BRENDA - Enzyme Database

The gene cluster for agmatine catabolism of Enterococcus faecalis: study of recombinant putrescine transcarbamylase and agmatine deiminase and a snapshot of agmatine deiminase catalyzing its reaction

Llacer, J.L.; Polo, L.M.; Tavarez, S.; Alarcon, B.; Hilario, R.; Rubio, V.; J. Bacteriol. 189, 1254-1265 (2007)

Data extracted from this reference:

Application
EC Number
Application
Commentary
Organism
2.7.2.2
additional information
putative gene for carbamate kinase is ef0735 on the DNA strand of the Enterococcus faecalis V583 chromosome. The arginine deiminase pathway of arginine catabolism probably supplies the genes for PTC and CK but not those for the agmatine/putrescine antiporter
Enterococcus faecalis
Cloned(Commentary)
EC Number
Commentary
Organism
2.1.3.6
expressed in Escherichia coli; gene ef0732, gene cluster organization, DNA and amino acid sequence determination and analysis, overexpression of His-tagged enzyme in Escherichia coli
Enterococcus faecalis
3.5.3.12
expressed in Escherichia coli BL21 (DE3) cells
Enterococcus faecalis
Crystallization (Commentary)
EC Number
Crystallization
Organism
2.1.3.6
purified recombinant enzyme in presence of inhibitor N-(phosphonoacetyl)-putrescine, X-ray diffraction structure determination and analysis at 3.0 A resolution; using the sparse-matrix sampling vapor-diffusion method. The addition of N-(phosphonoacetyl)-putrescine to the crystallization drop strongly improves the results of the crystallization
Enterococcus faecalis
3.5.3.12
hanging drop vapour diffusion method with in 50 mM Tris-HCl, pH 7.45, 1 mM dithiothreitol and 20 mM NaCl
Enterococcus faecalis
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
2.1.3.6
N-(phosphonoacetyl)-putrescine
; i.e. PAPU, highly potent and selective inhibitor
Enterococcus faecalis
2.1.3.6
phosphonoacetyl-L-aspartate
-
Enterococcus faecalis
2.1.3.6
phosphonoacetyl-L-ornithine
-
Enterococcus faecalis
3.5.3.12
arcaine
competitive inhibitor
Enterococcus faecalis
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.1.3.6
0.0023
-
putrescine
-
Enterococcus faecalis
2.1.3.6
0.058
-
Carbamoyl phosphate
-
Enterococcus faecalis
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
2.1.3.6
40000
-
gel filtration
Enterococcus faecalis
3.5.3.12
46000
-
SDS-PAGE
Enterococcus faecalis
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2.1.3.6
carbamoyl phosphate + L-ornithine
Enterococcus faecalis
low activity, reaction of EC 2.1.3.3
phosphate + N-carbamoyl-L-ornithine
-
-
?
2.1.3.6
carbamoyl phosphate + L-ornithine
Enterococcus faecalis ATCC 700802
low activity, reaction of EC 2.1.3.3
phosphate + N-carbamoyl-L-ornithine
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
Enterococcus faecalis
-
phosphate + N-carbamoyl-putrescine
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
Enterococcus faecalis ATCC 700802
-
phosphate + N-carbamoyl-putrescine
-
-
?
2.1.3.6
additional information
Enterococcus faecalis
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
?
-
-
-
2.1.3.6
additional information
Enterococcus faecalis ATCC 700802
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
?
-
-
-
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
2.1.3.6
Enterococcus faecalis
-
; strain SD10, gene ef0732
-
2.1.3.6
Enterococcus faecalis ATCC 700802
-
strain SD10, gene ef0732
-
2.7.2.2
Enterococcus faecalis
-
SD10 strain
-
2.7.2.2
Enterococcus faecalis ATCC 700802
-
SD10 strain
-
3.5.3.12
Enterococcus faecalis
Q837U5
strain SD10
-
3.5.3.12
Enterococcus faecalis ATCC 700802
Q837U5
strain SD10
-
Purification (Commentary)
EC Number
Commentary
Organism
2.1.3.6
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Enterococcus faecalis
3.5.3.12
HisTrap Ni-affinity column chromatography and Superdex 200 HR gel filtration
Enterococcus faecalis
Specific Activity [micromol/min/mg]
EC Number
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
2.1.3.6
460
-
non-recombinant enzyme from Enterococcus faecalis
Enterococcus faecalis
2.1.3.6
597
-
recombinant enzyme from Enterococcus faecalis
Enterococcus faecalis
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.1.3.6
carbamoyl phosphate + cadaverine
only weak activity with cadaverine a substrate
674316
Enterococcus faecalis
phosphate + N-carbamoylcadaverine
-
-
-
?
