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Information on EC 4.1.3.41 - 3-hydroxy-D-aspartate aldolase and Organism(s) Paracoccus denitrificans and UniProt Accession Q8GRC8

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EC Tree
     4 Lyases
         4.1 Carbon-carbon lyases
             4.1.3 Oxo-acid-lyases
                4.1.3.41 3-hydroxy-D-aspartate aldolase
IUBMB Comments
A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans IFO 13301, is strictly D-specific as to the alpha-position of the substrate, but accepts both the threo and erythro forms at the beta-position. The erythro form is a far better substrate (about 100-fold). The enzyme can also accept D-allothreonine, D-threonine, erythro-3-phenyl-D-serine and threo-3-phenyl-D-serine. Different from EC 4.1.3.14, erythro-3-hydroxy-L-aspartate aldolase. Requires a divalent cation, such as Mg2+, Mn2+ or Co2+.
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This record set is specific for:
Paracoccus denitrificans
UNIPROT: Q8GRC8
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The taxonomic range for the selected organisms is: Paracoccus denitrificans
The expected taxonomic range for this enzyme is: Bacteria, Archaea
Synonyms
d-3-hydroxyaspartate aldolase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D-3-hydroxyaspartate aldolase
-
D-3-hydroxyaspartate aldolase
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
3-hydroxy-D-aspartate glyoxylate-lyase (glycine-forming)
A pyridoxal-phosphate protein. The enzyme, purified from the bacterium Paracoccus denitrificans IFO 13301, is strictly D-specific as to the alpha-position of the substrate, but accepts both the threo and erythro forms at the beta-position. The erythro form is a far better substrate (about 100-fold). The enzyme can also accept D-allothreonine, D-threonine, erythro-3-phenyl-D-serine and threo-3-phenyl-D-serine. Different from EC 4.1.3.14, erythro-3-hydroxy-L-aspartate aldolase. Requires a divalent cation, such as Mg2+, Mn2+ or Co2+.
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2-amino-3-hydroxybutanedioic acid
aminoacetic acid + oxoacetic acid
show the reaction diagram
-
-
-
r
allo-threonine
?
show the reaction diagram
-
-
-
?
D-3-3,4-dihydroxyphenylserine
?
show the reaction diagram
-
-
-
?
D-erythro-3-3,4-methylenedioxyphenylserine
?
show the reaction diagram
-
-
-
?
D-erythro-3-hydroxyaspartate
glycine + glyoxylate
show the reaction diagram
the enzyme is strictly D-specific as to the alpha-position, whereas it does not distinguish between threo and erythro forms at the beta-position
-
-
?
D-erythro-3-phenylserine
?
show the reaction diagram
-
-
-
?
D-threo-3-3,4-methylenedioxyphenylserine
?
show the reaction diagram
-
-
-
?
D-threo-3-phenylserine
?
show the reaction diagram
-
-
-
?
additional information
?
-
the enzyme shows no activity towards L-erythro-3-hydroxyaspartate, L-threo-3-hydroxyaspartate, L-threonine, L-allo-threonine, L-erythro-3-phenylserine, L-threo-3-phenylserine, L-erythro-3-3,4-methylenedioxyphenylserine, and L-threo-3-3,4-methylenedioxyphenylserine
-
-
?
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
pyridoxal 5'-phosphate
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
2.0fold increase of specific activity in the presence of 1 mM Co2+
Mg2+
5.4fold increase of specific activity in the presence of 1 mM Mg2+
Mn2+
8.1fold increase of specific activity in the presence of 1 mM Mn2+
additional information
K+ and Na+ do not have an effect on the enzymatic activity
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
EDTA
82% inhibition at 1 mM
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.4
D-erythro-3-hydroxyaspartate
in 0.02 mM HEPES buffer, pH 8.0, at 30°C
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.36
after 50fold purification, using DL-threo-3-hydroxyaspartate as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
0.6
crude extract, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
14.6
after 50fold purification, using D-threo-3-3,4-methylenedioxyphenylserine as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
17.5
after 50fold purification, using D-erythro-3-3,4-methylenedioxyphenylserine as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
20
after 50fold purification, using D-threonine as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
25
after 50fold purification, using D-allo-threonine as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
30
after 50fold purification, using D-erythro-3-hydroxyaspartate as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
95
after 50fold purification, using D-threo-3-phenylserine as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
99
after 50fold purification, using D-erythro-3-phenylserine as substrate, in 0.02 mM HEPES buffer, pH 8.0, at 30°C
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain IFO 13301
UniProt
Manually annotated by BRENDA team
UNIPROT
ENTRY NAME
ORGANISM
NO. OF AA
NO. OF TRANSM. HELICES
MOLECULAR WEIGHT[Da]
SOURCE
SEQUENCE
LOCALIZATION PREDICTION?
BHCC_PARDE
387
0
41633
Swiss-Prot
-
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
41633
2 * 41633, calculated from amino acid sequence
43000
2 * 43000, SDS-PAGE
80000
gel filtration
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.5 - 8.5
the enzyme is stable between pH 6.5 and 8.5 for 30 min at 30°C
649407
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
45
the enzyme retains 50% activity upon heating at 45°C for 30 min
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
ammonium sulfate fractionation, hydroxyapatite column chromatography, DEAE-Toyopearl column chromatography, phenyl-Toyopearl column chromatography, Superdex 200 gel filtration, and Mono Q column chromatography
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
expressed in Escherichia coli XL1-Blue MRF‘ cells
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Liu, J.Q.; Dairi, T.; Itoh, N.; Kataoka, M.; Shimizu, S.
A novel enzyme, D-3-hydroxyaspartate aldolase from Paracoccus denitrificans IFO 13301: purification, characterization, and gene cloning
Appl. Microbiol. Biotechnol.
62
53-60
2003
Paracoccus denitrificans (Q8GRC8)
Manually annotated by BRENDA team