Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum

Giovanna Scapin, Sreelatha G. Reddy, John S. Blanchard

Research output: Contribution to journalArticle

47 Citations (Scopus)

Abstract

Diaminopimelate dehydrogenase catalyzes the NADPH-dependent reduction of ammonia and L-2-amino-6-ketopimelate to form meso-diaminopimelate, the direct precursor of L-lysine in the bacterial lysine biosynhetic pathway. Since mammals lack this metabolic pathway, inhibitors of enzymes in this pathway may be useful as antibiotics or herbicides. Diaminopimelate dehydrogenase catalyzes the only oxidative deamination of an amino acid of o configuration and must additionally distinguish between two chiral amino acid centers on the same symmetric substrate. The Corynebacterium glutamicum enzyme has been cloned, expressed in Escherichia coli, and purified to homogeneity using standard biochemical procedures [Reddy, S. G., Scapin, G., and Blanchard, J. S. (1996) Proteins: Structure, Funct. Genet. 25, 514-516]. The three- dimensional structure of the binary complex of diaminopimelate dehydrogenase with NADP+ has been solved using multiple isomorphous replacement procedures and noncrystallographic symmetry averaging. The resulting model has been refined against 2.2 Å diffraction data to a conventional crystallographic R- factor of 17.0%. Diaminopimelate dehydrogenase is a homodimer of structurally not identical subunits. Each subunit is composed of three domains. The N- terminal domain contains a modified dinucleotide binding domain, or Rossman fold (six central β-strands in a 213456 topology surrounded by five α- helices). The second domain contains two α-helices and three β-strands. This domain is referred to as the dimerization domain, since it is involved in forming the monomer-monomer interface of the dimer. The third or C- terminal domain is composed of six β-strands and five α-helices. The relative position of the N- and C-terminal domain in the two monomers is different, defining an open and a closed conformation that may represent the enzyme's binding and active state, respectively. In both monomers the nucleotide is bound in an extended conformation across the C-terminal portion of the β-sheet of the Rossman fold, with its C4 facing the C-terminal domain. In the closed conformer two molecules of acetate have been refined in this region, and we postulate that they define the DAP binding site. The structure of diaminopimelate dehydrogenase shows interesting similarities to the structure of glutamate dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W., Rob, A., and Stillmann, T. J. (1992a) J. Mol. Biol. 228, 662-671] and leucine dehydrogenase [Baker, P. J., Turnbull, A. P., Sedelnikova, S. E., Stillman, T. J., and Rice, D. W. (1995) Structure 3, 693-705] and also resembles the structure of dihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., and Sacchettini, J. C. (1995) Biochemistry 34, 3502-3512], the enzyme immediately preceding it in the diaminopimelic acid/lysine biosynthetic pathway.

Original languageEnglish (US)
Pages (from-to)13540-13551
Number of pages12
JournalBiochemistry
Volume35
Issue number42
DOIs
StatePublished - 1996

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diaminopimelate dehydrogenase
Diaminopimelic Acid
Corynebacterium glutamicum
Oxidoreductases
Monomers
Lysine
NADP
Dihydrodipicolinate Reductase
Leucine Dehydrogenase
Conformations
R388
Enzymes
Viverridae
Amino Acids
Glutamate Dehydrogenase
Deamination
Biochemistry
Mammals
Dimerization
Biosynthetic Pathways

ASJC Scopus subject areas

  • Biochemistry

Cite this

Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum. / Scapin, Giovanna; Reddy, Sreelatha G.; Blanchard, John S.

In: Biochemistry, Vol. 35, No. 42, 1996, p. 13540-13551.

