Any feedback?
Please rate this page
(enzyme.php)
(0/150)

BRENDA support

BRENDA Home
show all | hide all No of entries

Information on EC 4.3.3.7 - 4-hydroxy-tetrahydrodipicolinate synthase and Organism(s) Escherichia coli and UniProt Accession P0A6L2

for references in articles please use BRENDA:EC4.3.3.7
Please wait a moment until all data is loaded. This message will disappear when all data is loaded.
EC Tree
     4 Lyases
         4.3 Carbon-nitrogen lyases
             4.3.3 Amine-lyases
                4.3.3.7 4-hydroxy-tetrahydrodipicolinate synthase
IUBMB Comments
The reaction can be divided into three consecutive steps: Schiff base formation with pyruvate, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product. The product of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1,2], and the enzyme was classified accordingly as EC 4.2.1.52, dihydrodipicolinate synthase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual product of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate , and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate synthase. However, the identity of the product is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all .
Specify your search results
Select one or more organisms in this record: ?
This record set is specific for:
Escherichia coli
UNIPROT: P0A6L2
Show additional data
Do not include text mining results
Include (text mining) results
Include results (AMENDA + additional results, but less precise)
Word Map
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
Synonyms
dhdps, dihydrodipicolinate synthase, dhdps2, pa1010, dihydrodipicolinic acid synthase, cjdhdps, cdhdps, 4-hydroxy-tetrahydrodipicolinate synthase, mrsa-dhdps, dhdpa synthase, more
SYNONYM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dihydrodipicolinate synthase
-
EC 4.2.1.52
formerly
DHDPS
dihydrodipicolinate synthase
-
-
dihydrodipicolinic acid synthase
-
-
-
-
dihydropicolinate synthetase
-
-
-
-
pyruvate-aspartic semialdehyde condensing enzyme
-
-
-
-
synthase, dihydrodipicolinate
-
-
-
-
VEG81
-
-
-
-
Vegetative protein 81
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
show the reaction diagram
pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
-
-
SYSTEMATIC NAME
IUBMB Comments
L-aspartate-4-semialdehyde hydro-lyase [adding pyruvate and cyclizing; (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate-forming]
The reaction can be divided into three consecutive steps: Schiff base formation with pyruvate, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product. The product of the enzyme was initially thought to be (S)-2,3-dihydrodipicolinate [1,2], and the enzyme was classified accordingly as EC 4.2.1.52, dihydrodipicolinate synthase. Later studies of the enzyme from the bacterium Escherichia coli have suggested that the actual product of the enzyme is (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate [3], and thus the enzyme has been reclassified as 4-hydroxy-tetrahydrodipicolinate synthase. However, the identity of the product is still controversial, as more recently it has been suggested that it may be (S)-2,3-dihydrodipicolinate after all [5].
CAS REGISTRY NUMBER
COMMENTARY hide
9055-59-8
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
(S)-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
(S)-aspartate-4-semialdehyde + pyruvate
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
show the reaction diagram
-
-
-
?
L-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + 2 H2O
show the reaction diagram
L-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
pyruvate + L-aspartate-4-semialdehyde
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
show the reaction diagram
-
-
-
?
(S)-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
(S)-aspartate-4-semialdehyde + pyruvate
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
show the reaction diagram
L-aspartate 4-semialdehyde + pyruvate
(S)-2,3-dihydropyridine-2,6-dicarboxylate + 2 H2O
show the reaction diagram
-
-
-
-
?
L-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + 2 H2O
show the reaction diagram
L-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
-
-
-
-
?
L-aspartate-4-semialdehyde + pyruvate
?
show the reaction diagram
-
synthesis of the precursor of dipicolinic acid which plays a key role in bacterial sporulation process
-
-
?
L-aspartate-4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
pyruvate + (R,S)-aspartate-4-semialdehyde
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
show the reaction diagram
-
-
-
-
?
pyruvate + DL-aspartate-4-semialdehyde
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
show the reaction diagram
-
-
-
-
?
pyruvate + L-aspartate-4-semialdehyde
2,3-dihydrodipicolinate + ?
show the reaction diagram
-
2,3-dihydrodipicolinate is the product of the synthase reaction. One or more of the NMR peaks previously assigned to the product of the dihydrodipicolinate synthase reaction, presumed to be (4S)-4-hydroxy-2,3,4,5-tetrahydro-(2S)-dipicolinate, actually arises from a non-enzymatic reaction
-
-
?
additional information
?
-
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
(S)-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
(S)-aspartate-4-semialdehyde + pyruvate
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
show the reaction diagram
-
-
-
?
L-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
-
-
-
?
(S)-aspartate 4-semialdehyde + pyruvate
dihydrodipicolinate + H2O
show the reaction diagram
-
first step in the biosynthesis of lysine, overview
-
?
