BRENDA - Enzyme Database

Crystal structure of a Pseudomonas malonate decarboxylase holoenzyme hetero-tetramer

Maderbocus, R.; Fields, B.L.; Hamilton, K.; Luo, S.; Tran, T.H.; Dietrich, L.E.P.; Tong, L.; Nat. Commun. 8, 160 (2017)

Data extracted from this reference:

Activating Compound
EC Number
Activating Compound
Commentary
Organism
Structure
4.1.1.88
additional information
the enzyme is independent from biotin
Pseudomonas aeruginosa
Cloned(Commentary)
EC Number
Commentary
Organism
4.1.1.88
expressed in Escherichia coli BL21Star (DE3), BL21 Rosetta, and B834 (DE3) cells
Pseudomonas aeruginosa
Crystallization (Commentary)
EC Number
Crystallization
Organism
4.1.1.88
MdcD-MdcE subunits, sitting drop vapor diffusion method, using 0.1 M Bis-Tris (pH 5.8), 18% (w/v) PEG 3350, and 0.2 M ammonium acetate. Holoenzyme in complex with CoA and malonate, sitting drop vapor diffusion method, using 20% (w/v) PEG 3350 and 8% (w/v) tacsimate; the holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Structure of the MdcD-MdcE complex at 1.86 A resolution, and overall strcuture of the heterotetramer at 2.2 A resolution
Pseudomonas aeruginosa
Engineering
EC Number
Amino acid exchange
Commentary
Organism
4.1.1.88
Q100E
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
4.1.1.88
Q100E/Y102F
inactive
Pseudomonas aeruginosa
4.1.1.88
S142A
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
4.1.1.88
Y102F
the mutant of subunit MdcE has about wild type catalytic activity
Pseudomonas aeruginosa
Localization
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
4.1.1.88
membrane
-
Pseudomonas aeruginosa
16020
-
Molecular Weight [Da]
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
4.1.1.88
140000
-
gel filtration
Pseudomonas aeruginosa
Natural Substrates/ Products (Substrates)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
4.1.1.88
malonate + H+
Pseudomonas aeruginosa
-
acetate + CO2
-
-
?
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
4.1.1.88
Pseudomonas aeruginosa
Q9I6S7 and Q9I6S6
beta subunit MdcD and gamma subunit MdcE
-
4.1.1.88
Pseudomonas aeruginosa
Q9I6T0 and Q9I6S6
Q9I6T0 i.e. subunit MdcA, Q9I6S6 i.e. subunit MdcE
-
4.1.1.88
Pseudomonas aeruginosa DSM 22644
Q9I6T0 and Q9I6S6
Q9I6T0 i.e. subunit MdcA, Q9I6S6 i.e. subunit MdcE
-
Purification (Commentary)
EC Number
Commentary
Organism
4.1.1.88
nickel bead column chromatography and Sephacryl S-300 gel filtration
Pseudomonas aeruginosa
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.1.1.88
malonate + H+
-
748747
Pseudomonas aeruginosa
acetate + CO2
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
4.1.1.88
heterotetramer
x-ray crystallography
Pseudomonas aeruginosa
Activating Compound (protein specific)
EC Number
Activating Compound
Commentary
Organism
Structure
4.1.1.88
additional information
the enzyme is independent from biotin
Pseudomonas aeruginosa
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
4.1.1.88
expressed in Escherichia coli BL21Star (DE3), BL21 Rosetta, and B834 (DE3) cells
Pseudomonas aeruginosa
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
4.1.1.88
MdcD-MdcE subunits, sitting drop vapor diffusion method, using 0.1 M Bis-Tris (pH 5.8), 18% (w/v) PEG 3350, and 0.2 M ammonium acetate. Holoenzyme in complex with CoA and malonate, sitting drop vapor diffusion method, using 20% (w/v) PEG 3350 and 8% (w/v) tacsimate
Pseudomonas aeruginosa
4.1.1.88
the holoenzyme contains four subunits, having an acyl-carrier protein (MdcC subunit) with a distinct prosthetic group, as well as decarboxylase (MdcD-MdcE) and acyl-carrier protein transferase (MdcA) catalytic activities. Structure of the MdcD-MdcE complex at 1.86 A resolution, and overall strcuture of the heterotetramer at 2.2 A resolution
Pseudomonas aeruginosa
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
4.1.1.88
Q100E
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
4.1.1.88
Q100E/Y102F
inactive
Pseudomonas aeruginosa
4.1.1.88
S142A
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
4.1.1.88
Y102F
the mutant of subunit MdcE has about wild type catalytic activity
Pseudomonas aeruginosa
Localization (protein specific)
EC Number
Localization
Commentary
Organism
GeneOntology No.
Textmining
4.1.1.88
membrane
-
Pseudomonas aeruginosa
16020
-
Molecular Weight [Da] (protein specific)
EC Number
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
4.1.1.88
140000
-
gel filtration
Pseudomonas aeruginosa
Natural Substrates/ Products (Substrates) (protein specific)
EC Number
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
4.1.1.88
malonate + H+
Pseudomonas aeruginosa
-
acetate + CO2
-
-
?
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
4.1.1.88
nickel bead column chromatography and Sephacryl S-300 gel filtration
Pseudomonas aeruginosa
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4.1.1.88
malonate + H+
-
748747
Pseudomonas aeruginosa
acetate + CO2
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
4.1.1.88
heterotetramer
x-ray crystallography
Pseudomonas aeruginosa