BRENDA - Enzyme Database

Mechanistic insights into dimethylsulfoniopropionate lyase DddY, a new member of the cupin superfamily

Li, C.Y.; Zhang, D.; Chen, X.L.; Wang, P.; Shi, W.L.; Li, P.Y.; Zhang, X.Y.; Qin, Q.L.; Todd, J.D.; Zhang, Y.Z.; J. Mol. Biol. 429, 3850-3862 (2017)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
4.4.1.3
expression in Escherichia coli
Acinetobacter bereziniae
Crystallization (Commentary)
EC Number
Crystallization
Organism
4.4.1.3
to 1.5 A resolution. DddY contains a cap domain and a catalytic domain with a Zn2+ bound at its active site. Residues His265, Glu269, His338 and the acetate molecule participate in coordinating Zn2+. The DddY catalytic domain adopts a typical beta-barrel fold and contains two conserved cupin motifs. In the catalytic mechanism, residue Tyr271 acts as a general base to attack DMSP
Acinetobacter bereziniae
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.4.1.3
5
-
beta-dimethylsulfoniopropanoate
pH 8.0, 60°C
Acinetobacter bereziniae
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
4.4.1.3
Zinc
Zn2+ is bound at the active site
Acinetobacter bereziniae
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.4.1.3
Acinetobacter bereziniae
N8X9V6
-
-
4.4.1.3
Acinetobacter bereziniae NIPH 3
N8X9V6
-
-
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
-
748399
Acinetobacter bereziniae
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
beta-dimethylsulfoniopropanoate
-
748399
Acinetobacter bereziniae NIPH 3
dimethylsulfide + acrylate
-
-
-
?
Temperature Optimum [°C]
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
4.4.1.3
60
-
-
Acinetobacter bereziniae
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.4.1.3
8300
-
beta-dimethylsulfoniopropanoate
pH 8.0, 60°C
Acinetobacter bereziniae
pH Optimum
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.4.1.3
8
-
-
Acinetobacter bereziniae
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.4.1.3
expression in Escherichia coli
Acinetobacter bereziniae
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.4.1.3
to 1.5 A resolution. DddY contains a cap domain and a catalytic domain with a Zn2+ bound at its active site. Residues His265, Glu269, His338 and the acetate molecule participate in coordinating Zn2+. The DddY catalytic domain adopts a typical beta-barrel fold and contains two conserved cupin motifs. In the catalytic mechanism, residue Tyr271 acts as a general base to attack DMSP
Acinetobacter bereziniae
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
4.4.1.3
5
-
beta-dimethylsulfoniopropanoate
pH 8.0, 60°C
Acinetobacter bereziniae
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
4.4.1.3
Zinc
Zn2+ is bound at the active site
Acinetobacter bereziniae
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
-
748399
Acinetobacter bereziniae
dimethylsulfide + acrylate
-
-
-
?
4.4.1.3
beta-dimethylsulfoniopropanoate
-
748399
Acinetobacter bereziniae NIPH 3
dimethylsulfide + acrylate
-
-
-
?
Temperature Optimum [°C] (protein specific)
EC Number
Temperature Optimum [°C]
Temperature Optimum Maximum [°C]
Commentary
Organism
4.4.1.3
60
-
-
Acinetobacter bereziniae
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
4.4.1.3
8300
-
beta-dimethylsulfoniopropanoate
pH 8.0, 60°C
Acinetobacter bereziniae
pH Optimum (protein specific)
EC Number
pH Optimum Minimum
pH Optimum Maximum
Commentary
Organism
4.4.1.3
8
-
-
Acinetobacter bereziniae