Three-Dimensional Structure of meso-Diaminopimelic Acid Dehydrogenase from Corynebacterium glutamicum
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- 作者：Giovanna Scapin ; Sreelatha G. Reddy ; and John S. Blanchard
- 刊名：Biochemistry
- 出版年：1996
- 出版时间：October 22, 1996
- 年：1996
- 卷：35
- 期：42
- 页码：13540 - 13551
- 全文大小：627K
- 年卷期：v.35,no.42(October 22, 1996)
- ISSN：1520-4995
文摘
Diaminopimelate dehydrogenase catalyzes the NADPH-dependentreduction of ammonia andL-2-amino-6-ketopimelate to formmeso-diaminopimelate, the direct precursor of L-lysinein the bacteriallysine biosynthetic pathway. Since mammals lack this metabolicpathway, inhibitors of enzymes in thispathway may be useful as antibiotics or herbicides.Diaminopimelate dehydrogenase catalyzes the onlyoxidative deamination of an amino acid of D configurationand must additionally distinguish between twochiral amino acid centers on the same symmetric substrate. TheCorynebacterium glutamicum enzymehas been cloned, expressed in Escherichia coli, and purifiedto homogeneity using standard biochemicalprocedures [Reddy, S. G., Scapin, G., & Blanchard, J. S. (1996)Proteins: Structure, Funct. Genet.25,514-516]. The three-dimensional structure of the binary complexof diaminopimelate dehydrogenasewith NADP+ has been solved using multiple isomorphousreplacement procedures and noncrystallographicsymmetry averaging. The resulting model has been refined against2.2 Å diffraction data to a conventionalcrystallographic R-factor of 17.0%. Diaminopimelatedehydrogenase is a homodimer of structurally notidentical subunits. Each subunit is composed of three domains.The N-terminal domain contains a modifieddinucleotide binding domain, or Rossman fold (six central 
-strandsin a 213456 topology surrounded byfive 
-helices). The second domain contains two -helices andthree -strands. This domain is referredto as the dimerization domain, since it is involved in forming themonomer-monomer interface of thedimer. The third or C-terminal domain is composed of six-strands and five -helices. The relativeposition of the N- and C-terminal domain in the two monomers isdifferent, defining an open and aclosed conformation that may represent the enzyme's binding and activestate, respectively. In bothmonomers the nucleotide is bound in an extended conformation across theC-terminal portion of the-sheet of the Rossman fold, with its C4 facing the C-terminaldomain. In the closed conformer twomolecules of acetate have been refined in this region, and we postulatethat they define the DAP bindingsite. The structure of diaminopimelate dehydrogenase showsinteresting similarities to the structure ofglutamate dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W.,Rob, A., & Stillmann, T. J. (1992a)J. Mol. Biol. 228, 662-671] and leucinedehydrogenase [Baker, P. J., Turnbull, A. P., Sedelnikova, S.E.,Stillman, T. J., & Rice, D. W. (1995) Structure 3,693-705] and also resembles the structure ofdihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., &Sacchettini, J. C. (1995) Biochemistry 34,3502-3512], the enzyme immediately preceding it in thediaminopimelic acid/lysine biosynthetic pathway.
-strandsin a 213456 topology surrounded byfive -helices). The second domain contains two -helices andthree -strands. This domain is referredto as the dimerization domain, since it is involved in forming themonomer-monomer interface of thedimer. The third or C-terminal domain is composed of six-strands and five -helices. The relativeposition of the N- and C-terminal domain in the two monomers isdifferent, defining an open and aclosed conformation that may represent the enzyme's binding and activestate, respectively. In bothmonomers the nucleotide is bound in an extended conformation across theC-terminal portion of the-sheet of the Rossman fold, with its C4 facing the C-terminaldomain. In the closed conformer twomolecules of acetate have been refined in this region, and we postulatethat they define the DAP bindingsite. The structure of diaminopimelate dehydrogenase showsinteresting similarities to the structure ofglutamate dehydrogenase [Baker, P. J., Britton, K. L., Rice, D. W.,Rob, A., & Stillmann, T. J. (1992a)J. Mol. Biol. 228, 662-671] and leucinedehydrogenase [Baker, P. J., Turnbull, A. P., Sedelnikova, S.E.,Stillman, T. J., & Rice, D. W. (1995) Structure 3,693-705] and also resembles the structure ofdihydrodipicolinate reductase [Scapin, G., Blanchard, J. S., &Sacchettini, J. C. (1995) Biochemistry 34,3502-3512], the enzyme immediately preceding it in thediaminopimelic acid/lysine biosynthetic pathway.