(S)-aspartate-4-semialdehyde + pyruvate
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
show the reaction diagram
L-aspartate 4-semialdehyde + pyruvate
(S)-2,3-dihydropyridine-2,6-dicarboxylate + 2 H2O
show the reaction diagram
-
-
-
-
?
L-aspartate-4-semialdehyde + pyruvate
?
show the reaction diagram
-
synthesis of the precursor of dipicolinic acid which plays a key role in bacterial sporulation process
-
-
?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2E)-4-oxohept-2-enedioic acid
-
(2E,5E)-4-oxohepta-2,5-dienedioic acid
-
(S)-Lys
partial mixed inhibition with respect to pyruvate and partial non-competitive inhibition with resoect to L-aspartate 4-semialdehyde
(S)-lysine
2,2'-benzene-1,3-diylbis(oxoacetic acid)
-
2-oxopimelic acid
-
3-hydroxy-2-oxopropanoate
time-dependent inhibition, qualitatively followed by mass spectrometry, initial noncovalent adduct formation, followed by the slow formation of the covalent adduct
diethyl (2E)-4-oxohept-2-enedioate
-
diethyl (2E,5E)-4-oxohepta-2,5-dienedioate
-
dimethyl 2,2'-benzene-1,3-diylbis[(hydroxyimino)ethanoate]
-
dipicolinic acid
-
L-aspartate 4-semialdehyde
competitive inhibition at high substrate concentrations
L-lysine
lysine
inhibition of wild-type DHDPS by lysine with respect to pyruvate is partial and uncompetitive, and partial non-competitive with respect to L-aspartate 4-semialdehyde. Ethanolamine, n-butylamine, 1-amino-2-propanol, 3-amino-1-propanol, iso-butylamine and Tris-HCl cannot rescue activity
NaBH4
NaBH4 reduction of the pyruvyl-Schiff-base intermediate results in enzyme inactivation
Sodium borohydride
wild-type DHDPS is inactivated when incubated with pyruvate, whereas incubation with L-aspartate 4-semialdehyde has no effect
Succinate-semialdehyde
reversible inhibitor which is competitive with respect to L-aspartate-4-semialdehyde and uncompetitive with respect to pyruvate
(1SR,3R,5S)-1-hydroxy-3,5-bis(methoxycarbonyl)thiomorpholin-1-ium
-
30 mM, 18% inhibition
(1SS,3R,5S)-1-hydroxy-3,5-bis(methoxycarbonyl)thiomorpholin-1-ium
-
9 mM, 48% inhibition
(2R,6S)-piperidine-2,6-dicarboxylic acid
(3R,5R)-thiomorpholine-3,5-dicarboxylic acid
-
50 mM, 32% inhibition
(3R,5R)-thiomorpholine-3,5-dicarboxylic acid 1,1-dioxide
-
50 mM, 11% inhibition
(3R,5S)-thiomorpholine-3,5-dicarboxylic acid 1,1-dioxide
-
50 mM, 14% inhibition
(S)-lysine
2,2'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetic acid)
-
slow-tight inhibition
2,2'-benzene-1,3-diylbis(oxoacetic acid)
-
slow inhibition
2-oxobutyrate
-
competitive inhibitor of DHDPS
2-oxoglutarate
-
competitive inhibitor of DHDPS
3-Bromopyruvate
-
-
3-fluoro-2-oxopropanoate
-
-
3-Fluoropyruvate
-
competitive inhibitor of DHDPS, and a competitive substrates
3-hydroxypyruvate
-
competitive inhibitor of DHDPS and a competitive substrate
4-oxo-1,4-dihydropyridine-2,6-dicarboxylic acid
Bromopyruvate
-
is an irreversible inhibitor of DHDPS
cis-(1SS,3R5S)-3,5-thiomorpholinedicarboxylic acid, dimethyl ester, 1-oxide
-
20 mM, 8% inhibition
cis-piperidine-2,6-dicarboxylic acid
-
and derivatives
dimethyl (2R,6S)-piperidine-2,6-dicarboxylate
-
20 mM, 92% inhibition
dimethyl (3R,5R)-thiomorpholine-3,5-dicarboxylate
-
20 mM, 12% inhibition
dimethyl (3R,5R)-thiomorpholine-3,5-dicarboxylate 1,1-dioxide
dimethyl (3R,5S)-thiomorpholine-3,5-dicarboxylate
dimethyl 4-oxo-1,4-dihydropyridine-2,6-dicarboxylate
-
-
dimethyl chelidamate
-
IC50: 14 mM. 99% inhibition at 50 mM, noncompetitive with respect to both substrates
dimethyl piperidine-2,6-dicarboxylate
-
-
dimethyl pyridine-2,6-dicarboxylate
-
20 mM, 5% inhibition
dimethyl-(2E,2'E)-2,2'-benzene-1,3-diylbis[(hydroxyimino)ethanoate]
-
slow inhibition
dimethyl-2,2'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetate)
-
slow-tight inhibition
dipicolinic acid
dipicolinic acid di-imidate
-
-
dipicolinic acid N-oxide
-
0.8 mM 50% inhibition
L-lysine
L-threonine
-
at 100 mM 23% residual activity, at 100 mM 33% residual activity
pyridine-2,6-dicarboxylic acid
-
-
S-(2-aminoethyl)-L-cysteine
-
4.6 mM, 50% inhibition
Succinic semialdehyde
-
-
trans-(1SS,3R5S)-3,5-thiomorpholinedicarboxylic acid, dimethyl ester, 1-oxide
-
20 mM, 20% inhibition
additional information
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-methionine
-
at 10 mM 112% activity, at 100 mM 111% activity
meso-diaminopimelate
-
at 1 mM 108% activity, at 10 mM 122% activity
