Information on EC 4.2.1.6 - galactonate dehydratase

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

EC NUMBER
COMMENTARY
4.2.1.6
-
RECOMMENDED NAME
GeneOntology No.
galactonate dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
-
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
the immediate dehydration product is the enol which undergoes spontaneous ketonization
-
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
stereochemistry
-
D-galactonate = 2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
it is proposed that the mechanism of the enzyme-catalyzed reaction is initiated by abstraction of the alpha-proton to form a stabilized enolic ion. If the substrate binds at the active site in the extended conformation the stereochemical course of the beta-elimination reaction is expected to be anti
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
elimination
-
-
-
-
PATHWAY
KEGG Link
MetaCyc Link
D-galactonate degradation
-
Galactose metabolism
-
Metabolic pathways
-
Microbial metabolism in diverse environments
-
SYSTEMATIC NAME
IUBMB Comments
D-galactonate hydro-lyase (2-dehydro-3-deoxy-D-galactonate-forming)
The enzyme shows no activity with D-gluconate [2]. cf. EC 4.2.1.140, gluconate/galactonate dehydratase.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D-galactonate dehydrase
-
-
-
-
D-galactonate dehydratase
-
-
-
-
dehydratase, galactonate
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9024-38-8
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
Escherichia coli K10
K10
-
-
Manually annotated by BRENDA team
strain PRL-R3
-
-
Manually annotated by BRENDA team
Klebsiella pneumoniae PRL-R3
strain PRL-R3
-
-
Manually annotated by BRENDA team
Mycobacterium butyricum
-
-
-
Manually annotated by BRENDA team
Mycobacterium friburgensis
-
-
-
Manually annotated by BRENDA team
Mycobacterium jucho
-
-
-
Manually annotated by BRENDA team
strain 279; strain 607
-
-
Manually annotated by BRENDA team
strain 607
-
-
Manually annotated by BRENDA team
Mycobacterium sp. 279
strain 279
-
-
Manually annotated by BRENDA team
Mycobacterium sp. 607
strain 607
-
-
Manually annotated by BRENDA team
no activity in Botrytis cinerea
-
-
-
Manually annotated by BRENDA team
ATCC 27855
-
-
Manually annotated by BRENDA team
Salmonella enterica subsp. enterica serovar Typhimurium LT-12
strain LT-12
-
-
Manually annotated by BRENDA team
L5-30; UR23
-
-
Manually annotated by BRENDA team
Sinorhizobium meliloti L5-30
L5-30
-
-
Manually annotated by BRENDA team
Sinorhizobium meliloti UR23
UR23
-
-
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
D-fuconate
2-keto-3-deoxy-D-fuconate + H2O
show the reaction diagram
Klebsiella pneumoniae, Klebsiella pneumoniae PRL-R3
-
30% of the activity with D-galactonate
-
?
D-galactonate
?
show the reaction diagram
-
-
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium butyricum
-
the enzyme catalyzes the first reaction in the D-galactonate catabolic pathway of non-pathogenic mycobacteria
-
-
-
D-galactonate
?
show the reaction diagram
-
induced by growth on D-galactose, D-galactonate, D-fucose, and L-arabinose over the level present in glucose-grown cells
-
-
-
D-galactonate
?
show the reaction diagram
-
growth on D-galactonate, L-arabinose and D-fucose increases the enzyme activity over the level of cells grown in nutrient broth
-
-
-
D-galactonate
?
show the reaction diagram
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium jucho, Mycobacterium butyricum, Mycobacterium friburgensis
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 607
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 279
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium jucho, Mycobacterium butyricum, Mycobacterium friburgensis
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
-
the enzyme is strictly specific for D-galactonate
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium butyricum
-
the enzyme is strictly specific for D-galactonate
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Sinorhizobium meliloti UR23
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Salmonella enterica subsp. enterica serovar Typhimurium LT-12
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Klebsiella pneumoniae PRL-R3
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium sp. 607
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium sp. 607
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Escherichia coli K10
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Sinorhizobium meliloti L5-30
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Salmonella enterica subsp. enterica serovar Typhimurium LT-2
-
-
-
?
D-galactonate
2-dehydro-3-deoxy-D-galactonate + H2O
show the reaction diagram
Mycobacterium sp. 279
-
-
-
?