Research output: Contribution to journalArticle

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title = "Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum",
abstract = "Diaminopimelate dehydrogenase catalyzes the NADPH-dependent reduction of ammonia and L-2-amino-6-ketopimelate to form meso-diaminopimelate, the direct precursor of L-lysine in the bacterial lysine biosynhetic pathway. Since mammals lack this metabolic pathway, inhibitors of enzymes in this pathway may be useful as antibiotics or herbicides. Diaminopimelate dehydrogenase catalyzes the only oxidative deamination of an amino acid of o configuration and must additionally distinguish between two chiral amino acid centers on the same symmetric substrate. The Corynebacterium glutamicum enzyme has been cloned, expressed in Escherichia coli, and purified to homogeneity using standard biochemical procedures [Reddy, S. G., Scapin, G., and Blanchard, J. S. (1996) Proteins: Structure, Funct. Genet. 25, 514-516]. The three- dimensional structure of the binary complex of diaminopimelate dehydrogenase with NADP+ has been solved using multiple isomorphous replacement procedures and noncrystallographic symmetry averaging. The resulting model has been refined against 2.2 {\AA} diffraction data to a conventional crystallographic R- factor of 17.0{\%}. Diaminopimelate dehydrogenase is a homodimer of structurally not identical subunits. Each subunit is composed of three domains. The N- terminal domain contains a modified dinucleotide binding domain, or Rossman fold (six central β-strands in a 213456 topology surrounded by five α- helices). The second domain contains two α-helices and three β-strands. This domain is referred to as the dimerization domain, since it is involved in forming the monomer-monomer interface of the dimer. The third or C- terminal domain is composed of six β-strands and five α-helices. The relative position of the N- and C-terminal domain in the two monomers is different, defining an open and a closed conformation that may represent the enzyme's binding and active state, respectively. In both monomers the nucleotide is bound in an extended conformation across the C-terminal portion of the β-sheet of the Rossman fold, with its C4 facing the C-terminal domain. In the closed conformer two molecules of acetate have been refined in this region, and we postulate that they define the DAP binding site. The structure of diaminopimelate dehydrogenase shows interesting similarities to the structure of glutamate dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W., Rob, A., and Stillmann, T. J. (1992a) J. Mol. Biol. 228, 662-671] and leucine dehydrogenase [Baker, P. J., Turnbull, A. P., Sedelnikova, S. E., Stillman, T. J., and Rice, D. W. (1995) Structure 3, 693-705] and also resembles the structure of dihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., and Sacchettini, J. C. (1995) Biochemistry 34, 3502-3512], the enzyme immediately preceding it in the diaminopimelic acid/lysine biosynthetic pathway.",
author = "Giovanna Scapin and Reddy, {Sreelatha G.} and Blanchard, {John S.}",
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T1 - Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum

AU - Scapin, Giovanna

AU - Reddy, Sreelatha G.

AU - Blanchard, John S.

