Orn to activity with L-Lys is 2.6, compared to 0.69 for the wild-type enzyme
A52C/P54D/T55S
-
the ratio of activity with L-Orn to activity with L-Lys is 2.7, compared to 0.69 for the wild-type enzyme
M50V
-
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
-
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
-
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
-
the ratio of activity with L-Orn to activity with L-Lys is 4.0, compared to 0.69 for the wild-type enzyme
P54D
-
the ratio of activity with L-Orn to activity with L-Lys is 1.8, compared to 0.69 for the wild-type enzyme
P54D/T55S
-
the ratio of activity with L-Orn to activity with L-Lys is 1.8, compared to 0.69 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
additional information
disulfide bond-mediated spatial reconstitution can be a platform technology for development of enzymes with enhanced pyridoxal 5'-phosphate affinity
additional information
-
disulfide bond-mediated spatial reconstitution can be a platform technology for development of enzymes with enhanced pyridoxal 5'-phosphate affinity
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
35
30 min, 50% loss of activity without pyridoxal-5'-phosphate
50
30 min, 50% loss of activity in presence of pyridoxal 5'-phosphate
60
-
pH 6.5, 0.1 mM pyridoxal 5'-phosphate, 30% loss of activity after 5 min. 90% loss of activity within 5 min, at pH 6.5 in absence of pyridoxal 5'-phosphate
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-80°C, stable for one month in presence of 20% glycerol, loss of activity within 2 weeks without glycerol
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene Srldc, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
gene Srldc, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
gene Srldc, recombinant expression of His6-tagged enzyme in Escherichia coli strain BL21(DE3)
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
synthesis
enzyme LDC plays a crucial role in the synthesis of cadaverine, an important industrial platform chemical. Cadaverine is utilized with a variety of applications such as the production of polyamides, polyurethanes, chelating agents, and additives
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kamio, Y.; Terawaki, Y.
Purification and properties of Selenomonas ruminantium lysine decarboxylase
J. Bacteriol.
153
658-664
1983
Selenomonas ruminantium
Takatsuka, Y.; Onoda, M.; Sugiyama, T.; Muramoto, K.; Tomita, T.; Kamio, Y.
Novel characteristics of Selenomonas ruminantium lysine decarboxylase capable of decarboxylating both L-lysine and L-ornithine
Biosci. Biotechnol. Biochem.
63
1063-1069
1999
Selenomonas ruminantium (O50657), Selenomonas ruminantium
Takatsuka, Y.; Tomita, T.; Kamio, Y.
Identification of the amino acid residues conferring substrate specificity upon Selenomonas ruminantium lysine decarboxylase
Biosci. Biotechnol. Biochem.
63
1843-1846
1999
Selenomonas ruminantium
Takatsuka, Y.; Yamaguchi, Y.; Ono, M.; Kamio, Y.
Gene cloning and molecular characterization of lysine decarboxylase from Selenomonas ruminantium delineate its evolutionary relationship to ornithine decarboxylases from eukaryotes
J. Bacteriol.
182
6732-6741
2000
Selenomonas ruminantium (O50657), Selenomonas ruminantium
Sagong, H.Y.; Son, H.F.; Kim, S.; Kim, Y.H.; Kim, I.K.; Kim, K.J.
Crystal structure and pyridoxal 5-phosphate binding property of lysine decarboxylase from Selenomonas ruminantium
PLoS ONE
11
e0166667
2016
Selenomonas ruminantium (O50657), Selenomonas ruminantium
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