Information on EC 4.3.3.7 - 4-hydroxy-tetrahydrodipicolinate synthase

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

EC NUMBER
COMMENTARY hide
4.3.3.7
-
RECOMMENDED NAME
GeneOntology No.
4-hydroxy-tetrahydrodipicolinate synthase
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
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
-
-
-
-
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Biosynthesis of antibiotics
-
-
Biosynthesis of secondary metabolites
-
-
L-lysine biosynthesis I
-
-
L-lysine biosynthesis II
-
-
L-lysine biosynthesis III
-
-
L-lysine biosynthesis VI
-
-
Lysine biosynthesis
-
-
lysine metabolism
-
-
Metabolic pathways
-
-
Microbial metabolism in diverse environments
-
-
Monobactam biosynthesis
-
-
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]
Studies of the enzyme from the bacterium Escherichia coli have shown that the reaction can be divided into three consecutive steps: Schiff base formation between pyruvate and an active-site lysine, the addition of L-aspartate-semialdehyde, and finally transimination leading to cyclization with simultaneous dissociation of the product.
CAS REGISTRY NUMBER
COMMENTARY hide
9055-59-8
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
gene dapA or Aq_1143
UniProt
Manually annotated by BRENDA team
Sterne strain
UniProt
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
cabbage
-
-
Manually annotated by BRENDA team
DSM 15242T, JCM11007
SwissProt
Manually annotated by BRENDA team
gene dapA
-
-
Manually annotated by BRENDA team
Cucurbita sp.
-
-
-
Manually annotated by BRENDA team
gene dapA
-
-
Manually annotated by BRENDA team
strain XL1-Blue expressing the enzyme from a plasmid, gene dapA
-
-
Manually annotated by BRENDA team
-
Uniprot
Manually annotated by BRENDA team
barley
-
-
Manually annotated by BRENDA team
four isozymes, MtDHDPS, MtDHDPS2, MtDHDPS3, and MtDHDPS4
-
-
Manually annotated by BRENDA team
Medicago truncatula Jemalong 2HA
four isozymes, MtDHDPS, MtDHDPS2, MtDHDPS3, and MtDHDPS4
-
-
Manually annotated by BRENDA team
Methanothermobacter thermautotrophicum
-
-
-
Manually annotated by BRENDA team
strain MC58
UniProt
Manually annotated by BRENDA team
strain MC58
UniProt
Manually annotated by BRENDA team
tobacco
-
-
Manually annotated by BRENDA team
tobacco
-
-
Manually annotated by BRENDA team
no activity in Homo sapiens
-
-
-
Manually annotated by BRENDA team
Phaseolus sp.
bean
-
-
Manually annotated by BRENDA team
pea
-
-
Manually annotated by BRENDA team
gene dapA
-
-
Manually annotated by BRENDA team
gene dapA
-
-
Manually annotated by BRENDA team
spinach
-
-
Manually annotated by BRENDA team
strain COL
SwissProt
Manually annotated by BRENDA team
methicillin-resistent MRSA252 strain
SwissProt
Manually annotated by BRENDA team
strain OXC141
-
-
Manually annotated by BRENDA team
strain OXC141
-
-
Manually annotated by BRENDA team
wheat
-
-
Manually annotated by BRENDA team
-
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
malfunction
enzyme mutants with deleted dapA gene are viable and able to grow in a mouse lung infection model
metabolism
physiological function
additional information
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
(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
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
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
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
(S)-2,3-dihydropyridine-2,6-dicarboxylate + 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
pyruvate + L-aspartate-4-semialdehyde
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
show the reaction diagram
COFACTOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
FAD
-
produces a 5fold increase in dipicolinic acid production
FMN
-
results in a 3fold increase in dipicolinic acid production
additional information
-
neither NAD+ nor NADP+ are involved in the production of dipicolinic acid
