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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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  1. Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes. Paiardini A, Bossa F, Pascarella S. Protein Sci 13 2992-3005 (2004)
  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)


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  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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  2. The crystal structure of the RNA-dependent RNA polymerase from human rhinovirus: a dual function target for common cold antiviral therapy. Love RA, Maegley KA, Yu X, Ferre RA, Lingardo LK, Diehl W, Parge HE, Dragovich PS, Fuhrman SA. Structure 12 1533-1544 (2004)
  3. The crystal structure of 8-amino-7-oxononanoate synthase: a bacterial PLP-dependent, acyl-CoA-condensing enzyme. Alexeev D, Alexeeva M, Baxter RL, Campopiano DJ, Webster SP, Sawyer L. J Mol Biol 284 401-419 (1998)
  4. Crystal structure of human ornithine aminotransferase complexed with the highly specific and potent inhibitor 5-fluoromethylornithine. Storici P, Capitani G, Müller R, Schirmer T, Jansonius JN. J Mol Biol 285 297-309 (1999)
  5. gyrB-225, a mutation of DNA gyrase that compensates for topoisomerase I deficiency: investigation of its low activity and quinolone hypersensitivity. Heddle JG, Lu T, Zhao X, Drlica K, Maxwell A. J Mol Biol 309 1219-1231 (2001)
  6. Crystal Structure of human pyridoxal kinase: structural basis of M(+) and M(2+) activation. Musayev FN, di Salvo ML, Ko TP, Gandhi AK, Goswami A, Schirch V, Safo MK. Protein Sci 16 2184-2194 (2007)
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  9. Identification and molecular characterization of tryptophanase encoded by tnaA in Porphyromonas gingivalis. Yoshida Y, Sasaki T, Ito S, Tamura H, Kunimatsu K, Kato H. Microbiology (Reading) 155 968-978 (2009)
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  13. Pyridoxal 5'-phosphate inactivates DNA topoisomerase IB by modifying the lysine general acid. Vermeersch JJ, Christmann-Franck S, Karabashyan LV, Fermandjian S, Mirambeau G, Der Garabedian PA. Nucleic Acids Res 32 5649-5657 (2004)
  14. Chemogenomics of pyridoxal 5'-phosphate dependent enzymes. Singh R, Spyrakis F, Cozzini P, Paiardini A, Pascarella S, Mozzarelli A. J Enzyme Inhib Med Chem 28 183-194 (2013)
  15. Structures of apo- and holo-tyrosine phenol-lyase reveal a catalytically critical closed conformation and suggest a mechanism for activation by K+ ions. Milić D, Matković-Calogović D, Demidkina TV, Kulikova VV, Sinitzina NI, Antson AA. Biochemistry 45 7544-7552 (2006)
  16. Aromatic L-amino acid decarboxylase: conformational change in the flexible region around Arg334 is required during the transaldimination process. Ishii S, Hayashi H, Okamoto A, Kagamiyama H. Protein Sci 7 1802-1810 (1998)
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  18. New tryptophanase inhibitors: towards prevention of bacterial biofilm formation. Scherzer R, Gdalevsky GY, Goldgur Y, Cohen-Luria R, Bittner S, Parola AH. J Enzyme Inhib Med Chem 24 350-355 (2009)
  19. Potentiation of P2Y receptors by physiological elevations of extracellular K+ via a mechanism independent of Ca2+ influx. Pitt SJ, Martinez-Pinna J, Barnard EA, Mahaut-Smith MP. Mol Pharmacol 67 1705-1713 (2005)
  20. Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41. Almog O, Kogan A, Leeuw Md, Gdalevsky GY, Cohen-Luria R, Parola AH. Biopolymers 89 354-359 (2008)
  21. Inactivation of tyrosine phenol-lyase by Pictet-Spengler reaction and alleviation by T15A mutation on intertwined N-terminal arm. Lee SG, Hong SP, Kim DY, Song JJ, Ro HS, Sung MH. FEBS J 273 5564-5573 (2006)
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  23. Characterization of tryptophanase from Vibrio cholerae. Nuidate T, Tansila N, Chomchuen P, Phattaranit P, Eangchuan S, Vuddhakul V. Appl Biochem Biotechnol 175 243-252 (2015)
  24. Effects of salts on the conformation and catalytic properties of d-amino acid aminotransferase. Ro HS. J Biochem Mol Biol 35 306-312 (2002)
  25. Stereospecificity of isotopic exchange of C-α-protons of glycine catalyzed by three PLP-dependent lyases: the unusual case of tyrosine phenol-lyase. Koulikova VV, Zakomirdina LN, Gogoleva OI, Tsvetikova MA, Morozova EA, Komissarov VV, Tkachev YV, Timofeev VP, Demidkina TV, Faleev NG. Amino Acids 41 1247-1256 (2011)
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  27. Pyridoxal phosphate binding to wild type, W330F, and C298S mutants of Escherichia coli apotryptophanase: unraveling the cold inactivation. Erez T, Phillips RS, Parola AH. FEBS Lett 433 279-282 (1998)
  28. Inhibition of tyrosine phenol-lyase by tyrosine homologues. Do Q, Nguyen GT, Phillips RS. Amino Acids 48 2243-2251 (2016)
  29. Iterative projection algorithms in protein crystallography. II. Application. Lo VL, Kingston RL, Millane RP. Acta Crystallogr A Found Adv 71 451-459 (2015)
  30. The crystal structure of Proteus vulgaris tryptophan indole-lyase complexed with oxindolyl-L-alanine: implications for the reaction mechanism. Phillips RS, Buisman AA, Choi S, Hussaini A, Wood ZA. Acta Crystallogr D Struct Biol 74 748-759 (2018)
  31. Analysis of stability and catalytic properties of two tryptophanases from a thermophile. Kudo H, Natsume R, Nishiyama M, Horinouchi S. Protein Eng 12 687-692 (1999)
  32. Identification of pyridoxal phosphate-modified proteins using mass spectrometry. Wu Y, Chen J, Liu Z, Wang F. Rapid Commun Mass Spectrom 32 195-200 (2018)
  33. Synthesis of deuterium-labelled halogen derivatives of L-tryptophan catalysed by tryptophanase. Winnicka E, Szymańska J, Kańska M. Isotopes Environ Health Stud 52 231-238 (2016)
  34. The first steps. The attack on the carbonyl carbon of pyridoxal cofactor in pyridoxal-dependent enzymes. Sonnet PE, Mascavage LM, Dalton DR. Bioorg Med Chem Lett 18 744-748 (2008)
  35. A structural view of the dissociation of Escherichia coli tryptophanase. Green K, Qasim N, Gdaelvsky G, Kogan A, Goldgur Y, Parola AH, Lotan O, Almog O. Acta Crystallogr D Biol Crystallogr 71 2364-2371 (2015)
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Related citations provided by authors (2)

  1. X-Ray Study of Tryptophanase at 2.1 Angstrom Resolution. Isupov M, Dementieva I, Zakomirdina L, Wilson KS, Dauter Z, Antson AA, Dodson GG, Harutyunyan EH Biochemistry of Vitamin B6 and Pqq 183- (1994)
  2. Crystallization and preliminary X-ray investigation of holotryptophanases from Escherichia coli and Proteus vulgaris.. Dementieva IS, Zakomirdina LN, Sinitzina NI, Antson AA, Wilson KS, Isupov MN, Lebedev AA, Harutyunyan EH J Mol Biol 235 783-6 (1994)

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