2.1.3.6
carbamoyl phosphate + cadaverine
only weak activity with cadaverine a substrate
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoylcadaverine
-
-
-
?
2.1.3.6
carbamoyl phosphate + L-ornithine
low activity, reaction of EC 2.1.3.3
674316
Enterococcus faecalis
phosphate + N-carbamoyl-L-ornithine
-
-
-
?
2.1.3.6
carbamoyl phosphate + L-ornithine
low activity, reaction of EC 2.1.3.3
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoyl-L-ornithine
-
-
-
?
2.1.3.6
carbamoyl phosphate + ornithine
only weak activity with ornithine as a substrate
674316
Enterococcus faecalis
phosphate + N-carbamoylornithine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis
phosphate + N-carbamoylputrescine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoylputrescine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis
phosphate + N-carbamoyl-putrescine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoyl-putrescine
-
-
-
?
2.1.3.6
additional information
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
674316
Enterococcus faecalis
?
-
-
-
-
2.1.3.6
additional information
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
674316
Enterococcus faecalis ATCC 700802
?
-
-
-
-
3.5.3.12
agmatine + H2O
highly specific for agmatine
674316
Enterococcus faecalis
N-carbamoylputrescine + NH3
-
-
-
?
3.5.3.12
agmatine + H2O
highly specific for agmatine
674316
Enterococcus faecalis ATCC 700802
N-carbamoylputrescine + NH3
-
-
-
?
3.5.3.12
additional information
does not use L-arginine, L-argininamide, or arcaine (1,4-diguanidinobutane) as substrates
674316
Enterococcus faecalis
?
-
-
-
-
3.5.3.12
additional information
does not use L-arginine, L-argininamide, or arcaine (1,4-diguanidinobutane) as substrates
674316
Enterococcus faecalis ATCC 700802
?
-
-
-
-
Subunits
EC Number
Subunits
Commentary
Organism
2.1.3.6
trimer
; crystal strucutre
Enterococcus faecalis
3.5.3.12
tetramer
X-ray crystallography and gel filtration
Enterococcus faecalis
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
2.1.3.6
37
-
assay at
Enterococcus faecalis
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.1.3.6
7
-
assay at
Enterococcus faecalis
Ki Value [mM]
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
2.1.3.6
0.00001
-
N-(phosphonoacetyl)-putrescine
recombinant enzyme
Enterococcus faecalis
2.1.3.6
10
-
N-(phosphonoacetyl)-putrescine
-
Enterococcus faecalis
3.5.3.12
0.028
-
arcaine
at 37°C
Enterococcus faecalis
Application (protein specific)
EC Number
Application
Commentary
Organism
2.7.2.2
additional information
putative gene for carbamate kinase is ef0735 on the DNA strand of the Enterococcus faecalis V583 chromosome. The arginine deiminase pathway of arginine catabolism probably supplies the genes for PTC and CK but not those for the agmatine/putrescine antiporter
Enterococcus faecalis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
2.1.3.6
expressed in Escherichia coli; gene ef0732, gene cluster organization, DNA and amino acid sequence determination and analysis, overexpression of His-tagged enzyme in Escherichia coli
Enterococcus faecalis
3.5.3.12
expressed in Escherichia coli BL21 (DE3) cells
Enterococcus faecalis
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
2.1.3.6
purified recombinant enzyme in presence of inhibitor N-(phosphonoacetyl)-putrescine, X-ray diffraction structure determination and analysis at 3.0 A resolution; using the sparse-matrix sampling vapor-diffusion method. The addition of N-(phosphonoacetyl)-putrescine to the crystallization drop strongly improves the results of the crystallization
Enterococcus faecalis
3.5.3.12
hanging drop vapour diffusion method with in 50 mM Tris-HCl, pH 7.45, 1 mM dithiothreitol and 20 mM NaCl
Enterococcus faecalis
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
2.1.3.6
N-(phosphonoacetyl)-putrescine
; i.e. PAPU, highly potent and selective inhibitor
Enterococcus faecalis
2.1.3.6
phosphonoacetyl-L-aspartate
-
Enterococcus faecalis
2.1.3.6
phosphonoacetyl-L-ornithine
-
Enterococcus faecalis
3.5.3.12
arcaine
competitive inhibitor
Enterococcus faecalis
Ki Value [mM] (protein specific)
EC Number
Ki Value [mM]
Ki Value maximum [mM]
Inhibitor
Commentary
Organism
Structure
2.1.3.6
0.00001
-
N-(phosphonoacetyl)-putrescine
recombinant enzyme
Enterococcus faecalis
2.1.3.6
10
-
N-(phosphonoacetyl)-putrescine
-
Enterococcus faecalis
3.5.3.12
0.028
-
arcaine
at 37°C
Enterococcus faecalis
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
2.1.3.6
0.0023
-
putrescine
-
Enterococcus faecalis
2.1.3.6
0.058
-
Carbamoyl phosphate
-
Enterococcus faecalis
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
2.1.3.6
40000
-
gel filtration
Enterococcus faecalis
3.5.3.12
46000
-
SDS-PAGE
Enterococcus faecalis
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
2.1.3.6
carbamoyl phosphate + L-ornithine
Enterococcus faecalis
low activity, reaction of EC 2.1.3.3
phosphate + N-carbamoyl-L-ornithine
-
-
?
