Information on EC 4.2.1.81 - D(-)-tartrate dehydratase

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The expected taxonomic range for this enzyme is: Proteobacteria

EC NUMBER
COMMENTARY
4.2.1.81
-
RECOMMENDED NAME
GeneOntology No.
D(-)-tartrate dehydratase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
(S,S)-tartrate = oxaloacetate + H2O
show the reaction diagram
requires Fe2+; requires Fe2+ or Mn2+. cf. EC 4.2.1.32 L(+)-tartrate dehydratase
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
C-O bond cleavage by elimination of water
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
(S,S)-tartrate hydro-lyase (oxaloacetate-forming)
Requires Fe2+ or Mn2+. cf. EC 4.2.1.32 L(+)-tartrate dehydratase.
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
D-tartrate dehydratase
-
-
-
-
dehydratase, D-tartrate
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
82532-88-5
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
strains G2 and Ch
-
-
Manually annotated by BRENDA team
Rhodobacter sphaeroides Si4
Si4
-
-
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
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
-
-
-
ir
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
-
-
-
?
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
-
no substrates are L(+)-tartrate, meso-tartrate, glyceraldehyde, glycerate, glycerol, gluconate, 6-phosphogluconate, galactonate, mannonate, mannitol or sorbitol
at high or low pH-values or in the presence of metal ions spontaneous decarboxylation to pyruvate
ir
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
-
mechanism in which Lys 184 initiates the reaction by abstraction of the R-proton to generate a Mg2+-stabilized enediolate intermediate, and the vinylogous beta-elimination of the 3-OH group is general acid-catalyzed by the His 322, accomplishing the anti-elimination of water. The replacement of the leaving group by solvent-derived hydrogen is stereorandom
-
-
?
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
Rhodobacter sphaeroides Si4
-
-
-
ir
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
Rhodobacter sphaeroides Si4
-
no substrates are L(+)-tartrate, meso-tartrate, glyceraldehyde, glycerate, glycerol, gluconate, 6-phosphogluconate, galactonate, mannonate, mannitol or sorbitol
at high or low pH-values or in the presence of metal ions spontaneous decarboxylation to pyruvate
ir
additional information
?
-
-
involved in D-tartrate catabolism
-
-
-
additional information
?
-
-
involved in D-tartrate catabolism
-
-
-
additional information
?
-
Rhodobacter sphaeroides Si4
-
involved in D-tartrate catabolism
-
-
-
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
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
-
-
-
ir
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
-
-
-
?
(S,S)-tartrate
oxaloacetate + H2O
show the reaction diagram
Rhodobacter sphaeroides Si4
-
-
-
ir
additional information
?
-
-
involved in D-tartrate catabolism
-
-
-
additional information
?
-
-
involved in D-tartrate catabolism
-
-
-
additional information
?
-
Rhodobacter sphaeroides Si4
-
involved in D-tartrate catabolism
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
-
requirement, can replace Fe2+ or Co2+ with about 30% (strain G2) and 55% (strain Ch) efficiency
Co2+
-
requirement, 0.5 mM, equally effective as Fe2+
Divalent cations
-
not
Divalent cations
-
requirement
Fe2+
-
requirement, 0.1 mM, equally effective as Co2+
Mg2+
-
requirement, can replace Fe2+ or Co2+ with about 60% (strain G2) and 80% (strain Ch) efficiency
Mn2+
-
requirement, can replace Fe2+ or Co2+ with about 65% efficiency
Ni2+
-
requirement, can replace Fe2+ or Co2+ with about 30% (strain G2) and 80% (strain Ch) efficiency
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
beta-mercaptoethanol
-
-
D-malate
-
weak
dithioerythritol
-
-
EDTA
-
Fe2+ or Co2+ restores; strong
L(+)-Tartrate
-
weak
L(+)-Tartrate
-
weak
L-Malate
-
weak
meso-tartrate
-
-
meso-tartrate
-
competitive inhibitor
additional information
-
no inhibition by iodoacetamide, N-ethylmaleimide; no inhibition by iodoacetate
-
additional information
-
no inhibition by iodoacetate
-
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.035
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme K184R
0.048