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.09 - 2.7
(S)-aspartate 4-semialdehyde
0.12 - 37
L-aspartate 4-semialdehyde
0.08 - 35
pyruvate
0.21
(R,S)-aspartate-4-semialdehyde
-
pH 8.0, 30°C, with pyruvate
0.11
(S)-aspartate 4-semialdehyde
0.137 - 0.3
(S)-aspartate-4-semialdehyde
0.55
DL-aspartate-4-semialdehyde
-
-
0.11 - 0.14
L-aspartate 4-semialdehyde
0.25
L-aspartate-4-semialdehyde
-
-
0.13 - 0.827
pyruvate
additional information
additional information
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.12 - 124
(S)-aspartate 4-semialdehyde
0.038 - 12.4
L-aspartate 4-semialdehyde
0.038 - 78
pyruvate
124
(S)-aspartate 4-semialdehyde
-
30°C
9.8
L-aspartate 4-semialdehyde
-
pH 8.0, 30°C, recombinant wild-type enzyme
223
L-aspartate-4-semialdehyde
-
-
9.8 - 124
pyruvate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.26 - 600
L-aspartate 4-semialdehyde
0.13 - 488
pyruvate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
32.4
(2E)-4-oxohept-2-enedioic acid
mono-ene inhibitor
1.63
(2E,5E)-4-oxohepta-2,5-dienedioic acid
more potent than the corresponding mono-ene inhibitors
0.32 - 3.9
(S)-Lys
2.96
2,2'-benzene-1,3-diylbis(oxoacetic acid)
49% inhibition at 5 mM, mimics the substrate pyruvate, binding with the active site lysine residue, slow inhibition
0.17
2-oxopimelic acid
in 50 mM Tris-HCl (pH 8.2), at 22°C
0.21
3-hydroxy-2-oxopropanoate
time-dependent inhibition, value similar to that of (S)-lysine
10.9
diethyl (2E)-4-oxohept-2-enedioate
mono-ene inhibitor
4.95
diethyl (2E,5E)-4-oxohepta-2,5-dienedioate
best inhibitor
0.33
dimethyl 2,2'-benzene-1,3-diylbis[(hydroxyimino)ethanoate]
15% inhibition at 1 mM, binding with the active site lysine residue, kinetic analysis corresponds to slow-binding model of inhibition
0.18 - 4.1
L-lysine
0.12 - 0.23
lysine
0.3
Succinate-semialdehyde
in 50 mM Tris-HCl (pH 8.2), at 22°C
0.32 - 3.9
(S)-lysine
0.29
2,2'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetic acid)
-
pH 8.0, 30°C
2.96
2,2'-benzene-1,3-diylbis(oxoacetic acid)
-
pH 8.0, 30°C
22 - 24.8
4-oxo-1,4-dihydropyridine-2,6-dicarboxylic acid
6.9 - 14
dimethyl chelidamate
0.33
dimethyl-(2E,2'E)-2,2'-benzene-1,3-diylbis[(hydroxyimino)ethanoate]
-
pH 8.0, 30°C
0.04
dimethyl-2,2'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetate)
-
pH 8.0, 30°C
1 - 1.2
dipicolinic acid
0.8
dipicolinic acid N-oxide
-
-
0.21 - 3.9
L-lysine
4.6
S-(2-aminoethyl)-L-cysteine
-
-
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.21 - 0.22
L-lysine
20
(2R,6S)-piperidine-2,6-dicarboxylic acid
Escherichia coli
-
IC50: 20 mM, 83% inhibition at 50 mM
22
4-oxo-1,4-dihydropyridine-2,6-dicarboxylic acid
Escherichia coli
-
i.e. chelidamic acid, IC50: 22 mM, 99% inhibition at 50 mM, uncompetitive inhibitor with respect to both substrates
14
dimethyl chelidamate
Escherichia coli
-
IC50: 14 mM. 99% inhibition at 50 mM, noncompetitive with respect to both substrates
20
dipicolinic acid
Escherichia coli
-
IC50: 20 mM, competitive inhibitor
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.0034
purified mutant T44V
0.008
purified mutant Y133F
0.27
purified mutant Y107F
0.72
crude extract of mutant T44S
1.81
purified wild-type enzyme
14.52
20.7fold purified mutant T44S
1.11
-
purified enzyme
14.5
-
purified recombinant mutant L51K, pH 8.0, temperature not specified in the publication
19.2
-
purified recombinant mutant A49K, pH 8.0, temperature not specified in the publication
454.2
-
purified recombinant mutant H56K, pH 8.0, temperature not specified in the publication
478.1
-
purified recombinant mutant E84T, pH 8.0, temperature not specified in the publication
500.8
-
purified recombinant wild-type enzyme, pH 8.0, temperature not specified in the publication
559.4
-
purified recombinant mutant A49P, pH 8.0, temperature not specified in the publication
60.5
-
purified recombinant mutant L51T, pH 8.0, temperature not specified in the publication
81.6
-
purified recombinant mutant A49W, pH 8.0, temperature not specified in the publication
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.6
assay at, measured using a coupled assay with lactate dehydrogenase to detect pyruvate production
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23
-
assay at
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
metabolism
physiological function
complementation of the auxotrophy of Escherichia coli XL1-Blue KanRDELTAdapA cells only with the plasmid pUCX:dapA encoding wild-type DHDPS
