Abstract
Tryptophan synthase is a pyridoxal 5′-phosphate-dependent α2β2 complex catalyzing the last two steps of tryptophan biosynthesis in bacteria, plants and fungi. Structural, dynamic and functional studies, carried out over more than 40 years, have unveiled that: (1) α- and β-active sites are separated by about 20 Å and communicate via the selective stabilization of distinct conformational states, triggered by the chemical nature of individual catalytic intermediates and by allosteric ligands; (2) indole, formed at α-active site, is intramolecularly channeled to the β-active site; and (3) naturally occurring as well as genetically generated mutants have allowed to pinpoint functional and regulatory roles for several individual amino acids. These key features have made tryptophan synthase a text-book case for the understanding of the interplay between chemistry and conformational energy landscapes.
Similar content being viewed by others
Abbreviations
- GP:
-
Glycerol phosphate
- G3P:
-
d-glyceraldehyde-3-phosphate
- IA:
-
trans-3-indole-3′-acrylate
- IAD:
-
Indoleacetyl aspartate
- IAG:
-
Indoleacetyl glycine
- IAV:
-
Indoleacetyl valine
- IGP:
-
Indole-3-glycerol phosphate
- IPP:
-
Indole 3-propanol phosphate
- PLP:
-
Pyridoxal 5′-phosphate
- TS:
-
Tryptophan synthase
References
Huang X, Holden HM, Raushel FM (2001) Channeling of substrates and intermediates in enzyme-catalyzed reactions. Annu Rev Biochem 70:149–180
Barends TR, Dunn MF, Schlichting I (2008) Tryptophan synthase, an allosteric molecular factory. Curr Opin Chem Biol 12:593–600
Dunn MF, Niks D, Ngo H, Barends TR, Schlichting I (2008) Tryptophan synthase: the workings of a channeling nanomachine. Trends Biochem Sci 33:254–264
Kirschner K, Wiskocil RL, Foehn M, Rezeau L (1975) The tryptophan synthase from Escherichia coli: an improved purification procedure for the α-subunit and binding studies with substrate analogues. Eur J Biochem 60:513–523
Miles EW (1979) Tryptophan synthase: structure, function, and subunit interaction. Adv Enzymol Relat Areas Mol Biol 49:127–186
Miles EW (1991) Structural basis for catalysis by tryptophan synthase. Adv Enzymol Relat Areas Mol Biol 64:93–172
Miles EW (1995) Tryptophan synthase: structure, function, and protein engineering. Subcell Biochem 24:207–254
Miles EW, Rhee S, Davies DR (1999) The molecular basis of substrate channeling. J Biol Chem 274:12193–12196
Pan P, Woehl E, Dunn MF (1997) Protein architecture, dynamics and allostery in tryptophan synthase channeling. Trends Biochem Sci 22:22–27
Yanofsky C, Crawford IP (1972) In: The enzyme. Academy Press, NY, pp 1–13
Kallen RG, Korpela T, Martell AE, Matsushina Y, Metzler CM, Metzler DE, Yuru V, Ralson IM, Savin FA, Torchinski YM, Ueno H (1985). In: Christen P, Metzler DE (eds) Transaminases. Wiley, New York, pp 38–108
Hyde CC, Ahmed SA, Padlan EA, Miles EW, Davies DR (1988) Three-dimensional structure of the tryptophan synthase α2β2 multienzyme complex from Salmonella typhimurium. J Biol Chem 263:17857–17871
Schneider TR, Gerhardt E, Lee M, Liang PH, Anderson KS, Schlichting I (1998) Loop closure and intersubunit communication in tryptophan synthase. Biochemistry 37:5394–5406
Weyand M, Schlichting I, Herde P, Marabotti A, Mozzarelli A (2002) Crystal structure of the βSer178– > Pro mutant of tryptophan synthase: a “knock-out” allosteric enzyme. J Biol Chem 277:10653–10660
