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Literature summary extracted from

  • Atkinson, S.C.; Dogovski, C.; Downton, M.T.; Czabotar, P.E.; Dobson, R.C.; Gerrard, J.A.; Wagner, J.; Perugini, M.A.
    Structural, kinetic and computational investigation of Vitis vinifera DHDPS reveals new insight into the mechanism of lysine-mediated allosteric inhibition (2013), Plant Mol. Biol., 81, 431-446.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
4.3.3.7 gene dapA, expression of His-tagged enzyme in Escherichia coli strain BL21(DE3) Vitis vinifera

Crystallization (Commentary)

EC Number Crystallization (Comment) Organism
4.3.3.7 purified recombinant His-tagged enzyme, hanging drop vapor diffusion method, mixing of 0.002 ml of protein in 20 mM pyruvate and 20 mM lysine, with 0.002 ml of reservoir solution containing 0.1 M MES, pH 6.5, 6% v/v PEG 20000, X-ray diffraction structure determination and analysis at 2.40 A resolution Vitis vinifera

Inhibitors

EC Number Inhibitors Comment Organism Structure
4.3.3.7 L-lysine feedback inhibition, binding of lysine to the allosteric cleft of the enzyme, cooperative binding, structural mechanism for allosteric inhibition, overview. With respect to L-aspartate-4-semialdehyde, lysine is a noncompetitive inhibitor Vitis vinifera

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
4.3.3.7 additional information
-
 additional information Michaelis-Menten kinetics Vitis vinifera

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
4.3.3.7 pyruvate + L-aspartate-4-semialdehyde Vitis vinifera
-
 (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
4.3.3.7 Vitis vinifera D7U7T8 gene dapA
-

Purification (Commentary)

EC Number Purification (Comment) Organism
4.3.3.7 recombinant His-tagged enzyme from Escherichia coli strain BL21(DE3) by metal affinity chromatography Vitis vinifera

Reaction

EC Number Reaction Comment Organism Reaction ID
4.3.3.7 pyruvate + L-aspartate-4-semialdehyde = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O the reaction proceeds via a ping-pong kinetic mechanism in which pyruvate binds and forms a Schiff base to an active-site lysine residue (Lys184 in Vitis vinifera enzyme). L-aspartate-4-semialdehyde then reacts with the resultant enamine and following cyclization forms the product (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate Vitis vinifera
a

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
4.3.3.7 additional information coupled assay with dihydrodipicolinate reductase Vitis vinifera ?
-
 ?
4.3.3.7 pyruvate + L-aspartate-4-semialdehyde
-
 Vitis vinifera (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + H2O
-
 ?

Subunits

EC Number Subunits Comment Organism
4.3.3.7 homotetramer homotetramer of four identical (beta/alpha)8-barrel monomers, a dimer of tight dimers, with two tight-dimers binding in a head-to-head manner, with the active site situated near the center of the barrel, molecular dynamics simulations Vitis vinifera

Synonyms

EC Number Synonyms Comment Organism
4.3.3.7 DHDPS
-
 Vitis vinifera
4.3.3.7 dihydrodipicolinate synthase
-
 Vitis vinifera

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
4.3.3.7 30
-
 assay at Vitis vinifera

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
4.3.3.7 8
-
 assay at Vitis vinifera

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
4.3.3.7 additional information
-
 additional information kinetic and thermodynamics of allosteric inhibitin by lysine, overview Vitis vinifera
4.3.3.7 0.049
-
 L-lysine versus L-aspartate-4-semialdehyde, pH 8.0, 30°C, recombinant enzyme Vitis vinifera

General Information

EC Number General Information Comment Organism
4.3.3.7 metabolism lysine biosynthesis in plants is tightly regulated by feedback inhibition of the end product on dihydrodipicolinate synthase, the first enzyme of the lysine-specific branch Vitis vinifera