metabolism
physiological function
additional information
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
123000
tetramer size of mutant Y107W, analytical ultracentrifugation
125300
tetramer size of wild-type protein, mass spectrometry, mutant form Y107W reveals a mixture of primarily monomer and tetramer in solution
125400
tetramer size of mutant Y107W, mass spectrometry
31000
x * 31000, SDS-PAGE
31290
monomer size of mutant Y107W, deduced from sequence
31310
monomer size of wild-type, mass spectrometry
31320
monomer size of mutant Y107W, mass spectrometry
64000
dimer size of mutant Y107W, analytical ultracentrifugation
112000
-
gel filtration
134000
-
calculation from sedimentation and diffusion coefficient, Stokes' radius
31270
-
mass spectrometry
32000
-
4 * 32000, Lys161 is the active site, SDS-PAGE
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 31000, SDS-PAGE
homotetramer
tetramer
tetramer
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
by the hanging drop-vapour diffusion method, mutants K161A and K161R solved at resolutions of 2.0 and 2.1 A, respectively. They show no changes in their secondary or tertiary structures when compared to the wild-type structure. Crystal structure of mutant K161A with pyruvate bound at the active site solved at a resolution of 2.3 A, reveals a defined binding pocket for pyruvate that is thus not dependent upon lysine 161
complexed with pyruvate, the substrate analogs succinate alpha-semialdehyde and alpa-ketopimelic acid, the inhibitor dipicolinic acid, and the natural feedback inhibitor L-lysine, hanging drop vapor diffusion method, in the presence of beta-octyl glucoside using either potassium phosphate buffer (pH 10) or potassium citrate buffer (pH 7.0) as the precipitant
crystal structure of mutant enzyme R138H and R138A, hanging-drop vapor diffusion method
examination of the specificity of the active site of DHDPS, co-crystallization with the substrate analogue oxaloacetate, data-collection and refinement statistics
hanging-drop vapour-diffusion method, crystal struture of native and (S)-lysine-bound dihydropicolinate synthase are presented to 1.9 A and 2.0 A resolution, respectively
in complex with beta-hydroxypyruvate, hanging drop vapor-diffusion method, data processing and refinement statistics
mutant T44S, crystals are isomorphous to those of the wild-type enzyme, no significant modification in its tertiary or quaternary structure from that of the wild-type enzyme
mutant Y107W, hanging-drop vapor diffusion method, diffraction to beyond 2.0 A resolution, data collection and refinement statistics, solid-state structure of the mutant enzyme largely unchanged
purified enzyme in complex with pyruvate and substrate analogue succinic acid semialdehyde, hanging drop vapor diffusion method, mixing of 0.003 ml of 8 mg/mL protein in 20 mM Tris-HCl, pH 8.0, with 0.0012 ml of precipitant solution containing 1.8 M K2HPO4, pH 10, and 0.0006 ml of N-octyl-beta-R-glucopyranoside 6% w/v, 4°C, 3-4 days, soaking in cryoprotectant solution containing 1.8 M K2HPO4, pH 10, glycerol 20% v/v, and 120 mM succinic acid semialdehyde and 40 mM pyruvate, X-ray diffraction structure determination and analysis at 2.3 A resolution
purified recombinant wild-type and mutant enzymes, hanging or sitting drop vapour diffusion method, at 4°C and 21°C, 0.006 ml protein solutions: about 10 mg/ml protein, 1.8 M K2PO4, pH 10.0, N-octyl-beta-R-glucopyranoside 6% w/v, + 2 ml reservoir solution: 1.8 M K2PO4, pH 10.0, 3-4 days, X-ray diffraction structure determination and analysis at 2.35-2.5 A resolution
crystal structure at 2.5 A resolution
-
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D193A
removal of water mediated hydrogen-bond network
D193Y
removal of water mediated hydrogen-bond network and introduction of steric bulk to alter surface topology
H118Y
mutant enzyme H56K is more conducive to L-lysine production than mutant H118Y
H56K
mutant enzyme H56K is more conducive to L-lysine production than mutant H118Y
K161A
K161R
catalytically active, significant decrease in activity. Is not inactivated when incubated with pyruvate and the reducing agent sodium borohydride. Negligible heat production associated with pyruvate binding to the mutant enzyme, consistent with the lack of Schiff base formation
Q196D