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
D-galactonate
?
show the reaction diagram
-
-
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium butyricum
-
the enzyme catalyzes the first reaction in the D-galactonate catabolic pathway of non-pathogenic mycobacteria
-
-
-
D-galactonate
?
show the reaction diagram
-
induced by growth on D-galactose, D-galactonate, D-fucose, and L-arabinose over the level present in glucose-grown cells
-
-
-
D-galactonate
?
show the reaction diagram
-
growth on D-galactonate, L-arabinose and D-fucose increases the enzyme activity over the level of cells grown in nutrient broth
-
-
-
D-galactonate
?
show the reaction diagram
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium jucho, Mycobacterium butyricum, Mycobacterium friburgensis
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 607
-
enzyme of D-galactonate catabolism
-
-
-
D-galactonate
?
show the reaction diagram
Mycobacterium sp. 279
-
enzyme of D-galactonate catabolism
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Co2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+
Mg2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+; optimal concentration: 1 mM
Mg2+
Mycobacterium butyricum
-
highest activity at 0.3 mM MgCl2, Mg2+ or Mn2+ required
Mg2+
-
optimal concentration: 1 mM
Mg2+
-
activates
Mn2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+
Mn2+
Mycobacterium butyricum
-
highest activity at 0.02 mM MnCl2, Mn2+ or Mg2+ required
Ni2+
-
divalent cation required, in the order of decreasing effectiveness: Mg2+, Mn2+, Co2+, Ni2+
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
CdSO4
Mycobacterium butyricum
-
-
CuSO4
Mycobacterium butyricum
-
-
HgCl2
Mycobacterium butyricum
-
-
iodoacetamide
-
-
iodoacetate
Mycobacterium butyricum
-
-
NaF
Mycobacterium butyricum
-
-
PCMB
Mycobacterium butyricum
-
-
ZnSO4
Mycobacterium butyricum
-
reactivated by chelating agents
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
1.3
-
D-fuconate
-
-
0.9
-
D-galactonate
-
-
1
-
D-galactonate
Mycobacterium butyricum
-
-
1.14
-
D-galactonate
-
-
8.33
-
D-galactonate
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4.56
-
Mycobacterium butyricum
-
-
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7.1
-
-
glycylglycine buffer
7.8
8
Mycobacterium butyricum
-
in 100 mM tris-HCl buffer or 50 mM phosphate buffer
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5.9
8
-
pH 5.9: about 40% of maximal activity, pH 8.0: about 25% of maximal activity
6
9
-
about 25% of maximal activity at pH 6.0 and at pH 9.0
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
TEMPERATURE RANGE
TEMPERATURE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
20
60
-
about 45% of maximal activity at 20C and 60C
PDB
SCOP
CATH
ORGANISM
Ralstonia pickettii (strain 12J)
Ralstonia pickettii (strain 12J)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
240000
245000
-
gel filtration, sucrose density gradient centrifugation
240000
245000
-
-
270000
-
Mycobacterium butyricum
-
gel filtration
270000
-
-
-
290000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hexamer
-
6 * 46000, SDS-PAGE
hexamer
Klebsiella pneumoniae PRL-R3
-
6 * 46000, SDS-PAGE
-
tetramer
-
4 * 57000, SDS-PAGE
tetramer
-
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
53
-
-
half-life: more than 1 h
60
-
-
5 min, 6% loss of activity, 60 min, 30% loss of activity
70
-
Mycobacterium butyricum
-
15 min, about 10% loss of activity
70
-
-
5 min, 60% loss of activity. 60 min, 70% loss of activity
75
-
Mycobacterium butyricum
-
10 min, about 60% loss of activity. 15 min, about 90% loss of activity
81
-
-
half-life: 10 min
95
-
-
half-life: 3 min
additional information
-
-
Mg2+, dithiothreitol and D-galactonate increase the rate of thermal inactivation
additional information
-
Mycobacterium butyricum
-
dithiothreitol increases heat sensitivity
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
insensitive to repeated freeze-thaw cycles
-
stable to lyophilization in 0.05 M glycine/0.01 M sodium cacodylate, pH 8.8
-
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
4C or -20C, stable for at least 1 month
-
-20C, 0.05 M glycine-0.01 M sodium cacodylate, pH 8.8, stable for 6 months
-
-20C, 6 months, stable
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-
Mycobacterium butyricum
-