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Information on EC 4.3.3.7 - 4-hydroxy-tetrahydrodipicolinate synthase and Organism(s) Pseudomonas aeruginosa and UniProt Accession Q9I4W3

for references in articles please use BRENDA:EC4.3.3.7
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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 .
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Pseudomonas aeruginosa
UNIPROT: Q9I4W3
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The taxonomic range for the selected organisms is: Pseudomonas aeruginosa
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
DHDPS
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dihydrodipicolinic acid synthase
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dihydropicolinate synthetase
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pyruvate-aspartic semialdehyde condensing enzyme
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synthase, dihydrodipicolinate
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VEG81
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Vegetative protein 81
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
elimination
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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
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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
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
show the reaction diagram
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?
L-aspartate 4-semialdehyde + pyruvate
(S)-2,3-dihydropyridine-2,6-dicarboxylate + 2 H2O
show the reaction diagram
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?
additional information
?
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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
(2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinic acid + H2O
show the reaction diagram
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?
L-aspartate 4-semialdehyde + pyruvate
(S)-2,3-dihydropyridine-2,6-dicarboxylate + 2 H2O
show the reaction diagram
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?
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
L-lysine
binds at three sites to the enzyme, binding structure, overview
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.17
L-aspartate 4-semialdehyde
pH 8.0, 37°C, recombinant His-tagged enzyme
0.9
pyruvate
pH 8.0, 37°C, recombinant His-tagged enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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
the enzyme catalyzes the first step in the diaminopimelic acid pathway of lysine biosynthesis
additional information
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
dimer
three-dimensional structure determination shows that DHDPS forms a homodimer which is stabilized by several hydrogen bonds and van der Waals forces at the interface, active site structure, overview. Each monomer is composed of two domains, the N-terminal domain consists of residues 1-224, and forms an 8-fold parallel alpha/beta barrel
additional information
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
purified recombinant DHDPS, free or in complex with inhibitor (S)-lysine, 15 mg/ml protein in 50 mM Tris-HCl, pH 8.5, at 20°C using hanging drop vapour diffusion method, mixing of 0.005 ml protein solution with 0.005 ml well solution containing 30% w/v PEG-3350, 170 mM MgCl2, 70 mM Tris-HCl, pH 8.5, and 6% v/v propylene glycol. Crystals obtained without 6% propylene glycol are soaked in the reservoir containing 20 mg/ml (S)-lysine, X-ray diffraction structure determination and analysis at 2.65-2.85 A resolution
purified recombinant His6-tagged enzyme, hanging drop vapour diffusion method, mixing of 0.002 m of 12.5 mg/ml protein solution with 0.002 ml of reservoir solution containing 18% of PEG6000, 0.2 M MgCl2, and 0.1 M TRIS-HCl, pH 7.6, X-ray diffraction structure determination and analysis at 1.6 A resolution, molecular replacement
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65
the recombinant enzyme adopts a characteristic alpha/beta conformation which is retained up to 65°C
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged DHDPS from Escherichia coli strain BL21(DE3) by nickel affinity chromatography
recombinant His6-tagged enzyme from Escherichia coli strain BL21(DE3) by nickel affinity chromatography, the proteolytic cleavage by TEV protease does not remove the N-terminal His6-tag efficiently
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
gene dapA, DNA and amino acid sequence determination and analysis, expression of His-tagged DHDPS in Escherichia coli strain BL21(DE3)
gene dapA, expression of N-terminally His6-tagged enzyme in Escherichia coli strain BL21(DE3)
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
drug development
the intracellular enzyme dihydrodipicolinate synthase a potential drug target because it is essential for the growth of bacteria while it is absent in humans
additional information
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Kaur, N.; Gautam, A.; Kumar, S.; Singh, A.; Singh, N.; Sharma, S.; Sharma, R.; Tewari, R.; Singh, T.P.
Biochemical studies and crystal structure determination of dihydrodipicolinate synthase from Pseudomonas aeruginosa
Int. J. Biol. Macromol.
48
779-787
2011
no activity in Homo sapiens, Pseudomonas aeruginosa (Q9I4W3), Pseudomonas aeruginosa
Manually annotated by BRENDA team
Schnell, R.; Oehlmann, W.; Sandalova, T.; Braun, Y.; Huck, C.; Maringer, M.; Singh, M.; Schneider, G.
Tetrahydrodipicolinate N-succinyltransferase and dihydrodipicolinate synthase from Pseudomonas aeruginosa: structure analysis and gene deletion
PLoS ONE
7
e31133
2012
Pseudomonas aeruginosa (Q9I4W3), Pseudomonas aeruginosa
Manually annotated by BRENDA team