BRENDA - Enzyme Database

Characterization and inactivation of an agmatine deiminase from Helicobacter pylori

Jones, J.E.; Causey, C.P.; Lovelace, L.; Knuckley, B.; Flick, H.; Lebioda, L.; Thompson, P.R.; Bioorg. Chem. 38, 62-73 (2010)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
3.5.3.12
expression in Escherichia coli
Helicobacter pylori
Crystallization (Commentary)
EC Number
Crystallization
Organism
3.5.3.12
to 2.1 A resolution. Residue D198 is the key residue for agmatine recognition
Helicobacter pylori
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.3.12
Co2+
-
Helicobacter pylori
3.5.3.12
N-(4-aminobutyl)-2-chloro-ethanimidamide
i.e. ABCA , haloacetamidine-containing agmatine analogue
Helicobacter pylori
3.5.3.12
N-(4-aminobutyl)-2-fluoro-ethanimidamide
i.e. ABFA, haloacetamidine-containing agmatine analogue
Helicobacter pylori
3.5.3.12
Ni2+
-
Helicobacter pylori
3.5.3.12
Zn2+
-
Helicobacter pylori
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
3.5.3.12
0.033
-
agmatine
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.17
-
agmatine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.5.3.12
Helicobacter pylori
Q9ZN18
-
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.5.3.12
Ac-SGRGK + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
agmatine + H2O
-
711375
Helicobacter pylori
N-carbamoylputrescine + NH3
major products. Ammonia and N-carbamoylputrescine are produced in approximately equimolar amounts
-
-
?
3.5.3.12
guanidine + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
L-arginine + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
N-alpha-benzoyl-L-arginine amide + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
N-alpha-benzoyl-L-arginine ethyl ester + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
N-alpha-benzoyl-L-arginine methyl ester + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
streptomycin + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
3.5.3.12
0.0047
-
agmatine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.082
-
agmatine
wild-type, pH 8.0, 37C
Helicobacter pylori
IC50 Value
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
3.5.3.12
0.00087
-
wild-type, pH 8.0, 37C
Helicobacter pylori
N-(4-aminobutyl)-2-chloro-ethanimidamide
3.5.3.12
0.0068
-
wild-type, pH 8.0, 37C
Helicobacter pylori
N-(4-aminobutyl)-2-fluoro-ethanimidamide
3.5.3.12
0.013
-
wild-type, pH 8.0, 37C
Helicobacter pylori
Co2+
3.5.3.12
0.03
-
wild-type, pH 8.0, 37C
Helicobacter pylori
Zn2+
3.5.3.12
0.1
-
wild-type, pH 8.0, 37C
Helicobacter pylori
Ni2+
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.5.3.12
expression in Escherichia coli
Helicobacter pylori
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
3.5.3.12
to 2.1 A resolution. Residue D198 is the key residue for agmatine recognition
Helicobacter pylori
IC50 Value (protein specific)
EC Number
IC50 Value
IC50 Value Maximum
Commentary
Organism
Inhibitor
Structure
3.5.3.12
0.00087
-
wild-type, pH 8.0, 37C
Helicobacter pylori
N-(4-aminobutyl)-2-chloro-ethanimidamide
3.5.3.12
0.0068
-
wild-type, pH 8.0, 37C
Helicobacter pylori
N-(4-aminobutyl)-2-fluoro-ethanimidamide
3.5.3.12
0.013
-
wild-type, pH 8.0, 37C
Helicobacter pylori
Co2+
3.5.3.12
0.03
-
wild-type, pH 8.0, 37C
Helicobacter pylori
Zn2+
3.5.3.12
0.1
-
wild-type, pH 8.0, 37C
Helicobacter pylori
Ni2+
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
3.5.3.12
Co2+
-
Helicobacter pylori
3.5.3.12
N-(4-aminobutyl)-2-chloro-ethanimidamide
i.e. ABCA , haloacetamidine-containing agmatine analogue
Helicobacter pylori
3.5.3.12
N-(4-aminobutyl)-2-fluoro-ethanimidamide
i.e. ABFA, haloacetamidine-containing agmatine analogue
Helicobacter pylori
3.5.3.12
Ni2+
-
Helicobacter pylori
3.5.3.12
Zn2+
-
Helicobacter pylori
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
3.5.3.12
0.033
-
agmatine
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.17
-
agmatine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.5.3.12
Ac-SGRGK + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
agmatine + H2O
-
711375
Helicobacter pylori
N-carbamoylputrescine + NH3
major products. Ammonia and N-carbamoylputrescine are produced in approximately equimolar amounts
-
-
?
3.5.3.12
guanidine + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
L-arginine + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
N-alpha-benzoyl-L-arginine amide + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
N-alpha-benzoyl-L-arginine ethyl ester + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
N-alpha-benzoyl-L-arginine methyl ester + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
3.5.3.12
streptomycin + H2O
-
711375
Helicobacter pylori
? + NH3
-
-
-
?
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
3.5.3.12
0.0047
-
agmatine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.082
-
agmatine
wild-type, pH 8.0, 37C
Helicobacter pylori
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
3.5.3.12
0.0000038
-
Ac-SGRGK
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000017
-
L-arginine
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000235
-
Ac-SGRGK
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000033
-
streptomycin
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000377
-
streptomycin
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000678
-
guanidine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000072
-
N-alpha-benzoyl-L-arginine amide
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000812
-
guanidine
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000847
-
N-alpha-benzoyl-L-arginine ethyl ester
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0001038
-
N-alpha-benzoyl-L-arginine methyl ester
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0001285
-
N-alpha-benzoyl-L-arginine amide
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0001383
-
N-alpha-benzoyl-L-arginine ethyl ester
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000149
-
L-arginine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0002183
-
N-alpha-benzoyl-L-arginine methyl ester
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0283
-
agmatine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
2.45
-
agmatine
wild-type, pH 8.0, 37C
Helicobacter pylori
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
3.5.3.12
0.0000038
-
Ac-SGRGK
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000017
-
L-arginine
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000235
-
Ac-SGRGK
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000033
-
streptomycin
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000377
-
streptomycin
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000678
-
guanidine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000072
-
N-alpha-benzoyl-L-arginine amide
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000812
-
guanidine
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0000847
-
N-alpha-benzoyl-L-arginine ethyl ester
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0001038
-
N-alpha-benzoyl-L-arginine methyl ester
wild-type, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0001285
-
N-alpha-benzoyl-L-arginine amide
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0001383
-
N-alpha-benzoyl-L-arginine ethyl ester
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.000149
-
L-arginine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0002183
-
N-alpha-benzoyl-L-arginine methyl ester
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
0.0283
-
agmatine
mutant D198A, pH 8.0, 37C
Helicobacter pylori
3.5.3.12
2.45
-
agmatine
wild-type, pH 8.0, 37C
Helicobacter pylori