Information on EC 4.1.1.47 - Tartronate-semialdehyde synthase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY
4.1.1.47
-
RECOMMENDED NAME
GeneOntology No.
Tartronate-semialdehyde synthase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
2 glyoxylate = 2-hydroxy-3-oxopropanoate + CO2
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
condensation
-
-
-
-
decarboxylation
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
glycolate and glyoxylate degradation
-
-
glycolate and glyoxylate degradation I
-
-
Glyoxylate and dicarboxylate metabolism
-
-
Metabolic pathways
-
-
SYSTEMATIC NAME
IUBMB Comments
glyoxylate carboxy-lyase (dimerizing; tartronate-semialdehyde-forming)
A flavoprotein.
SYNONYMS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Glyoxalate carboligase
-
-
-
-
Glyoxylate carbo-ligase
-
-
-
-
Glyoxylate carboligase
-
-
-
-
Glyoxylate carboxy-lyase
-
-
-
-
Glyoxylate carboxy-lyase (dimerizing and reducing)
-
-
-
-
Glyoxylic carbo-ligase
-
-
-
-
Hydroxymalonic semialdehyde carboxylase
-
-
-
-
Synthase, tartronate semialdehyde
-
-
-
-
Tartronate semialdehyde carboxylase
-
-
-
-
Tartronate-semialdehyde synthase
-
-
-
-
Tartronic semialdehyde carboxylase
-
-
-
-
Tartronic semialdehyde synthase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9027-24-1
-
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain 83
-
-
Manually annotated by BRENDA team
Bacillus fastidiosus 83
strain 83
-
-
Manually annotated by BRENDA team
basonym Alcaligenes eutrophus; strain H16
-
-
Manually annotated by BRENDA team
strain OX1
-
-
Manually annotated by BRENDA team
Cupriavidus oxalaticus OX1
strain OX1
-
-
Manually annotated by BRENDA team
Gloeomonas sp.
-
-
-
Manually annotated by BRENDA team
Pseudomonas putida JM37
-
-
-
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
malfunction
-
a mutation of tartronate semialdehyde synthase does not influence glyoxylic acid conversion
malfunction
Pseudomonas putida JM37
-
a mutation of tartronate semialdehyde synthase does not influence glyoxylic acid conversion
-
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2 glyoxylate
tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2 glyoxylate
tartronate semialdehyde + CO2
show the reaction diagram
P0AEP7
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
Gloeomonas sp.
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
Pseudomonas putida JM37
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
Cupriavidus oxalaticus OX1
-
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
Bacillus fastidiosus 83
-
-
-
-
Glyoxylate
?
show the reaction diagram
-
enzyme of the glyoxylate metabolism
-
-
-
Glyoxylate
?
show the reaction diagram
-
the enzyme is stimulated by light and inhibited during nitrogen starvation, activity is only partially recovered after reintroduction of nitrate
-
-
-
Glyoxylate
?
show the reaction diagram
-
synthesis of the enzyme and thus the degradation of purine derivatives is repressed by high concentrations of adenine
-
-
-
Glyoxylate
?
show the reaction diagram
Bacillus fastidiosus 83
-
enzyme of the glyoxylate metabolism
-
-
-
additional information
?
-
-
the enzyme is unreactive with 2-ketoacids
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
2 glyoxylate
tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
2 glyoxylate
tartronate semialdehyde + CO2
show the reaction diagram
P0AEP7
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
?
show the reaction diagram
-
enzyme of the glyoxylate metabolism
-
-
-
Glyoxylate
?
show the reaction diagram
-
the enzyme is stimulated by light and inhibited during nitrogen starvation, activity is only partially recovered after reintroduction of nitrate
-
-
-
Glyoxylate
?
show the reaction diagram
-
synthesis of the enzyme and thus the degradation of purine derivatives is repressed by high concentrations of adenine
-
-
-
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
-
-
-
-
?
Glyoxylate
Tartronate semialdehyde + CO2
show the reaction diagram
Pseudomonas putida JM37
-
-
-
-
?
Glyoxylate
?
show the reaction diagram
Bacillus fastidiosus 83
-
enzyme of the glyoxylate metabolism
-
-
-
COFACTOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
1,5-Dihydro-5-deaza-FADH2
-
reconstitution of the apoenzyme with 50% recovery of the ativity, Km: 0.00071
5-deaza-FAD
-
can reconstitute the apoenzyme to full activity, Km: 0.00074 mM
FAD
-
1 mol of FAD per mol of dimer, Km: 0.00025 mM; coenzyme
FAD
-
coenzyme
thiamine diphosphate
Gloeomonas sp.
-
cofactor
thiamine diphosphate
-
the structure of glyoxylate carboligase reveals that there is no glutamate in a position to interact with N1 of thiamine diphosphate, the position homologous to the conserved glutamate is occupied by Val51
thiamine diphosphate
P0AEP7
-
thiamine diphosphate
-
dependent on
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Gloeomonas sp.
-
required
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.2
glyoxylate
Gloeomonas sp.