removal of hydrogen bonds and charge-charge repulsion, shortened side chain places charged carboxyl groups proximal at interface
Q234D
removal of hydrogen bond and charge-charge repulsion with negatively charged E175. Quaternary structure appears closest to that of the wild-type enzyme
R138A
activity is approximately 0.1% of wild-type activity, Km-value for L-aspartate 4-semialdehyde is significantly higher than the wild-type value, shows the same IC50 values as the wild-type enzyme, but different partial inhibition patterns
R138H
activity is approximately 0.1% of wild-type activity, Km-value for L-aspartate 4-semialdehyde is significantly higher than the wild-type value, shows the same IC50 values as the wild-type enzyme, but different partial inhibition patterns
T44S
the active site is intact, returns much but not all activity likely due to the flexibility of Ser44. Increased flexibility in the active site, which appears to facilitate the binding/reaction of substrate analogues
T44V
site-directed mutagenesis, reduced activity, structure is similar to the wild-type enzyme
Y107F
Y107W
mutant, site-directed mutagenesis
Y133F
site-directed mutagenesis, reduced activity, structure is similar to the wild-type enzyme
A49K
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
A49P
-
site-directed mutagenesis, the mutant shows increased activity compared to the wild-type enzyme and is still sensitive to L-lysine
A49W
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
E84T
-
site-directed mutagenesis, the mutant shows slightly reduced activity compared to the wild-type enzyme and is insensitive to L-lysine
H56K
-
site-directed mutagenesis, the mutant shows slightly reduced activity compared to the wild-type enzyme and is insensitive to L-lysine
L197D/Y107W
-
site-directed mutagenesis, the mutant forms a monomer that is catalytically active, but with reduced catalytic efficiency, displaying 8% of the specific activity of the wild-type enzyme. The Michaelis constants for the substrates pyruvate and for (S)-aspartate semialdehyde increase by an order of magnitude. L197D/Y107W is expressed as a folded monomer
L51K
-
site-directed mutagenesis, the mutant shows highly reduced activity compared to the wild-type enzyme
L51T
-
site-directed mutagenesis, the mutant shows reduced activity compared to the wild-type enzyme and is sill sensitive to L-lysine
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
20 - 95
-
purified recombinnat wild-type enzyme
59.5
-
melting temperature in the absence of substrates
61.3
-
is thermally stabilised by the first substrate, pyruvate
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
repeated freezing/thawing causes loss of activity
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20°C, 20 mM Tris-HCl buffer, pH 8.0
-20°C, 0.06 M phosphate buffer, pH 7.5, 3 months, no loss of activity
-
-20°C, 10 mM triethanolamine buffer, pH 7.5, 10 mM 2-mercaptoethanol, stable for at least 6 months
-
-20°C, addition of glycerol, several months, no loss of activity
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
gel filtration
mutant T44S, no pyruvate added to the crude extract prior to sonication, purified by heat shock and ion-exchange chromatography, 20.7fold with a yield of 123%
recombinant enzyme 5.7fold from Escherichia coli strain XL-1 Blue
recombinant wild-type 5.8fold, recombinant mutant Y107F 17.6fold, recombinant mutant T44V 15.8fold, and recombinant mutant Y133F 18fold
wild-type and mutants, by gel filtration
wild-type DHDPS, and the coupling enzyme, DHDPR, by ammonium sulphate fractionation
by centrifugation and gel filtration
-
enzyme expressed from plasmid in strain XL1-Blue, 69fold
-
recombinant His-tagged wild-type and mutant enzymes from Escherichia coli strain BL21 Star (DE3) by nickel affinity chromatography and gel filtration
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
DHDPS mutants expressed in Escherichia coli strain AT997r-
DHDPS overexpressed in Escherichia coli AT997recA-, transformed with site-directed mutants based on the pBluescript plasmid pJG001
expressed in Escherichia coli XL-1 Blue harbouring the plasmid pJG001
expressed in Escherichia coli XL1-blue, pBluescript vector, recombinant protein
expressed in Escherichia coli, pJG001 plasmid for site-directed mutagenesis, mutant Y107W expressed in dapA-negative strain AT997r-
mutant T44S expressed in dapA-deficient Escherichia coli AT997r-
