Information on EC 4.1.1.85 - 3-dehydro-L-gulonate-6-phosphate decarboxylase

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The expected taxonomic range for this enzyme is: Bacteria

EC NUMBER
COMMENTARY
4.1.1.85
-
RECOMMENDED NAME
GeneOntology No.
3-dehydro-L-gulonate-6-phosphate decarboxylase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
-
-
-
-
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
formation and stabilization of an enediolate anion intermediate is part of reaction mechanism, mechanism overview, the active site is located at the dimer interface, structure-function relationship, overview
P39304
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
active site structure, substrate binding structure, formation of a cis-1,2-enediolate anion intermediate, intermediate structure and reaction mechanism involving residues Lys64, Asp67, and His136, overview
-
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
catalytic mechanism, formation and Mg2+-stabilization of an cis-1,2-enediolate anion intermediate, important residues for the stereospecific exchange of the pro-1S hydrogen are Lys64, Asp67, Glu112, Arg139, and Lys64, the latter stabilizes the intermediate via hydrogen bonds to O1 and O2 of the intermediate involving conserved active site residue Asp67, His136 takes part in hydrogen exchange with solvent of the 1-hydroxymethylene group of the product, overview
-
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
formation and stabilization of an 1,2-enediolate anion intermediate, protonation of the intermediate involving residues Glu112, His136, and Arg139, active site structure-function relationship, overview
-
3-dehydro-L-gulonate 6-phosphate + H+ = L-xylulose 5-phosphate + CO2
show the reaction diagram
active site structure, substrate binding structure, structure-function relationship, overview
P39304
PATHWAY
KEGG Link
MetaCyc Link
Ascorbate and aldarate metabolism
-
L-ascorbate degradation I (bacterial, anaerobic)
-
L-ascorbate degradation II (bacterial, aerobic)
-
Metabolic pathways
-
Microbial metabolism in diverse environments
-
Pentose and glucuronate interconversions
-
SYSTEMATIC NAME
IUBMB Comments
3-dehydro-L-gulonate-6-phosphate carboxy-lyase (L-xylulose-5-phosphate-forming)
Requires Mg2+. Along with EC 5.1.3.22, L-ribulose-5-phosphate 3-epimerase, this enzyme is involved in a pathway for the utilization of L-ascorbate by Escherichia coli.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3-keto-L-gulonate 6-phosphate decarboxylase
-
-
3-keto-L-gulonate 6-phosphate decarboxylase
-
-
3-keto-L-gulonate 6-phosphate decarboxylase
-
-
3-keto-L-gulonate 6-phosphate decarboxylase
-
-
3-keto-L-gulonate 6-phosphate decarboxylase
-
-
-
additional information
-
the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily
additional information
-
the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily, overview
additional information
-
the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily
additional information
-
the enzyme belongs to the orotidine 5'-monophosphate decarboxylase OMPDC suprafamily
CAS REGISTRY NUMBER
COMMENTARY
406722-60-9
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
gene ulaD
Uniprot
Manually annotated by BRENDA team
gene ulaD or sgaH encoded in the yia-sga operon, and gene sgbH encoded in the yia-sgb operon
-
-
Manually annotated by BRENDA team
strain UA159
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-, P39304
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
P39304
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
P39304
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
stereochemistry
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
P39304
substrate binding structure
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
SgaH/UlaD and SgbH
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
step in the catabolic pathway of L-ascorbate utilization
-
-
?
additional information
?
-
-
enzyme catalyzes one step in the L-ascorbate utilization pathway, L-ascorbate is converted to L-xylulose, overview, enzymes SgaH/UlaD and SgbH are not active with 3-dehydro-L-gulonate
-
-
-
additional information
?
-
-
the D-arabino-hex-3-ulose 6-phosphate synthase of Methylomonas aminofaciens also performs the 3-keto-L-gulonate 6-phosphate decarboxylase reaction with lower activity than for the preferred reaction catalyzing Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate, proton exchange reaction rates, overview
-
-
-
additional information
?
-
P39304
the enzyme also performs the Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase reaction with low activity catalyzing Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate, while the Methylomonas aminofaciens enzyme also performs the 3-keto-L-gulonate 6-phosphate decarboxylase reaction, overview
-
-
-
additional information
?
-
-
the enzyme also performs the Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase reaction with low activity catalyzing Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate, while the Methylomonas aminofaciens enzyme also performs the 3-keto-L-gulonate 6-phosphate decarboxylase reaction, proton exchange reaction rates, overview
-
-
-
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
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-, P39304
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
P39304
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
P39304
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
-
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
SgaH/UlaD and SgbH
-
-
?
