3dap
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C. GLUTAMICUM DAP DEHYDROGENASE IN COMPLEX WITH NADP+ AND THE INHIBITOR 5S-ISOXAZOLINE
OverviewOverview
The three-dimensional structures of Corynebacterium glutamicum, diaminopimelate dehydrogenase as a binary complex with the substrate, meso-diaminopimelate (meso-DAP) and a ternary complex with NADP+ and an, isoxazoline inhibitor [Abbot, S.D., Lane-Bell, P., Kanwar, P.S.S., and, Vederas, J. C. (1994) J. Am. Chem. Soc. 116, 6513-6520] have been solved, and refined against X-ray diffraction data to 2.2 A. Diaminopimelate, dehydrogenase is a homodimer of approximately 35,000 molecular weight, subunits and is the only dehydrogenase present in the bacterial, diaminopimelate/lysine biosynthetic pathway. Inhibitors of the enzymes of, L-lysine biosynthesis have been proposed as potential antibiotics or, herbicides, since mammals lack this metabolic pathway. Diaminopimelate, dehydrogenase catalyzes the unique, reversible, pyridine, dinucleotide-dependent oxidative deamination of the D-amino acid, stereocenter of meso-diaminopimelate to generate L-2-amino-6-oxopimelate., The enzyme is absolutely specific for the meso stereoisomer of DAP and, must distinguish between two opposite chiral amino acid centers on the, same symmetric substrate. The determination of the three-dimensional, structure of the enzyme--meso-diaminopimelate complex allows a description, of the molecular basis of this stereospecific discrimination. The, substrate is bound in an elongated cavity, in which the distribution of, residues that act as hydrogen bond donors or acceptors defines a single, orientation in which the substrate may bind in order to position the, D-amino acid center of meso-DAP near the oxidized nucleotide. The, previously described isoxazoline inhibitor binds at the same site as DAP, but has its L-amino acid center positioned where the D-amino acid center, of meso-DAP would normally be located, thereby generating a nonproductive, inhibitor complex. The relative positions of the N-terminal dinucleotide, and C-terminal substrate-binding domains in the diaminopimelate, dehydrogenase--NADP+, diaminopimelate dehydrogenase--DAP, and, diaminopimelate dehydrogenase--NADP(+)--inhibitor complexes confirm our, previous observations that the enzyme undergoes significant conformational, changes upon binding of both dinucleotide and substrate.
About this StructureAbout this Structure
3DAP is a Single protein structure of sequence from Corynebacterium glutamicum with NDP and DA3 as ligands. Active as Diaminopimelate dehydrogenase, with EC number 1.4.1.16 Structure known Active Sites: INH, N1 and N2. Full crystallographic information is available from OCA.
ReferenceReference
Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase., Scapin G, Cirilli M, Reddy SG, Gao Y, Vederas JC, Blanchard JS, Biochemistry. 1998 Mar 10;37(10):3278-85. PMID:9521647
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