Substrate and Inhibitor Binding Sites in Corynebacterium glutamicum Diaminopimelate Dehydrogenase

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• 作者：Giovanna Scapin ; Maurizio Cirilli ; Sreelatha G. Reddy ; Yong Gao ; John C. Vederas ; and John S. Blanchard
• 刊名：Biochemistry
• 出版年：1998
• 出版时间：March 10, 1998
• 年：1998
• 卷：37
• 期：10
• 页码：3278 - 3285
• 全文大小：246K
• 年卷期：v.37,no.10(March 10, 1998)
• ISSN：1520-4995

文摘

The three-dimensional structures ofCorynebacterium glutamicum diaminopimelatedehydrogenase as a binary complex with the substratemeso-diaminopimelate (meso-DAP) and a ternarycomplexwith 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 againstX-ray diffractiondata to 2.2 Å. Diaminopimelate dehydrogenase is a homodimer ofapproximately 35 000 molecular weightsubunits and is the only dehydrogenase present in the bacterialdiaminopimelate/lysine biosynthetic pathway.Inhibitors of the enzymes of L-lysine biosynthesishave been proposed as potential antibiotics or herbicides,since mammals lack this metabolic pathway. Diaminopimelatedehydrogenase catalyzes the unique,reversible, pyridine dinucleotide-dependent oxidative deamination ofthe D-amino acid stereocenter ofmeso-diaminopimelate to generateL-2-amino-6-oxopimelate. The enzyme is absolutelyspecific for themeso stereoisomer of DAP and must distinguish between twoopposite chiral amino acid centers on thesame symmetric substrate. The determination of thethree-dimensional structure of theenzyme-meso-diaminopimelate complex allows a description of the molecular basis ofthis stereospecific discrimination.The substrate is bound in an elongated cavity, in which thedistribution of residues that act as hydrogenbond donors or acceptors defines a single orientation in which thesubstrate may bind in order to positionthe D-amino acid center of meso-DAP near theoxidized nucleotide. The previously describedisoxazolineinhibitor binds at the same site as DAP but has its L-aminoacid center positioned where the D-amino acidcenter of meso-DAP would normally be located, therebygenerating a nonproductive inhibitor complex.The relative positions of the N-terminal dinucleotide andC-terminal substrate-binding domains in thediaminopimelate dehydrogenase-NADP⁺, diaminopimelatedehydrogenase-DAP, and diaminopimelatedehydrogenase-NADP⁺-inhibitor complexes confirm ourprevious observations that the enzyme undergoessignificant conformational changes upon binding of both dinucleotideand substrate.