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme H322N
0.086
-
(S,S)-Tartrate
-
25C, pH 7.5, wild-type enzyme
0.18
-
(S,S)-Tartrate
-
-
0.18
-
(S,S)-Tartrate
-
strain Ch
0.6
-
(S,S)-Tartrate
-
strain G2
6.2
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme H322A
7.7
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme H322Q
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.0019
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme H322Q
0.0027
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme H322A
0.0058
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme K184R
0.0069
-
(S,S)-Tartrate
-
25C, pH 7.5, mutant enzyme H322N
7.3
-
(S,S)-Tartrate
-
25C, pH 7.5, wild-type enzyme
19.8
-
D-Tartrate
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
3.1
-
-
strain Ch
13.6
-
-
strain G2
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
-
highest activity in Tris-HCl buffer, less effective are N-2'-hydroxyethylpiperazine-2-ethanesulfonic acid, glycylglycine, triethanolamine-HCl, N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid, imidazole or potassium phosphate buffer
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
assay at
pI VALUE
pI VALUE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
5.5
-
-
isoelectric focusing
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
Rhodobacter sphaeroides Si4
-
-
-
Manually annotated by BRENDA team
PDB
SCOP
CATH
ORGANISM
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
Bradyrhizobium diazoefficiens (strain JCM 10833 / IAM 13628 / NBRC 14792 / USDA 110)
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
72000
-
-
strain Ch, gel filtration
78000
-
-
strain G2, gel filtration
158000
-
-
gel filtration, ultracentrifugation
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
2 * 38500, SDS-PAGE
tetramer
-
4 * 39500, SDS-PAGE
tetramer
Rhodobacter sphaeroides Si4
-
4 * 39500, SDS-PAGE
-
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
all crystals, wild type TarD liganded with Mg2+, selenomethionine-substituted TarD liganded with Mg2+, wild-type TarD liganded with Mg2+ and meso-tartrate, and the K184A mutant liganded with Mg2+ and D-tartrate, are grown by the hanging drop method at room temperature
-
pH STABILITY
pH STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
4.9
-
-
5 min, 50% loss of activity at 30C
6
8.7
-
stable at least 5 min at 30C
9.4
-
-
5 min, 50% loss of activity at 30C
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
30
-
-
stable at least 5 min at pH 6-8.7, 50% loss of activity at pH 4.9 and pH 9.4 after 5 min
45
-
-
30 min, 50% loss of activity
50
-
-
3 min, 50% loss of activity
55
-
-
1 min, 50% loss of activity
60
-
-
12 s, 50% loss of activity
GENERAL STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
omission of Mg2+ from standard buffer results in rapid inactivation during purification with irreversible loss of activity after ammonium sulfate precipitation, Mg2+, Mn2+, Zn2+, Ca2+ or Co2+ stabilizes, not Ni2+
-
OXIDATION STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
insensitive to O2, no thiols required for protection, 15 h stable at 22C
-
648404
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-20C, 1.5 mg enzyme/ml 0.1 M Tris-HCl buffer, pH 7.2, 1 mM MgCl2, 20% loss of activity within 5 months
-
22C, 50% loss of activity within 10 days
-
4C, 50% loss of activity within 6 weeks
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
to near homogeneity
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression in Escherichia coli strain BL21
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
H322A
-
kcatKm is 193000fold lower than wild-type value
H322N
-
kcatKm is 607fold lower than wild-type value
H322Q
-
kcatKm is 340000fold lower than wild-type value
K102A
-
inactive mutant protein
K102M
-
inactive mutant protein
K184A
-
inactive mutant enzyme
K184R
-
reduced activity. kcat/Km is 500fold lower than wild-type value
additional information
-
selection of strains for constitutive production of enzyme for selective cleavage of racemic tartaric acid and quantitative detection of D(-)-tartrate
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
biotechnology
-
constitutive production of enzyme for selective cleavage of racemic tartaric acid and quantitative detection of D(-)-tartrate