BRENDA - Enzyme Database
show all sequences of 4.1.1.88

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
Activating Compound
Commentary
Organism
Structure
additional information
the enzyme is independent from biotin
Pseudomonas aeruginosa
Cloned(Commentary)
Commentary
Organism
expressed in Escherichia coli BL21Star (DE3), BL21 Rosetta, and B834 (DE3) cells
Pseudomonas aeruginosa
Crystallization (Commentary)
Crystallization
Organism
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
Amino acid exchange
Commentary
Organism
Q100E
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
Q100E/Y102F
inactive
Pseudomonas aeruginosa
S142A
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
Y102F
the mutant of subunit MdcE has about wild type catalytic activity
Pseudomonas aeruginosa
Localization
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
-
Pseudomonas aeruginosa
16020
-
Molecular Weight [Da]
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
140000
-
gel filtration
Pseudomonas aeruginosa
Natural Substrates/ Products (Substrates)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
malonate + H+
Pseudomonas aeruginosa
-
acetate + CO2
-
-
?
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Pseudomonas aeruginosa
Q9I6S7 and Q9I6S6
beta subunit MdcD and gamma subunit MdcE
-
Pseudomonas aeruginosa
Q9I6T0 and Q9I6S6
Q9I6T0 i.e. subunit MdcA, Q9I6S6 i.e. subunit MdcE
-
Pseudomonas aeruginosa DSM 22644
Q9I6T0 and Q9I6S6
Q9I6T0 i.e. subunit MdcA, Q9I6S6 i.e. subunit MdcE
-
Purification (Commentary)
Commentary
Organism
nickel bead column chromatography and Sephacryl S-300 gel filtration
Pseudomonas aeruginosa
Substrates and Products (Substrate)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
malonate + H+
-
748747
Pseudomonas aeruginosa
acetate + CO2
-
-
-
?
Subunits
Subunits
Commentary
Organism
heterotetramer
x-ray crystallography
Pseudomonas aeruginosa
Activating Compound (protein specific)
Activating Compound
Commentary
Organism
Structure
additional information
the enzyme is independent from biotin
Pseudomonas aeruginosa
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli BL21Star (DE3), BL21 Rosetta, and B834 (DE3) cells
Pseudomonas aeruginosa
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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
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)
Amino acid exchange
Commentary
Organism
Q100E
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
Q100E/Y102F
inactive
Pseudomonas aeruginosa
S142A
the mutant of subunit MdcE has a roughly 10fold lower catalytic activity compared to the wild type enzyme
Pseudomonas aeruginosa
Y102F
the mutant of subunit MdcE has about wild type catalytic activity
Pseudomonas aeruginosa
Localization (protein specific)
Localization
Commentary
Organism
GeneOntology No.
Textmining
membrane
-
Pseudomonas aeruginosa
16020
-
Molecular Weight [Da] (protein specific)
Molecular Weight [Da]
Molecular Weight Maximum [Da]
Commentary
Organism
140000
-
gel filtration
Pseudomonas aeruginosa
Natural Substrates/ Products (Substrates) (protein specific)
Natural Substrates
Organism
Commentary (Nat. Sub.)
Natural Products
Commentary (Nat. Pro.)
Organism (Nat. Pro.)
Reversibility
malonate + H+
Pseudomonas aeruginosa
-
acetate + CO2
-
-
?
Purification (Commentary) (protein specific)
Commentary
Organism
nickel bead column chromatography and Sephacryl S-300 gel filtration
Pseudomonas aeruginosa
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
malonate + H+
-
748747
Pseudomonas aeruginosa
acetate + CO2
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
heterotetramer
x-ray crystallography
Pseudomonas aeruginosa
Other publictions for EC 4.1.1.88
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [C]
Temperature Range [C]
Temperature Stability [C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [C] (protein specific)
Temperature Range [C] (protein specific)
Temperature Stability [C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
748747
Maderbocus
Crystal structure of a Pseudo ...
Pseudomonas aeruginosa, Pseudomonas aeruginosa DSM 22644
Nat. Commun.
8
160
2017
1
-
1
1
4
-
-
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1
-
1
1
-
6
-
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1
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1
1
-
-
-
-
-
-
-
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-
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1
-
1
-
2
4
-
-
-
-
-
1
-
1
1
-
-
-
1
-
-
-
-
1
1
-
-
-
-
-
-
-
-
-
-
-
-
-
-
685057
Hoenke
Identification of the active s ...
Klebsiella pneumoniae
Biochemistry
39
13233-13240
2000
-
-
-
-
-
-
-
-
-
-
-
-
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4
-
-
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-
-
-
-
-
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1
-
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-
-
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-
1
-
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1
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-
-
1
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-
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684660
Handa
Stereochemical course of bioti ...
Acinetobacter calcoaceticus, Pseudomonas fluorescens
Arch. Biochem. Biophys.
370
93-96
1999
-
-
-
-
-
-
-
-
-
-
-
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5
-
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2
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686494
Koo
Functional evaluation of the g ...
Acinetobacter calcoaceticus
Eur. J. Biochem.
266
683-690
1999
-
-
1
-
-
-
-
3
-
-
-
-
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2
-
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-
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1
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2
1
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-
-
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1
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1
1
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3
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1
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2
1
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685309
Koo
Cloning and sequencing of gene ...
Acinetobacter calcoaceticus
Biochim. Biophys. Acta
1354
49-54
1997
-
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1
-
1
-
-
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5
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1
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1
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1
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1
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-
686492
Hoenke
Sequence of a gene cluster fro ...
Klebsiella pneumoniae
Eur. J. Biochem.
246
530-538
1997
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1
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-
-
-
-
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4
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-
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1
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1
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1
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687464
Byun
-
Subunit organization of bacter ...
Acinetobacter calcoaceticus, Pseudomonas fluorescens
J. Biochem. Mol. Biol.
30
132-137
1997
3
-
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-
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-
12
-
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-
10
-
-
2
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2
2
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2
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2
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2
2
-
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3
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12
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10
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2
2
2
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2
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2
2
-
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-
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-
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-
-
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686490
Schmid
Malonate decarboxylase of Kleb ...
Klebsiella pneumoniae
Eur. J. Biochem.
237
221-228
1996
-
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-
-
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2
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4
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2
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1
1
1
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2
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1
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2
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687489
Kim
Purification and properties of ...
Acinetobacter calcoaceticus
J. Biol. Chem.
269
29636-29641
1994
-
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-
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1
5
1
1
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5
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2
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1
1
1
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2
5
1
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1
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1
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1
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1
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1
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5
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1
1
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5
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1
1
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2
5
1
-
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1
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1
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