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Crystal structure of tryptophanase.

Isupov MN, Antson AA, Dodson EJ, Dodson GG, Dementieva IS, Zakomirdina LN, Wilson KS, Dauter Z, Lebedev AA, Harutyunyan EH
J Mol Biol 276 603-23 (1998)
Cited: 57 times
EuropePMC logo PMID: 9551100

Abstract

The X-ray structure of tryptophanase (Tnase) reveals the interactions responsible for binding of the pyridoxal 5'-phosphate (PLP) and atomic details of the K+ binding site essential for catalysis. The structure of holo Tnase from Proteus vulgaris (space group P2(1)2(1)2(1) with a = 115.0 A, b = 118.2 A, c = 153.7 A) has been determined at 2.1 A resolution by molecular replacement using tyrosine phenol-lyase (TPL) coordinates. The final model of Tnase, refined to an R-factor of 18.7%, (Rfree = 22.8%) suggests that the PLP-enzyme from observed in the structure is a ketoenamine. PLP is bound in a cleft formed by both the small and large domains of one subunit and the large domain of the adjacent subunit in the so-called "catalytic" dimer. The K+ cations are located on the interface of the subunits in the dimer. The structure of the catalytic dimer and mode of PLP binding in Tnase resemble those found in aspartate amino-transferase, TPL, omega-amino acid pyruvate aminotransferase, dialkylglycine decarboxylase (DGD), cystathionine beta-lyase and ornithine decarboxylase. No structural similarity has been detected between Tnase and the beta 2 dimer of tryptophan synthase which catalyses the same beta-replacement reaction. The single monovalent cation binding site of Tnase is similar to that of TPL, but differs from either of those in DGD.

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  2. C-S bond cleavage by a polyketide synthase domain. Ma M, Lohman JR, Liu T, Shen B. Proc Natl Acad Sci U S A 112 10359-10364 (2015)
  3. Synthetic receptors as models for alkali metal cation-pi binding sites in proteins. De Wall SL, Meadows ES, Barbour LJ, Gokel GW. Proc Natl Acad Sci U S A 97 6271-6276 (2000)
  4. A new suite of tnaA mutants suggests that Escherichia coli tryptophanase is regulated by intracellular sequestration and by occlusion of its active site. Li G, Young KD. BMC Microbiol 15 14 (2015)
  5. Conformational changes and loose packing promote E. coli Tryptophanase cold lability. Kogan A, Gdalevsky GY, Cohen-Luria R, Goldgur Y, Phillips RS, Parola AH, Almog O. BMC Struct Biol 9 65 (2009)
  6. Structures of Escherichia coli tryptophanase in holo and 'semi-holo' forms. Kogan A, Raznov L, Gdalevsky GY, Cohen-Luria R, Almog O, Parola AH, Goldgur Y. Acta Crystallogr F Struct Biol Commun 71 286-290 (2015)
  7. Exploration of Catalytic Selectivity for Aminotransferase (BtrR) Based on Multiple Molecular Dynamics Simulations. Liu Y, Wan Y, Zhu J, Li M, Yu Z, Han J, Zhang Z, Han W. Int J Mol Sci 20 E1188 (2019)
  8. Structure and Mechanism of d-Glucosaminate-6-phosphate Ammonia-lyase: A Novel Octameric Assembly for a Pyridoxal 5'-Phosphate-Dependent Enzyme, and Unprecedented Stereochemical Inversion in the Elimination Reaction of a d-Amino Acid. Phillips RS, Ting SC, Anderson K. Biochemistry 60 1609-1618 (2021)


Reviews citing this publication (9)

  1. Structure, evolution and action of vitamin B6-dependent enzymes. Jansonius JN. Curr Opin Struct Biol 8 759-769 (1998)
  2. The manifold of vitamin B6 dependent enzymes. Schneider G, Käck H, Lindqvist Y. Structure 8 R1-6 (2000)
  3. Role of Na+ and K+ in enzyme function. Page MJ, Di Cera E. Physiol Rev 86 1049-1092 (2006)
  4. Molecular Mechanisms of Enzyme Activation by Monovalent Cations. Gohara DW, Di Cera E. J Biol Chem 291 20840-20848 (2016)
  5. Stereospecificity for the hydrogen transfer of pyridoxal enzyme reactions. Soda K, Yoshimura T, Esaki N. Chem Rec 1 373-384 (2001)
  6. Pyridoxal 5'-Phosphate-Dependent Enzymes at the Crossroads of Host-Microbe Tryptophan Metabolism. Cellini B, Zelante T, Dindo M, Bellet MM, Renga G, Romani L, Costantini C. Int J Mol Sci 21 E5823 (2020)
  7. Molecular modelling studies on the interactions of human DNA topoisomerase IB with pyridoxal-compounds. Christmann-Franck S, Fermandjian S, Mirambeau G, Der Garabedian PA. Biochimie 89 468-473 (2007)
  8. The role of substrate strain in the mechanism of the carbon-carbon lyases. Phillips RS, Demidkina TV, Faleev NG. Bioorg Chem 57 198-205 (2014)
  9. Structural Basis for Allostery in PLP-dependent Enzymes. Tran JU, Brown BL. Front Mol Biosci 9 884281 (2022)

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