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
-
no effect: Cd2+, Mg2+, Mn2+, Zn2+
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(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
(2E)-4-oxohept-2-enedioic acid
-
-
(2E,5E)-4-oxohepta-2,5-dienedioic acid
-
-
(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)-aspartate 4-semialdehyde
-
-
(S)-aspartate-4-semialdehyde
substrate inhibition
(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'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetic acid)
-
slow-tight inhibition
-
2,2'-benzene-1,3-diylbis(oxoacetic acid)
2-fluoropyruvate
-
-
-
2-oxobutyrate
2-oxoglutarate
-
competitive inhibitor of DHDPS
2-oxopimelic acid
-
-
3-Bromopyruvate
3-bromopyruvate ethyl ester
-
1.2 mM, 85% inhibition
3-Fluoropyruvate
-
competitive inhibitor of DHDPS, and a competitive substrates
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
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
cis-piperidine-2,6-dicarboxylic acid
-
and derivatives
D-Lysine
allosteric inhibitor
diethyl (2E)-4-oxohept-2-enedioate
-
-
diethyl (2E,5E)-4-oxohepta-2,5-dienedioate
-
-
dimethyl (2R,6S)-piperidine-2,6-dicarboxylate
dimethyl (3R,5R)-thiomorpholine-3,5-dicarboxylate
dimethyl (3R,5R)-thiomorpholine-3,5-dicarboxylate 1,1-dioxide
dimethyl (3R,5R)-thiomorpholine-3,5-dicarboxylate 1-oxide
dimethyl (3R,5S)-thiomorpholine-3,5-dicarboxylate
dimethyl (3R,5S)-thiomorpholine-3,5-dicarboxylate 1,1-dioxide
-
20 mM, 19% inhibition; 20 mM, 6% inhibition
dimethyl 2,2'-benzene-1,3-diylbis[(hydroxyimino)ethanoate]
-
-
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
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
DL-diaminopimelic acid
glyoxylic acid
-
-
isoleucine
KCl
-
1 M, 35% inactivation, 2 M, 55% inactivation
L-alpha-(2-aminoethoxyvinyl)-glycine
-
1.2 mM, 100% inhibition
L-arginine
L-aspartate
competitive inhibition, L-aspartate 4-semialdehyde as varied substrate
L-aspartate 4-semialdehyde
L-homoserine
-
1 mM, 13% inhibition
L-lysine
L-methionine
-
at 10 or 100 mM 80% residual activity
L-threonine
Lys
-
strong inhibition
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
lysine ethyl ester
-
-
NaBH4
-
NaBH4 reduction of the pyruvyl-Schiff-base intermediate results in enzyme inactivation
oxaloacetate
non-competitive inhibition, pyruvate as varied substrate
PMSF
-
-
pyridine-2,6-dicarboxylic acid
S-(2-aminoethyl)-L-cysteine
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
Succinic semialdehyde
threo-4-hydroxy-L-lysine
trans-(1SS,3R5S)-3,5-thiomorpholinedicarboxylic acid, dimethyl ester, 1-oxide
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
(2R,3S,6S)-2,6-diamino-3-hydroxyheptanedioic acid
-
134% of the activity without
(2R,6S)-2,6-diamino-2-methyl-3-heptenedioic acid
-
110% of the activity without
(2R,6S/S)-2,6-diamino-6-phosphonohexanoic acid
-
113% of the activity without
2-mercaptoethanol
-
activation
cysteine
-
activation
isocitric acid
-
activation
L-lysine
-
mutagenesis of the lysine binding sites of the Corynebacterium glutamicum enzyme according to the residues in the Escherichia coli enzyme does not conver the expected feedback inhibition but an activation of the nezyme by L-lysine
L-methionine
-
at 10 mM 112% activity, at 100 mM 111% activity
meso-diaminopimelate
-
at 1 mM 108% activity, at 10 mM 122% activity
additional information
-
meso-diaminopimelate has no effect
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.21
(R,S)-aspartate 4-semialdehyde
-
pH 8.0, 30C, with pyruvate
-
0.09 - 2.7
(S)-aspartate 4-semialdehyde
0.137 - 0.32
(S)-aspartate-4-semialdehyde
0.55
DL-aspartate-4-semialdehyde
-
-
0.05 - 37
L-aspartate 4-semialdehyde
0.25 - 5
L-aspartate-4-semialdehyde
0.05 - 35
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 - 465
L-aspartate 4-semialdehyde
223
L-aspartate-4-semialdehyde
Escherichia coli
-
-
0.038 - 465
pyruvate
kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.26 - 898
