Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase

Giovanna Scapin, Maurizio Cirilli, Sreelatha G. Reddy, Yong Gao, John C. Vederas, John S. Blanchard

Research output: Contribution to journalArticle

33 Citations (Scopus)

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 Å. 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- mesodiaminopimelate 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.

Original languageEnglish (US)
Pages (from-to)3278-3285
Number of pages8
JournalBiochemistry
Volume37
Issue number10
DOIs
StatePublished - Mar 10 1998

Fingerprint

diaminopimelate dehydrogenase
Corynebacterium glutamicum
Binding Sites
Amino Acids
Substrates
NADP
Lysine
Enzymes
NADPH Dehydrogenase
Deamination
Stereoisomerism
Mammals
Biosynthesis
Biosynthetic Pathways
Herbicides
Enzyme Inhibitors
Metabolic Networks and Pathways
X-Ray Diffraction
Hydrogen
Hydrogen bonds

ASJC Scopus subject areas

  • Biochemistry

Cite this

Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase. / Scapin, Giovanna; Cirilli, Maurizio; Reddy, Sreelatha G.; Gao, Yong; Vederas, John C.; Blanchard, John S.

In: Biochemistry, Vol. 37, No. 10, 10.03.1998, p. 3278-3285.

Research output: Contribution to journalArticle

Scapin, Giovanna ; Cirilli, Maurizio ; Reddy, Sreelatha G. ; Gao, Yong ; Vederas, John C. ; Blanchard, John S. / Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase. In: Biochemistry. 1998 ; Vol. 37, No. 10. pp. 3278-3285.
@article{060dfc86ac2d464eb5704bb8ca3027ad,
title = "Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase",
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 {\AA}. 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- mesodiaminopimelate 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.",
author = "Giovanna Scapin and Maurizio Cirilli and Reddy, {Sreelatha G.} and Yong Gao and Vederas, {John C.} and Blanchard, {John S.}",
year = "1998",
month = "3",
day = "10",
doi = "10.1021/bi9727949",
language = "English (US)",
volume = "37",
pages = "3278--3285",
journal = "Biochemistry",
issn = "0006-2960",
publisher = "American Chemical Society",
number = "10",

}

TY - JOUR

T1 - Substrate and inhibitor binding sites in Corynebacterium glutamicum diaminopimelate dehydrogenase

AU - Scapin, Giovanna

AU - Cirilli, Maurizio

AU - Reddy, Sreelatha G.

AU - Gao, Yong

AU - Vederas, John C.

AU - Blanchard, John S.

PY - 1998/3/10

Y1 - 1998/3/10

N2 - 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 Å. 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- mesodiaminopimelate 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.

AB - 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 Å. 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- mesodiaminopimelate 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.

UR - http://www.scopus.com/inward/record.url?scp=0032502243&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=0032502243&partnerID=8YFLogxK

U2 - 10.1021/bi9727949

DO - 10.1021/bi9727949

M3 - Article

C2 - 9521647

AN - SCOPUS:0032502243

VL - 37

SP - 3278

EP - 3285

JO - Biochemistry

JF - Biochemistry

SN - 0006-2960

IS - 10

ER -