Involved in the biosynthesis of lysine in bacteria (including cyanobacteria) and higher plants. The 1992 edition of the Enzyme List erroneously gave the name 2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase to this enzyme.
tetrahydrodipicolinate N-succinyltransferase catalyses the transfer of the succinyl moiety of succinyl-CoA to the alpha-amino group of tetrahydrodipicolinate, the first committed step in the succinylase branch of the DAP biosynthesis pathway, diaminopimelic acid pathway of lysine biosynthesis, overview
no activity ith L-lysine, adipic acid, alpha-amino-adipic acid, L-epsilon-acetyl-lysine, L-glutamate, L-glutamine, L-norleucine, substrate specificity for DapD, overview. Binding of CoA to PaDapD does not induce any large conformational changes, ternary complex structure of DapD with bound CoA and succinate, overview
the enzyme is absolutely specific for the L-2-aminopimelate enantiomer, L-2-aminopimelate and weak inhibitor D-2-aminopimelate bind at the same site of the enzyme. Binding interaction analysis of the ligands in the enzyme active site suggests a misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition
very weak competitive inhibition, L-2-aminopimelate and D-2-aminopimelate bind at the same site of the enzyme. Binding interaction analysis of the ligands in the enzyme active site suggests a misalignment of the amino group of D-2-aminopimelate for nucleophilic attack on the succinate moiety of the co-substrate succinyl-CoA as the structural basis of specificity and inhibition
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structure in complex with succinyl-CoA. Enzyme functions as a trimer, and each monomer consists of an N-terminal helical domain, a left-handed beta-helix domain, and a beta C-terminal domain. The position of the C-terminal domain changes slightly as the cofactor binds to the enzyme. The structure of DapD in complex with the substrate analogue 2-aminopimelate reveals that the analogue is stabilized by conserved residues
crystal structure of DapD from Escherichia coli at 2.0 A resolution is shown. Comparison of the structure with the homologous enzyme from Mycobacterium bovis reveals the C-terminal helix undergoes a large rearrangement upon substrate binding, which contributes to cooperativity in substrate binding
crystal structure in complex with L-2-aminopimelate/coenzyme A and L-2-amino-6-oxopimelate/coenzyme A at 2.0 A resolution, hanging drop vapor diffusion from solutions of 10-13% poly(ethylene glycol) 4000, 94 mM MES, pH 6.4, 94 mM ammonium sulfate, and 4.7% 2-propanol in the presence of 16 mM (D,L)-2-aminopimelate and 2.5 mM CoA
crystal structure of the enzyme in ternary complexes with pimelate/succinyl-CoA and L-2-aminopimelate with the nonreactive cofactor analog succinamide-CoA, 2.3 and 2.0 A resolution, crystals are prepared by cocrystallization using the hanging drop vapor diffusion method, drops are formed by mixing 0.005 ml 27 mg/ml enzyme with an equal volume of 17% poly(ethylene glycol) 4000, 188 mM ammonium sulfate, 94 mM MES, pH 6.4, 4.7% 2-propanol, 20 mM pimelate, and 5 mM succinyl-CoA or 5 mM succinamide-CoA
crystallized from solutions of 16% poly(ethylene glycol) 4000, 200 mM ammonium sulfate, 100 mM HEPES, pH 7.5, and 10% 2-propanol, crystals belong to space group P21, X-ray structure refined to 2.2 A resolution
crystallized in the cubic space group I23 or I213. Diffraction data analysis indicates the presence of five molecules per asymmetric unit. Data exhibit icosahedral point-group symmetry. Enzyme might assembles into a 60-mer exhibiting 235 point-group symmetry and crystallizes as such in space group I23. In this case, the combination of crystallographic and noncrystallographic symmetry elements results in an arrangement of the icosahedrons in the cubic crystal with one pentamer in the asymmetric unit. Another explanation is that the packing of the molecules itself mimics icosahedral symmetry. In this case both space groups I23 and I213 would be possible
purified recombinant His6-tagged DapD with bound L-2-aminopimelate and D-2-aminopimelate or in complex with CoA/succinate, hanging drop vapour diffusion method, mixing of 0.002 ml of 26 mg/ml protein in 25 mM Tris-HCl pH 8.0, and 150 mM NaCl, with or without 10-15 mM CoA, with 0.002 ml of reservoir solution containing 19-20% of PEG3350, 0.3-0.4 M succinate, pH 6.2, and equilibration against reservoir solution for 1-2 days, incubation of the enzyme with formyl-CoA leads to better crystals, soaking of apoenzyme crystals in solution containing L-2-aminopimelate and D-2-aminopimelate, the CoA-complex also contains a succinatemolecule bound next to the acceptor arm of the CoA in the active site cleft, X-ray diffraction structure determination and analysis at 1.8-2.95 A resolution, molecular replacement