-
-
0.2
glyoxylate
P0AEP7
mutant V51D
0.54
glyoxylate
P0AEP7
mutant V51E
0.9
glyoxylate
P0AEP7
wild-type enzyme
1.1
glyoxylate
P0AEP7
mutant V51S
1.2
glyoxylate
P0AEP7
mutant E52Q
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.25
glyoxylate
P0AEP7
mutant V51D
2.9
glyoxylate
P0AEP7
mutant V51E
18.5
glyoxylate
P0AEP7
mutant V51S
18.9
glyoxylate
P0AEP7
wild-type enzyme
19.7
glyoxylate
P0AEP7
mutant E52Q
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.58
glyoxylate
-
mutant enzyme I479V, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
101
0.65
glyoxylate
-
mutant enzyme I393V, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
101
1.3
glyoxylate
P0AEP7
mutant V51D
101
1.3
glyoxylate
-
mutant enzyme V51D, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
101
1.79
glyoxylate
-
mutant enzyme L478A, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
101
2.06
glyoxylate
-
mutant enzyme I393A, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
101
5.3
glyoxylate
P0AEP7
mutant V51E
101
16.5
glyoxylate
P0AEP7
mutant E52Q
101
17.3
glyoxylate
P0AEP7
mutant V51S
101
21
glyoxylate
P0AEP7
wild-type enzyme
101
21
glyoxylate
-
wild type enzyme, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
101
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
0.06
-
mutant enzyme L478A, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
0.2
P0AEP7
mutant V51D catalyzes the formation of the product nearly two orders of magnitude more slowly than the wild-type enzyme
0.2
-
mutant enzyme V51D, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
0.68
-
mutant enzyme I393A, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
0.84
-
mutant enzyme I479V, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
0.93
-
mutant enzyme I393V, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
2.7
P0AEP7
mutant V51E is about seven times slower than the wild-type enzyme
17.1
P0AEP7
mutant V51S is nearly as active as the wild-type enzyme
17.5
P0AEP7
wild-type enzyme
17.5
-
wild type enzyme, in 50 mM KH2PO4 (pH 7.7), 0.06 M KCl, 0.1 mM thiamin diphosphate, 5 mM MgCl2, at 37C
18.3
P0AEP7
mutant E52Q
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
7 - 7.7
-
-
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
145000
-
gel filtration
4584
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
?
-
x * 66000, SDS-PAGE
?
-
x * 64738, calculation from DNA sequence
dimer
-
2 * 68000, SDS-PAGE
homotetramer
P0AEP7
the apparent functional unit is a dimer with a pair of identical thiamine diphosphate binding sites at the dimer interface
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
glyoxylate carboligase crystallizes with 6 monomers (a tetramer and a dimer) in an asymmetric unit, vapor diffusion hanging-drop, 2-4 microlitre of protein solution (5-15 mg/ml, 100 micromolar ThDP, 10 micromolar FAD, 1mM MgCl2 and 10 mM quinone Q0) are mixed with equal volume of reservoir solution (0.5% PEG6000, 0.5M NaCl, 40 mM DTT), pH 8.00, temperature 294K, space group P41212, resolution 2.70 A
P0AEP7
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
HiTrap Chelating Ni column chromatography
-
nickel affinity chromatography
P0AEP7
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expressed in Nicotiana tabacum cultivar Petit Havana
-
expression in Escherichia coli
P0AEP7
EXPRESSION
ORGANISM
UNIPROT
LITERATURE
in ethylene glycol-treated cells glyoxylate carboligase expression is induced 9.6fold
-
in ethylene glycol-treated cells glyoxylate carboligase expression is induced 9.6fold
Pseudomonas putida JM37
-
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
I393A
-
the mutation leads to a lower catalytic efficiency (3.9%) compared to the wild type enzyme. The enzyme is converted to an acetolactate synthase which can use pyruvate as a substrate with a catalytic efficiency (kcat/Km) of about 20times higher than that of the wild type enzyme
I393V
-
the mutation leads to a lower catalytic efficiency (5.3%) compared to the wild type enzyme
I479V
-
the mutation leads to a lower catalytic efficiency (4.8%) compared to the wild type enzyme
L478A
-
the mutation leads to a lower catalytic efficiency (0.34%) compared to the wild type enzyme
V51D
-
replacement of Val51 by an amino acid with a carboxylate in its side chain (glutamate or aspartate) has striking and significant effects, V51D variant of glyoxylate carboligase undergoes proton exchange at a rate 6fold higher than the wild-type enzyme
V51D
-
the substitution shifts the pH optimum to 6.0-6.2, the mutant is less active (1.2%) than the wild type enzyme (turnover rates are 2 orders of magnitude lower) despite having higher rate of activation of the coenzyme
V51D/I393A
-
the enzyme is converted to an acetolactate synthase which can use pyruvate as a substrate with a catalytic efficiency (kcat/Km) of about 20times higher than that of the wild type enzyme
V51E
-
the mutant is less active than the wild type enzyme (turnover rates are 7fold lower) despite having higher rate of activation of the coenzyme
E52Q
P0AEP7
site-directed mutagenesis
V51D
P0AEP7
site-directed mutagenesis
V51E
P0AEP7
site-directed mutagenesis
V51S
P0AEP7
site-directed mutagenesis