3-dehydro-L-gulonate 6-phosphate + H+
L-xylulose 5-phosphate + CO2
show the reaction diagram
-
step in the catabolic pathway of L-ascorbate utilization
-
-
?
additional information
?
-
-
enzyme catalyzes one step in the L-ascorbate utilization pathway, L-ascorbate is converted to L-xylulose, overview
-
-
-
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
L-gulonate 6-phosphate
P39304
binding structure involving Glu33 and Asp62 and Mg2+
L-xylitol 5-phosphate
-
binding structure
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.15
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112Q/H136A
0.22
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112Q/H136A/R139V
0.27
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant D67A/H136A
0.3
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutants K64R and D67N/H136A
0.31
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112Q
0.34
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112A
0.36
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant R139V
0.37
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant H136N
0.41
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant D67N
0.44
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64R/H136A
0.5
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant D67A
0.51
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A
0.52
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant H136Q
0.55
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/E112Q/H136A
0.58
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/H136A
0.65
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112A/H136A
0.67
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant wild-type enzyme
0.7
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant H136A
0.77
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112A/H136A/R139V
0.9
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/R139V
0.91
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112D/R139V/T169A
1.4
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutants H136A/R139V and K64A/E112A/H136A/R139V
5.4
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant enzyme
additional information
-
additional information
-
analysis of kinetics and activity of the mutant enzymes, overview
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.19
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant D67A/H136A
0.2
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112Q/H136A/R139V
0.21
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112A/H136A/R139V
0.23
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112Q/H136A
0.26
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/E112A/H136A/R139V
0.3
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112A
0.45
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112A/H136A
0.75
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/H136A
1.1
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant D67N
1.2
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/R139V
1.3
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant D67N/H136A
1.4
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant H136Q
2.4
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutants D67A and H136A
2.4
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112D/R139V/T169A
2.9
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A/E112Q/H136A
4
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant E112Q
4.2
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64R/H136A
4.3
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant H136N
8.3
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64A
8.9
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant R139V
9.2
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant H136A/R139V
15
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant enzyme
17
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant mutant K64R
51
-
3-dehydro-L-gulonate 6-phosphate
-
pH 7.5, 25C, recombinant wild-type enzyme
51
-
3-dehydro-L-gulonate 6-phosphate
-
SgaH, pH 7.5, 25C
64
-
3-dehydro-L-gulonate 6-phosphate
-
SgbH, pH 7.5, 25C
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.5
-
-
assay at
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
25
-
-
assay at
PDB
SCOP
CATH
ORGANISM
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
E112Q
-
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
E112Q/H136A
-
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
H136A
-
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
K64A
-
site-directed mutagenesis, crystal structure determination and analysis, the mutant enzyme shows altered reaction intermediate binding at the active site, reaction mechanism, and stereochemistry
D67A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
D67A/H136A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
D67N
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
D67N/H136A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
E112A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
E112A/H136A
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
E112A/H136A/R139V
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
E112D/R139V
P39304
site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme
E112D/R139V/T169A
-
site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme
E112D/R139V/T169A/R192A
-
site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme
E112D/T169A
P39304
site-directed mutagenesis, mutations alter the Escherichia coli residues to those of Methylomonas aminofaciens D-arabino-hex-3-ulose 6-phosphate synthase, a homologous enzyme, also altering the enzyme activity of the 3-keto-L-gulonate 6-phosphate decarboxylase performing th Mg2+-dependent aldol condensation between formaldehyde and D-ribulose 5-phosphate with highly increased activity compared to the wild-type enzyme
E112Q
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
E112Q/H136A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
E112Q/H136A/R139V
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
E33K
-
site-directed mutagenesis, inactive mutant
H136A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
H136A/R139V
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
H136N
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
H136Q
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
K64A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
K64A/E112A/H136A/R139V
-
site-directed mutagenesis, highly reduced activity compared to the wild-type enzyme
K64A/E112Q/H136A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
K64A/H136A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
K64A/R139V
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
K64R
-
site-directed mutagenesis, slightly reduced activity compared to the wild-type enzyme
K64R/H136A
-
site-directed mutagenesis, reduced activity compared to the wild-type enzyme
R139V
-
site-directed mutagenesis, slightly reduced activity compared to the wild-type enzyme