BRENDA - Enzyme Database

Structural and molecular basis for the novel catalytic mechanism and evolution of DddP, an abundant peptidase-like bacterial dimethylsulfoniopropionate lyase a new enzyme from an old fold

Wang, P.; Chen, X.L.; Li, C.Y.; Gao, X.; Zhu, D.Y.; Xie, B.B.; Qin, Q.L.; Zhang, X.Y.; Su, H.N.; Zhou, B.C.; Xun, L.Y.; Zhang, Y.Z.; Mol. Microbiol. 98, 289-301 (2015)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
4.4.1.3
expression in Escherichia coli
Ruegeria lacuscaerulensis
Crystallization (Commentary)
EC Number
Crystallization
Organism
4.4.1.3
wild-type in complex with inhibitor 2-(N-morpholino)ethanesulfonic acid or PO43-, to 2.1 A resolution, and mutants Y366A and D377N bound to acrylate
Ruegeria lacuscaerulensis
Engineering
EC Number
Amino acid exchange
Commentary
Organism
4.4.1.3
D377A
complete loss of activity
Ruegeria lacuscaerulensis
4.4.1.3
D377N
about 10% residual activity
Ruegeria lacuscaerulensis
4.4.1.3
Y366A
20% residual activity
Ruegeria lacuscaerulensis
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
4.4.1.3
1,10-phenanthroline
10 mM, almost complete inhibition
Ruegeria lacuscaerulensis
4.4.1.3
2-(N-morpholino)ethanesulfonic acid
-
Ruegeria lacuscaerulensis
4.4.1.3
bipyridyl
10 mM, 50% inhibition
Ruegeria lacuscaerulensis
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.4.1.3
17.1
-
beta-dimethylsulfoniopropanoate
pH 6.0, 60°C
Ruegeria lacuscaerulensis
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.4.1.3
Ruegeria lacuscaerulensis
D0CY07
-
-
4.4.1.3
Ruegeria lacuscaerulensis DSM 11314
D0CY07
-
-
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.4.1.3
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis DSM 11314
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis
?
-
-
-
-
4.4.1.3
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis DSM 11314
?
-
-
-
-
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
4.4.1.3
60
-
-
Ruegeria lacuscaerulensis
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.4.1.3
6
-
-
Ruegeria lacuscaerulensis
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.4.1.3
expression in Escherichia coli
Ruegeria lacuscaerulensis
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.4.1.3
wild-type in complex with inhibitor 2-(N-morpholino)ethanesulfonic acid or PO43-, to 2.1 A resolution, and mutants Y366A and D377N bound to acrylate
Ruegeria lacuscaerulensis
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
4.4.1.3
D377A
complete loss of activity
Ruegeria lacuscaerulensis
4.4.1.3
D377N
about 10% residual activity
Ruegeria lacuscaerulensis
4.4.1.3
Y366A
20% residual activity
Ruegeria lacuscaerulensis
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
4.4.1.3
1,10-phenanthroline
10 mM, almost complete inhibition
Ruegeria lacuscaerulensis
4.4.1.3
2-(N-morpholino)ethanesulfonic acid
-
Ruegeria lacuscaerulensis
4.4.1.3
bipyridyl
10 mM, 50% inhibition
Ruegeria lacuscaerulensis
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.4.1.3
17.1
-
beta-dimethylsulfoniopropanoate
pH 6.0, 60°C
Ruegeria lacuscaerulensis
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.4.1.3
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
beta-dimethylsulfoniopropanoate
-
748685
Ruegeria lacuscaerulensis DSM 11314
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis
?
-
-
-
-
4.4.1.3
additional information
enzyme shows no detectable activity toward the typical substrate (Val-Pro) of M24 peptidases
748685
Ruegeria lacuscaerulensis DSM 11314
?
-
-
-
-
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
4.4.1.3
60
-
-
Ruegeria lacuscaerulensis
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.4.1.3
6
-
-
Ruegeria lacuscaerulensis
Expression
EC Number
Organism
Commentary
Expression
4.4.1.3
Ruegeria lacuscaerulensis
the expression of the dddP gene is significantly induced by DMSP but not by peptide Val-Pro or casein
up
Expression (protein specific)
EC Number
Organism
Commentary
Expression
4.4.1.3
Ruegeria lacuscaerulensis
the expression of the dddP gene is significantly induced by DMSP but not by peptide Val-Pro or casein
up