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N2 - Diaminopimelate dehydrogenase catalyzes the NADPH-dependent reduction of ammonia and L-2-amino-6-ketopimelate to form meso-diaminopimelate, the direct precursor of L-lysine in the bacterial lysine biosynhetic pathway. Since mammals lack this metabolic pathway, inhibitors of enzymes in this pathway may be useful as antibiotics or herbicides. Diaminopimelate dehydrogenase catalyzes the only oxidative deamination of an amino acid of o configuration and must additionally distinguish between two chiral amino acid centers on the same symmetric substrate. The Corynebacterium glutamicum enzyme has been cloned, expressed in Escherichia coli, and purified to homogeneity using standard biochemical procedures [Reddy, S. G., Scapin, G., and Blanchard, J. S. (1996) Proteins: Structure, Funct. Genet. 25, 514-516]. The three- dimensional structure of the binary complex of diaminopimelate dehydrogenase with NADP+ has been solved using multiple isomorphous replacement procedures and noncrystallographic symmetry averaging. The resulting model has been refined against 2.2 Å diffraction data to a conventional crystallographic R- factor of 17.0%. Diaminopimelate dehydrogenase is a homodimer of structurally not identical subunits. Each subunit is composed of three domains. The N- terminal domain contains a modified dinucleotide binding domain, or Rossman fold (six central β-strands in a 213456 topology surrounded by five α- helices). The second domain contains two α-helices and three β-strands. This domain is referred to as the dimerization domain, since it is involved in forming the monomer-monomer interface of the dimer. The third or C- terminal domain is composed of six β-strands and five α-helices. The relative position of the N- and C-terminal domain in the two monomers is different, defining an open and a closed conformation that may represent the enzyme's binding and active state, respectively. In both monomers the nucleotide is bound in an extended conformation across the C-terminal portion of the β-sheet of the Rossman fold, with its C4 facing the C-terminal domain. In the closed conformer two molecules of acetate have been refined in this region, and we postulate that they define the DAP binding site. The structure of diaminopimelate dehydrogenase shows interesting similarities to the structure of glutamate dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W., Rob, A., and Stillmann, T. J. (1992a) J. Mol. Biol. 228, 662-671] and leucine dehydrogenase [Baker, P. J., Turnbull, A. P., Sedelnikova, S. E., Stillman, T. J., and Rice, D. W. (1995) Structure 3, 693-705] and also resembles the structure of dihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., and Sacchettini, J. C. (1995) Biochemistry 34, 3502-3512], the enzyme immediately preceding it in the diaminopimelic acid/lysine biosynthetic pathway.

AB - Diaminopimelate dehydrogenase catalyzes the NADPH-dependent reduction of ammonia and L-2-amino-6-ketopimelate to form meso-diaminopimelate, the direct precursor of L-lysine in the bacterial lysine biosynhetic pathway. Since mammals lack this metabolic pathway, inhibitors of enzymes in this pathway may be useful as antibiotics or herbicides. Diaminopimelate dehydrogenase catalyzes the only oxidative deamination of an amino acid of o configuration and must additionally distinguish between two chiral amino acid centers on the same symmetric substrate. The Corynebacterium glutamicum enzyme has been cloned, expressed in Escherichia coli, and purified to homogeneity using standard biochemical procedures [Reddy, S. G., Scapin, G., and Blanchard, J. S. (1996) Proteins: Structure, Funct. Genet. 25, 514-516]. The three- dimensional structure of the binary complex of diaminopimelate dehydrogenase with NADP+ has been solved using multiple isomorphous replacement procedures and noncrystallographic symmetry averaging. The resulting model has been refined against 2.2 Å diffraction data to a conventional crystallographic R- factor of 17.0%. Diaminopimelate dehydrogenase is a homodimer of structurally not identical subunits. Each subunit is composed of three domains. The N- terminal domain contains a modified dinucleotide binding domain, or Rossman fold (six central β-strands in a 213456 topology surrounded by five α- helices). The second domain contains two α-helices and three β-strands. This domain is referred to as the dimerization domain, since it is involved in forming the monomer-monomer interface of the dimer. The third or C- terminal domain is composed of six β-strands and five α-helices. The relative position of the N- and C-terminal domain in the two monomers is different, defining an open and a closed conformation that may represent the enzyme's binding and active state, respectively. In both monomers the nucleotide is bound in an extended conformation across the C-terminal portion of the β-sheet of the Rossman fold, with its C4 facing the C-terminal domain. In the closed conformer two molecules of acetate have been refined in this region, and we postulate that they define the DAP binding site. The structure of diaminopimelate dehydrogenase shows interesting similarities to the structure of glutamate dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W., Rob, A., and Stillmann, T. J. (1992a) J. Mol. Biol. 228, 662-671] and leucine dehydrogenase [Baker, P. J., Turnbull, A. P., Sedelnikova, S. E., Stillman, T. J., and Rice, D. W. (1995) Structure 3, 693-705] and also resembles the structure of dihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., and Sacchettini, J. C. (1995) Biochemistry 34, 3502-3512], the enzyme immediately preceding it in the diaminopimelic acid/lysine biosynthetic pathway.

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