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Phenylalanine dehydrogenase from Rhodococcus sp. M4: high-resolution X-ray analyses of inhibitory ternary complexes reveal key features in the oxidative deamination mechanism.

Vanhooke JL, Thoden JB, Brunhuber NM, Blanchard JS, Holden HM
Biochemistry 38 2326-39 (1999)
Cited: 24 times
EuropePMC logo PMID: 10029526

Abstract

The molecular structures of recombinant L-phenylalanine dehydrogenase from Rhodococcus sp. M4 in two different inhibitory ternary complexes have been determined by X-ray crystallographic analyses to high resolution. Both structures show that L-phenylalanine dehydrogenase is a homodimeric enzyme with each monomer composed of distinct globular N- and C-terminal domains separated by a deep cleft containing the active site. The N-terminal domain binds the amino acid substrate and contributes to the interactions at the subunit:subunit interface. The C-terminal domain contains a typical Rossmann fold and orients the dinucleotide. The dimer has overall dimensions of approximately 82 A x 75 A x 75 A, with roughly 50 A separating the two active sites. The structures described here, namely the enzyme.NAD+.phenylpyruvate, and enzyme. NAD+.beta-phenylpropionate species, represent the first models for any amino acid dehydrogenase in a ternary complex. By analysis of the active-site interactions in these models, along with the currently available kinetic data, a detailed chemical mechanism has been proposed. This mechanism differs from those proposed to date in that it accounts for the inability of the amino acid dehydrogenases, in general, to function as hydroxy acid dehydrogenases.

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  1. Role of Na+ and K+ in enzyme function. Page MJ, Di Cera E. Physiol. Rev. 86 1049-1092 (2006)
  2. Enzymatic asymmetric synthesis of chiral amino acids. Xue YP, Cao CH, Zheng YG. Chem Soc Rev 47 1516-1561 (2018)
  3. L-aspartate dehydrogenase: features and applications. Li Y, Ogola HJ, Sawa Y. Appl. Microbiol. Biotechnol. 93 503-516 (2012)

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  2. A structurally conserved water molecule in Rossmann dinucleotide-binding domains. Bottoms CA, Smith PE, Tanner JJ. Protein Sci. 11 2125-2137 (2002)
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  4. Structure of alanine dehydrogenase from Archaeoglobus: active site analysis and relation to bacterial cyclodeaminases and mammalian mu crystallin. Gallagher DT, Monbouquette HG, Schröder I, Robinson H, Holden MJ, Smith NN. J. Mol. Biol. 342 119-130 (2004)
  5. The three-dimensional structure of the ternary complex of Corynebacterium glutamicum diaminopimelate dehydrogenase-NADPH-L-2-amino-6-methylene-pimelate. Cirilli M, Scapin G, Sutherland A, Vederas JC, Blanchard JS. Protein Sci. 9 2034-2037 (2000)
  6. Crystal structures of the Mycobacterium tuberculosis secretory antigen alanine dehydrogenase (Rv2780) in apo and ternary complex forms captures "open" and "closed" enzyme conformations. Tripathi SM, Ramachandran R. Proteins 72 1089-1095 (2008)
  7. A novel chimeric amine dehydrogenase shows altered substrate specificity compared to its parent enzymes. Bommarius BR, Schürmann M, Bommarius AS. Chem. Commun. (Camb.) 50 14953-14955 (2014)
  8. Conversion of a glutamate dehydrogenase into methionine/norleucine dehydrogenase by site-directed mutagenesis. Wang XG, Britton KL, Stillman TJ, Rice DW, Engel PC. Eur. J. Biochem. 268 5791-5799 (2001)
  9. Efficient screening for new amino acid dehydrogenase activity: directed evolution of Bacillus sphaericus phenylalanine dehydrogenase towards activity with an unsaturated non-natural amino acid. Chen S, Engel PC. J. Biotechnol. 142 127-134 (2009)
  10. Kinetic analysis of phenylalanine dehydrogenase mutants designed for aliphatic amino acid dehydrogenase activity with guidance from homology-based modelling. Seah SY, Britton KL, Rice DW, Asano Y, Engel PC. Eur. J. Biochem. 270 4628-4634 (2003)
  11. Enhancement of stability of L-tryptophan dehydrogenase from Nostoc punctiforme ATCC29133 and its application to L-tryptophan assay. Matsui D, Okazaki S, Matsuda M, Asano Y. J. Biotechnol. 196-197 27-32 (2015)
  12. A close-packed planar 4-atom motif serves as a variable-pathway mechanistic switching device in enzymatic catalysis. Fisher HF, Maniscalco SJ. Bioorg. Chem. 30 199-210 (2002)
  13. Engineering of alanine dehydrogenase from Bacillus subtilis for novel cofactor specificity. Lerchner A, Jarasch A, Skerra A. Biotechnol. Appl. Biochem. 63 616-624 (2016)
  14. Rational Engineering of Bacillus cereus Leucine Dehydrogenase Towards α-keto Acid Reduction for Improving Unnatural Amino Acid Production. Zhou J, Wang Y, Chen J, Xu M, Yang T, Zheng J, Zhang X, Rao Z. Biotechnol J 14 e1800253 (2019)
  15. Fragmentary form of thermostable leucine dehydrogenase of Bacillus stearothermophilus: its construction and reconstitution of active fragmentary enzyme. Oikawa T, Kataoka K, Jin Y, Suzuki S, Soda K. Biochem. Biophys. Res. Commun. 280 1177-1182 (2001)
  16. Functional Classification of Super-Large Families of Enzymes Based on Substrate Binding Pocket Residues for Biocatalysis and Enzyme Engineering Applications. Sirota FL, Maurer-Stroh S, Li Z, Eisenhaber F, Eisenhaber B. Front Bioeng Biotechnol 9 701120 (2021)


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