2.1.3.6
carbamoyl phosphate + L-ornithine
Enterococcus faecalis ATCC 700802
low activity, reaction of EC 2.1.3.3
phosphate + N-carbamoyl-L-ornithine
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
Enterococcus faecalis
-
phosphate + N-carbamoyl-putrescine
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
Enterococcus faecalis ATCC 700802
-
phosphate + N-carbamoyl-putrescine
-
-
?
2.1.3.6
additional information
Enterococcus faecalis
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
?
-
-
-
2.1.3.6
additional information
Enterococcus faecalis ATCC 700802
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
?
-
-
-
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
2.1.3.6
recombinant His-tagged enzyme from Escherichia coli by nickel affinity chromatography
Enterococcus faecalis
3.5.3.12
HisTrap Ni-affinity column chromatography and Superdex 200 HR gel filtration
Enterococcus faecalis
Specific Activity [micromol/min/mg] (protein specific)
EC Number
Specific Activity Minimum [µmol/min/mg]
Specific Activity Maximum [µmol/min/mg]
Commentary
Organism
2.1.3.6
460
-
non-recombinant enzyme from Enterococcus faecalis
Enterococcus faecalis
2.1.3.6
597
-
recombinant enzyme from Enterococcus faecalis
Enterococcus faecalis
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
2.1.3.6
carbamoyl phosphate + cadaverine
only weak activity with cadaverine a substrate
674316
Enterococcus faecalis
phosphate + N-carbamoylcadaverine
-
-
-
?
2.1.3.6
carbamoyl phosphate + cadaverine
only weak activity with cadaverine a substrate
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoylcadaverine
-
-
-
?
2.1.3.6
carbamoyl phosphate + L-ornithine
low activity, reaction of EC 2.1.3.3
674316
Enterococcus faecalis
phosphate + N-carbamoyl-L-ornithine
-
-
-
?
2.1.3.6
carbamoyl phosphate + L-ornithine
low activity, reaction of EC 2.1.3.3
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoyl-L-ornithine
-
-
-
?
2.1.3.6
carbamoyl phosphate + ornithine
only weak activity with ornithine as a substrate
674316
Enterococcus faecalis
phosphate + N-carbamoylornithine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis
phosphate + N-carbamoylputrescine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoylputrescine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis
phosphate + N-carbamoyl-putrescine
-
-
-
?
2.1.3.6
carbamoyl phosphate + putrescine
-
674316
Enterococcus faecalis ATCC 700802
phosphate + N-carbamoyl-putrescine
-
-
-
?
2.1.3.6
additional information
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
674316
Enterococcus faecalis
?
-
-
-
-
2.1.3.6
additional information
the enzyme catalyzes the second of three steps of ATP synthesis from agmatine
674316
Enterococcus faecalis ATCC 700802
?
-
-
-
-
3.5.3.12
agmatine + H2O
highly specific for agmatine
674316
Enterococcus faecalis
N-carbamoylputrescine + NH3
-
-
-
?
3.5.3.12
agmatine + H2O
highly specific for agmatine
674316
Enterococcus faecalis ATCC 700802
N-carbamoylputrescine + NH3
-
-
-
?
3.5.3.12
additional information
does not use L-arginine, L-argininamide, or arcaine (1,4-diguanidinobutane) as substrates
674316
Enterococcus faecalis
?
-
-
-
-
3.5.3.12
additional information
does not use L-arginine, L-argininamide, or arcaine (1,4-diguanidinobutane) as substrates
674316
Enterococcus faecalis ATCC 700802
?
-
-
-
-
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
2.1.3.6
trimer
; crystal strucutre
Enterococcus faecalis
3.5.3.12
tetramer
X-ray crystallography and gel filtration
Enterococcus faecalis
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
2.1.3.6
37
-
assay at
Enterococcus faecalis
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
2.1.3.6
7
-
assay at
Enterococcus faecalis