PDBsum entry 2dap

Oxidoreductase

PDB id: 2dap

Contents

Protein chain

320 a.a. *

Ligands

API

Waters ×150

* Residue conservation analysis

PDB id:

2dap

Name:

Oxidoreductase

Title:

C. Glutamicum dap dehydrogenase in complex with dap

Structure:

Diaminopimelic acid dehydrogenase. Chain: a. Synonym: dapdh. Ec: 1.4.1.16

Source:

Corynebacterium glutamicum. Organism_taxid: 1718. Atcc: 13032. Plasmid: pet23a

Biol. unit:

Dimer (from PDB file)

Resolution:

2.20Å R-factor: 0.170 R-free: 0.258

Authors:

G.Scapin,M.Cirilli,S.G.Reddy,Y.Gao,J.C.Vederas,J.S.Blanchard

Key ref:

G.Scapin et al. (1998). Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase. Biochemistry, 37, 3278-3285. PubMed id: 9521647 DOI: 10.1021/bi9727949

Date:

23-Dec-97 Release date: 08-Apr-98

Protein chain

P04964  (DAPDH_CORGL) -  Meso-diaminopimelate D-dehydrogenase from Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / BCRC 11384 / JCM 1318 / LMG 3730 / NCIMB 10025)

Seq: 320 a.a.

Struc: 320 a.a.

Enzyme reactions

• Enzyme class: E.C.1.4.1.16 - diaminopimelate dehydrogenase.
• Reaction: meso-2,6-diaminopimelate + NADP⁺ + H2O = (S)-2-amino-6-oxoheptanedioate + NH4⁺ + NADPH + H⁺

meso-2,6-diaminopimelate + NADP(+) (Bound ligand (Het Group name = API) corresponds exactly) + H2O = (S)-2-amino-6-oxoheptanedioate + NH4(+) + NADPH + H(+)

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1021/bi9727949

Biochemistry 37:3278-3285 (1998)

PubMed id: 9521647

Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase.

G.Scapin, M.Cirilli, S.G.Reddy, Y.Gao, J.C.Vederas, J.S.Blanchard.

ABSTRACT

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.