overexpression of wild-type and mutant enzymes in strain XL1-Blue
recombinant enzyme expression in Escherichia coli strain XL-1 Blue using plasmid pJG001
the dapA and dapA-H225* genes introduced into the vector pUCX, to transform the auxotrophic Escherichia coli XL1-Blue KanRDELTAdapA cells, under the control of a lac promoter/repressor system. Mutations in dapA introduced into the pET-151/D-TOPO plasmid. C-terminal truncated DHDPS (H225*) expressed in Escherichia coli BL21 Star (DE3)
wild-type and mutant cloned into plasmid pET-151/D-TOPO and expressed in Escherichia coli BL21 Star (DE3) competent cells
as His-tagged constructs
-
expression in Escherichia coli
-
expression in Nicotina tabacum
-
expression in Solanum tuberosum
-
gene dapA, overexpression of His-tagged wild-type and mutant enzymes in Escherichia coli strain BL21 Star (DE3)
-
gene dapA, recombinant expression of lysine-insensitive mutants in Escherichia coli strain MG1655 with a yield improved by 46% compared to the wild-type enzyme
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
the enzyme is an attractive target for the design and synthesis of herbicides and antibiotics
food industry
L-lysine, one of the essential amino acids required for nutrition in animals and humans, is widely used in the food industry, medical industry, etc. L-lysine has been mainly produced by microbial fermentation employing mutant strains of bacteria. An L-lysine high-yielding strain is developed by modification of aspartokinase III and dihydrodipicolinate synthetase
medicine
L-lysine, one of the essential amino acids required for nutritionin animals and humans, is widely used in the food industry, medical industry, etc. L-lysine has been mainly produced by microbial fermentation employing mutant strains of bacteria. An L-lysine high-yielding strain is developed by modification of aspartokinase III and dihydrodipicolinate synthetase
biotechnology
-
enzyme is a target for herbicide and anti-microbial action
medicine
-
development of species-specific inhibitors of DHDPS as potential antibacterials
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Shedlarski, J.G.
Pyruvate-aspartic semialdehyde condensing enzyme (Escherichia coli)
Methods Enzymol.
17B
129-134
1971
Escherichia coli
-
Manually annotated by BRENDA team
Shedlarski, J.G.; Gilvarg, C.
The pyruvate-aspartic semialdehyde condensing enzyme of Escherichia coli
J. Biol. Chem.
245
1362-1373
1970
Escherichia coli
Manually annotated by BRENDA team
Laber, B.; Gomis-Rueth, F.X.; Romao, M.J.; Huber, R.
Escherichia coli dihydrodipicolinate synthase. Identification of the active site and crystallization
Biochem. J.
268
691-695
1992
Escherichia coli
-
Manually annotated by BRENDA team
Mirwaldt, C.; Korndoerfer, I.; Huber, R.
The crystal structure of dihydrodipicolinate synthase from Escherichia coli at 2.5 A resolution
J. Mol. Biol.
246
227-239
1995
Escherichia coli
Manually annotated by BRENDA team
Perl, A.; Shaul, O.; Galili, G.
Regulation of lysine synthesis in transgenic potato plants expressing a bacterial dihydrodipicolinate synthase in their chloroplasts
Plant Mol. Biol.
19
815-823
1992
Escherichia coli, Solanum tuberosum
Manually annotated by BRENDA team
Shaul, O.; Galili, G.
Concerted regulation of lysine and threonine synthesis in tobacco plants expressing bacterial feedback-insensitive aspartate kinase and dihydrodipicolinate synthase
Plant Mol. Biol.
23
759-768
1993
Escherichia coli, Nicotiana tabacum
Manually annotated by BRENDA team
Couper, L.; McKendrick, J.E.; Robins, D.J.
Pyridine and piperidine derivatives as inhibitors of dihydrdipicolinic acid synthase, a key enzyme in the diaminopimelate pathway to L-lysine
Bioorg. Med. Chem. Lett.
4
2267-2272
1994
Escherichia coli
-
Manually annotated by BRENDA team
Karsten, W.E.
Dihydrodipicolinate synthase from Escherichia coli: pH dependent changes in the kinetic mechanism and kinetic mechanism of allosteric inhibition by L-lysine
Biochemistry
36
1730-1739
1997
Escherichia coli
Manually annotated by BRENDA team
Blickling, S.; Knaeblein, J.
Feedback inhibition of dihydrodipicolinate synthase enzymes by L-lysine
Biol. Chem.
378
207-210
1997
Escherichia coli
Manually annotated by BRENDA team
Dobson, R.C.; Gerrard, J.A.; Pearce, F.G.
Dihydrodipicolinate synthase is not inhibited by its substrate, (S)-aspartate beta-semialdehyde
Biochem. J.
