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Information on EC 4.3.3.7 - 4-hydroxy-tetrahydrodipicolinate synthase and Organism(s) Thermotoga maritima and UniProt Accession Q9X1K9

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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Thermotoga maritima
UNIPROT: Q9X1K9
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The taxonomic range for the selected organisms is: Thermotoga maritima
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
dihydrodipicolinate synthase
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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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additional information
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the enzyme belongs to the TIM-barrel family of enzymes
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
dihydrodipicolinate + H2O
show the reaction diagram
catalyses the branch point in lysine biosynthesis
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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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the active site of the monomer is well conserved, with most active-site residues in the same conformation
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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
dihydrodipicolinate + H2O
show the reaction diagram
catalyses the branch point in lysine biosynthesis
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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
additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.15 - 2.2
L-aspartate 4-semialdehyde
0.05 - 2.6
pyruvate
additional information
additional information
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Michaelis-Menten kinetics for wild-type and mutant enzymes, overview
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
35 - 465
L-aspartate 4-semialdehyde
35 - 465
pyruvate
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30 - 45
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assay at 30°C and at 45°C
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Uniprot
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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pyruvate binding occurs near the large interface of DHDPS, and is likely, therefore, to stabilize this solvent-accessible face, which favors the formation of a dimer rather than a monomer. For the DELTAAsp168/Arg237 and DELTAAsp168/Asp171 DHDPS variants addition of pyruvate shifts the equilibrium from primarily monomer to favor almost exclusively dimers. On the other hand, for the DELTAAsp168 DHDPS variant, the monomer-tetramer equilibrium shifts from primarily monomer to primarily tetramer on addition of pyruvate
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
133000
sedimentation equilibrium analysis
33800
4 * 33800, calculated from sequence
130000
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gel filtration
34000
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4 * 34000, SDS-PAGE, role of quaternary structure in the TIM-barrel family of enzymes, overview. Unlike other DHDPS enzymes, but like many thermophilic enzymes, Tm-DHDPS has a large number of charged residues at the quaternary interface. Removal of electrostatic interactions disrupts quaternary structure
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
tetramer
4 * 33800, calculated from sequence
tetramer
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4 * 34000, SDS-PAGE, role of quaternary structure in the TIM-barrel family of enzymes, overview. Unlike other DHDPS enzymes, but like many thermophilic enzymes, Tm-DHDPS has a large number of charged residues at the quaternary interface. Removal of electrostatic interactions disrupts quaternary structure
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
the X-ray crystal structure is described
purified recombinant Tm-DHDPS-DELTAArg-237, vapor diffusion method, mixing of 150 nl protein solution, containing 11.2 mg/ml protein in 20 mM Tris-HCl, pH 8.0, with 150 nl reservoir solution, containing 40% v/v PEG 300, 100 mM phosphate-citrate, buffer, pH 4.2, and 0.02% w/v sodium azide, X-ray diffraction structure determination and analysis at 1.9-2.1 A resolution
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PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information
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construction of mutants Tm-DHDPS-DELTAAsp168, DELTAAsp171, or DELTAArg237 by mutating charged residues, reduction of the number of salt bridges at one of the two tetramerization interface of the enzyme and its interactions results in variants with altered quaternary structure, e.g. monomeric, as shown by analytical ultracentrifugation, gel filtration liquid chromatography, and small angle X-ray scattering, and X-ray crystallographic studies, overview
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
90
7 h, 40% loss of activity. When the enzyme is incubated at 90°C in 8M urea, 60% of the activity is lost after 90 min
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Pearce, F.G.; Perugini, M.A.; McKerchar, H.J.; Gerrard, J.A.
Dihydrodipicolinate synthase from Thermotoga maritima
Biochem. J.
400
359-366
2006
Thermotoga maritima (Q9X1K9), Thermotoga maritima
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
Pearce, F.G.; Dobson, R.C.; Jameson, G.B.; Perugini, M.A.; Gerrard, J.A.
Characterization of monomeric dihydrodipicolinate synthase variant reveals the importance of substrate binding in optimizing oligomerization
Biochim. Biophys. Acta
1814
1900-1909
2011
Thermotoga maritima
Manually annotated by BRENDA team