L-aspartate 4-semialdehyde
0.13 - 820
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
0.07
(S)-aspartate 4-semialdehyde
-
substrate inhibition
0.15
(S)-aspartate-4-semialdehyde
pH and temperature not specified in the publication
0.32 - 3.9
(S)-Lys
3.9 - 4.7
(S)-lysine
0.29
2,2'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetic acid)
-
pH 8.0, 30C
-
2.96
2,2'-benzene-1,3-diylbis(oxoacetic acid)
0.17
2-oxopimelic acid
-
in 50 mM Tris-HCl (pH 8.2), at 22C
0.21
3-hydroxy-2-oxopropanoate
-
time-dependent inhibition, value similar to that of (S)-lysine
22 - 24.8
4-oxo-1,4-dihydropyridine-2,6-dicarboxylic acid
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
6.9 - 14
dimethyl chelidamate
0.33
dimethyl-(2E,2'E)-2,2'-benzene-1,3-diylbis[(hydroxyimino)ethanoate]
-
pH 8.0, 30C
0.04
dimethyl-2,2'-(2-hydroxy-1,3-phenylene)bis(2-oxoacetate)
-
pH 8.0, 30C
-
1 - 1.2
dipicolinic acid
0.8
dipicolinic acid N-oxide
-
-
5.4
L-aspartate 4-semialdehyde
-
-
0.049 - 4.1
L-lysine
0.12 - 0.23
lysine
0.19 - 0.57
pyruvate
pH and temperature not specified in the publication
4.6
S-(2-aminoethyl)-L-cysteine
-
-
0.3
Succinate-semialdehyde
-
in 50 mM Tris-HCl (pH 8.2), at 22C
additional information
additional information
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
20
(2R,6S)-piperidine-2,6-dicarboxylic acid
Escherichia coli
-
IC50: 20 mM, 83% inhibition at 50 mM
0.065
(S)-lysine
Campylobacter jejuni
-
pH and temperature not specified in the publication
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
0.053 - 660
L-lysine
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
0.81
-
crude extract
1.11
-
purified enzyme
1.5
-
purified enzyme, recombinant enzyme in the absence of the substrate pyruvate
1.61
-
2fold purified enzyme
1.81
-
purified wild-type enzyme
2
-
crude extract, recombinant enzyme in the absence of the substrate pyruvate
12
-
crude extract, recombinant enzyme in the presence of the substrate pyruvate
14.5
-
purified recombinant mutant L51K, pH 8.0, temperature not specified in the publication
14.52
-
20.7fold purified mutant T44S
19.2
-
purified recombinant mutant A49K, pH 8.0, temperature not specified in the publication
33
-
purified enzyme, recombinant enzyme in the presence of the substrate pyruvate
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
104
-
purified recombinant His-tagged enzyme, pH not specified in the publication, temperature not specified in the publication
174
purified recombinant His-tagged enzyme, coupled assay, pH and 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
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
7.9 - 8.2
-
-
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
23
-
assay at
25
-
isothermal titration microcalorimetry at
30 - 45
-
assay at 30C and at 45C
85
specific condensation of pyruvate and (S)-aspartate 4-semialdehyde optimally at, assay performed at 60C, structural model reveals that the active site is well conserved
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6.24
sequence analysis
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
Cucurbita sp.
-
-
Manually annotated by BRENDA team
Phaseolus sp.
-
-
Manually annotated by BRENDA team
rarely present
Manually annotated by BRENDA team
additional information
PDB
SCOP
CATH
ORGANISM
UNIPROT
Agrobacterium sp. (strain H13-3)
Agrobacterium sp. (strain H13-3)
Agrobacterium sp. (strain H13-3)
Aquifex aeolicus (strain VF5)
Bacillus clausii (strain KSM-K16)
Bartonella henselae (strain ATCC 49882 / DSM 28221 / Houston 1)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Campylobacter jejuni subsp. jejuni serotype O:2 (strain ATCC 700819 / NCTC 11168)
Clostridium botulinum (strain ATCC 19397 / Type A)
Clostridium botulinum (strain Hall / ATCC 3502 / NCTC 13319 / Type A)
Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / LMG 3730 / NCIMB 10025)
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)