377
757-762
2004
Escherichia coli, Escherichia coli XL1-Blue
Manually annotated by BRENDA team
Dobson, R.C.; Valegard, K.; Gerrard, J.A.
The crystal structure of three site-directed mutants of Escherichia coli dihydrodipicolinate synthase: further evidence for a catalytic triad
J. Mol. Biol.
338
329-339
2004
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Dobson, R.C.; Griffin, M.D.; Jameson, G.B.; Gerrard, J.A.
The crystal structures of native and (S)-lysine-bound dihydrodipicolinate synthase from Escherichia coli with improved resolution show new features of biological significance
Acta Crystallogr. Sect. D
61
1116-1124
2005
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Dobson, R.C.; Devenish, S.R.; Turner, L.A.; Clifford, V.R.; Pearce, F.G.; Jameson, G.B.; Gerrard, J.A.
Role of arginine 138 in the catalysis and regulation of Escherichia coli dihydrodipicolinate synthase
Biochemistry
44
13007-13013
2005
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Dobson, R.C.; Griffin, M.D.; Roberts, S.J.; Gerrard, J.A.
Dihydrodipicolinate synthase (DHDPS) from Escherichia coli displays partial mixed inhibition with respect to its first substrate, pyruvate
Biochimie
86
311-315
2004
Escherichia coli
Manually annotated by BRENDA team
Turner, J.J.; Gerrard, J.A.; Hutton, C.A.
Heterocyclic inhibitors of dihydrodipicolinate synthase are not competitive
Bioorg. Med. Chem.
13
2133-2140
2005
Escherichia coli
Manually annotated by BRENDA team
Mitsakos, V.; Dobson, R.C.; Pearce, F.G.; Devenish, S.R.; Evans, G.L.; Burgess, B.R.; Perugini, M.A.; Gerrard, J.A.; Hutton, C.A.
Inhibiting dihydrodipicolinate synthase across species: Towards specificity for pathogens?
Bioorg. Med. Chem. Lett.
18
842-844
2007
Escherichia coli, Mycobacterium tuberculosis, Staphylococcus aureus
Manually annotated by BRENDA team
Devenish, S.R.; Gerrard, J.A.; Jameson, G.B.; Dobson, R.C.
The high-resolution structure of dihydrodipicolinate synthase from Escherichia coli bound to its first substrate, pyruvate
Acta Crystallogr. Sect. F
64
1092-1095
2008
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Pearce, F.G.; Dobson, R.C.; Weber, A.; Lane, L.A.; McCammon, M.G.; Squire, M.A.; Perugini, M.A.; Jameson, G.B.; Robinson, C.V.; Gerrard, J.A.
Mutating the tight-dimer interface of dihydrodipicolinate synthase disrupts the enzyme quaternary structure: toward a monomeric enzyme
Biochemistry
47
12108-12117
2008
Escherichia coli (P0A6L2)
Manually annotated by BRENDA team
Boughton, B.A.; Griffin, M.D.; ODonnell, P.A.; Dobson, R.C.; Perugini, M.A.; Gerrard, J.A.; Hutton, C.A.
Irreversible inhibition of dihydrodipicolinate synthase by 4-oxo-heptenedioic acid analogues
Bioorg. Med. Chem.
16
9975-9983
2008
Escherichia coli (P0A6L2)
Manually annotated by BRENDA team
Boughton, B.A.; Dobson, R.C.; Gerrard, J.A.; Hutton, C.A.
Conformationally constrained diketopimelic acid analogues as inhibitors of dihydrodipicolinate synthase
Bioorg. Med. Chem. Lett.
18
460-463
2008
Escherichia coli (P0A6L2)
Manually annotated by BRENDA team
Dobson, R.C.; Griffin, M.D.; Devenish, S.R.; Pearce, F.G.; Hutton, C.A.; Gerrard, J.A.; Jameson, G.B.; Perugini, M.A.
Conserved main-chain peptide distortions: a proposed role for Ile203 in catalysis by dihydrodipicolinate synthase
Protein Sci.
17
2080-2090
2008
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Griffin, M.D.; Dobson, R.C.; Gerrard, J.A.; Perugini, M.A.
Exploring the dihydrodipicolinate synthase tetramer: how resilient is the dimer-dimer interface?
Arch. Biochem. Biophys.
494
58-63
2010
Escherichia coli (P0A6L2)
Manually annotated by BRENDA team
Guo, B.B.; Devenish, S.R.; Dobson, R.C.; Muscroft-Taylor, A.C.; Gerrard, J.A.
The C-terminal domain of Escherichia coli dihydrodipicolinate synthase (DHDPS) is essential for maintenance of quaternary structure and efficient catalysis
Biochem. Biophys. Res. Commun.
380
802-806
2009
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Devenish, S.R.; Huisman, F.H.; Parker, E.J.; Hadfield, A.T.; Gerrard, J.A.
