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 ACCESSION NO.
LITERATURE
2 glyoxylate = 2-hydroxy-3-oxopropanoate + CO2
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
condensation
-
-
-
-
decarboxylation
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
glycolate and glyoxylate degradation
BRENDA
BRENDA
BRENDA
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 ACCESSION NO.
COMMENTARY
LITERATURE
GCL
-
gene name
GCL
Pseudomonas putida JM37
-
;
-
Glyoxalate carboligase
-
-
-
-
Glyoxylate carbo-ligase
-
-
-
-
Glyoxylate carboligase
-
-
-
-
Glyoxylate carboligase
-
-
Glyoxylate carboligase
P0AEP7
-
Glyoxylate carboligase
-
-
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
-
-
tartronate semialdehyde synthase
Pseudomonas putida JM37
-
;
-
Tartronate-semialdehyde synthase
-
-
-
-
Tartronic semialdehyde carboxylase
-
-
-
-
Tartronic semialdehyde synthase
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9027-24-1
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
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 ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
COMMENTARY
LITERATURE
Mg2+
Gloeomonas sp.
-
required
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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]
kcat/KM VALUE [1/mMs-1] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
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]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
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
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
145000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
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 ACCESSION NO.
LITERATURE
HiTrap Chelating Ni column chromatography
-
nickel affinity chromatography
P0AEP7
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expressed in Nicotiana tabacum cultivar Petit Havana
-
expression in Escherichia coli
P0AEP7
EXPRESSION
ORGANISM
UNIPROT ACCESSION NO.
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 ACCESSION NO.
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