Cloning and characterisation of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis
Biochim. Biophys. Acta
1794
1168-1174
2009
Escherichia coli, Neisseria meningitidis (Q9JZR4), Neisseria meningitidis, Neisseria meningitidis MC58 (Q9JZR4)
Manually annotated by BRENDA team
Domigan, L.J.; Scally, S.W.; Fogg, M.J.; Hutton, C.A.; Perugini, M.A.; Dobson, R.C.; Muscroft-Taylor, A.C.; Gerrard, J.A.; Devenish, S.R.
Characterisation of dihydrodipicolinate synthase (DHDPS) from Bacillus anthracis
Biochim. Biophys. Acta
1794
1510-1516
2009
Escherichia coli, Bacillus anthracis (Q81WN7), Bacillus anthracis
Manually annotated by BRENDA team
Dobson, R.C.; Perugini, M.A.; Jameson, G.B.; Gerrard, J.A.
Specificity versus catalytic potency: The role of threonine 44 in Escherichia coli dihydrodipicolinate synthase mediated catalysis
Biochimie
91
1036-1044
2009
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Muscroft-Taylor, A.C.; Soares da Costa, T.P.; Gerrard, J.A.
New insights into the mechanism of dihydrodipicolinate synthase using isothermal titration calorimetry
Biochimie
92
254-262
2010
Thermotoga maritima, Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Soares da Costa, T.P.; Muscroft-Taylor, A.C.; Dobson, R.C.; Devenish, S.R.; Jameson, G.B.; Gerrard, J.A.
How essential is the essential active-site lysine in dihydrodipicolinate synthase?
Biochimie
92
837-845
2010
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Devenish, S.R.; Blunt, J.W.; Gerrard, J.A.
NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase
J. Med. Chem.
53
4808-4812
2010
Escherichia coli
Manually annotated by BRENDA team
Muscroft-Taylor, A.C.; Catchpole, R.J.; Dobson, R.C.; Pearce, F.G.; Perugini, M.A.; Gerrard, J.A.
Disruption of quaternary structure in Escherichia coli dihydrodipicolinate synthase (DHDPS) generates a functional monomer that is no longer inhibited by lysine
Arch. Biochem. Biophys.
503
202-206
2010
Escherichia coli
Manually annotated by BRENDA team
Blickling, S.; Renner, C.; Laber, B.; Pohlenz, H.; Holak, T.; Huber, R.
Reaction mechanism of Escherichia coli dihydrodipicolinate synthase investigated by X-ray crystallography and NMR spectroscopy
Biochemistry
36
24-33
1997
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Geng, F.; Chen, Z.; Zheng, P.; Sun, J.; Zeng, A.
Exploring the allosteric mechanism of dihydrodipicolinate synthase by reverse engineering of the allosteric inhibitor binding sites and its application for lysine production
Appl. Microbiol. Biotechnol.
97
1963-1971
2012
Corynebacterium glutamicum, Corynebacterium glutamicum ATCC 13032, Escherichia coli, Escherichia coli MG1655
Manually annotated by BRENDA team
Boughton, B.A.; Hor, L.; Gerrard, J.A.; Hutton, C.A.
1,3-Phenylene bis(ketoacid) derivatives as inhibitors of Escherichia coli dihydrodipicolinate synthase
Bioorg. Med. Chem.
20
2419-2426
2012
Escherichia coli
Manually annotated by BRENDA team
Reboul, C.F.; Porebski, B.T.; Griffin, M.D.; Dobson, R.C.; Perugini, M.A.; Gerrard, J.A.; Buckle, A.M.
Structural and dynamic requirements for optimal activity of the essential bacterial enzyme dihydrodipicolinate synthase
PLoS Comput. Biol.
8
e1002537
2012
Escherichia coli, Staphylococcus aureus
Manually annotated by BRENDA team
Boughton, B.; Dobson, R.; Hutton, C.
The crystal structure of dihydrodipicolinate synthase from Escherichia coli with bound pyruvate and succinic acid semialdehyde: unambiguous resolution of the stereochemistry of the condensation product
Proteins
80
2117-2122
2012
Escherichia coli (P0A6L2), Escherichia coli
Manually annotated by BRENDA team
Karsten, W.E.; Nimmo, S.A.; Liu, J.; Chooback, L.
Identification of 2, 3-dihydrodipicolinate as the product of the dihydrodipicolinate synthase reaction from Escherichia coli
Arch. Biochem. Biophys.
653
50-62
2018
Escherichia coli, Escherichia coli JM109
Manually annotated by BRENDA team
Xu, J.; Han, M.; Ren, X.; Zhang, W.
Modification of aspartokinase III and dihydrodipicolinate synthetase increases the production of L-lysine in Escherichia coli
Biochem. Eng. J.
114
79-86
2016
Escherichia coli (P0A6L2), Escherichia coli LATR11 (P0A6L2)
-
Manually annotated by BRENDA team