Raboni S, Mozzarelli A, Cook PF (2007) Control of ionizable residues in the catalytic mechanism of tryptophan synthase from Salmonella typhimurium. Biochemistry 46:13223–13234
Barends TR, Domratcheva T, Kulik V, Blumenstein L, Niks D, Dunn MF, Schlichting I (2008) Structure and mechanistic implications of a tryptophan synthase quinonoid intermediate. Chembiochem 9:1024–1028
Grishin NV, Phillips MA, Goldsmith EJ (1995) Modeling of the spatial structure of eukaryotic ornithine decarboxylases. Protein Sci 4:1291–1304
Rhee S, Parris KD, Ahmed SA, Miles EW, Davies DR (1996) Exchange of K+ or Cs+ for Na+ induces local and long-range changes in the three-dimensional structure of the tryptophan synthase α2β2 complex. Biochemistry 35:4211–4221
Rhee S, Parris KD, Hyde CC, Ahmed SA, Miles EW, Davies DR (1997) Crystal structures of a mutant (βK87T) tryptophan synthase α2β2 complex with ligands bound to the active sites of the α- and β-subunits reveal ligand-induced conformational changes. Biochemistry 36:7664–7680
Anderson KS, Miles EW, Johnson KA (1991) Serine modulates substrate channeling in tryptophan synthase: a novel intersubunit triggering mechanism. J Biol Chem 266:8020–8033
Dunn MF, Aguilar V, Brzovic P, Drewe WF Jr, Houben KF, Leja CA, Roy M (1990) The tryptophan synthase bienzyme complex transfers indole between the α- and β-sites via a 25–30 Å long tunnel. Biochemistry 29:8598–8607
Nagata S, Hyde CC, Miles EW (1989) The α-subunit of tryptophan synthase. Evidence that aspartic acid 60 is a catalytic residue and that the double alteration of residues 175 and 211 in a second-site revertant restores the proper geometry of the substrate binding site. J Biol Chem 264:6288–6296
Yutani K, Ogasahara K, Tsujita T, Kanemoto K, Matsumoto M, Tanaka S, Miyashita T, Matsushiro A, Sugino Y, Miles EW (1987) Tryptophan synthase α-subunit glutamic acid 49 is essential for activity: studies with 19 mutants at position 49. J Biol Chem 262:13429–13433
Kulik V, Hartmann E, Weyand M, Frey M, Gierl A, Niks D, Dunn MF, Schlichting I (2005) On the structural basis of the catalytic mechanism and the regulation of the α-subunit of tryptophan synthase from Salmonella typhimurium and BX1 from maize, two evolutionarily related enzymes. J Mol Biol 352:608–620
Miles EW, McPhie P, Yutani K (1988) Evidence that glutamic acid 49 of tryptophan synthase α-subunit is a catalytic residue: inactive mutant proteins substituted at position 49 bind ligands and transmit ligand-dependent to the β-subunit. J Biol Chem 263:8611–8614
Lane AN, Kirschner K (1983) The catalytic mechanism of tryptophan synthase from Escherichia coli: kinetics of the reaction of indole with the enzyme-l-serine complexes. Eur J Biochem 129:571–582
Weischet WO, Kirschner K (1976) The mechanism of the synthesis of indoleglycerol phosphate catalyzed by tryptophan synthase from Escherichia coli: steady-state kinetic studies. Eur J Biochem 65:365–373
Marabotti A, Cozzini P, Mozzarelli A (2000) Novel allosteric effectors of the tryptophan synthase α2β2 complex identified by computer-assisted molecular modeling. Biochim Biophys Acta 1476:287–299
Weyand M, Schlichting I, Marabotti A, Mozzarelli A (2002) Crystal structures of a new class of allosteric effectors complexed to tryptophan synthase. J Biol Chem 277:10647–10652
Sachpatzidis A, Dealwis C, Lubetsky JB, Liang PH, Anderson KS, Lolis E (1999) Crystallographic studies of phosphonate-based α-reaction transition-state analogues complexed to tryptophan synthase. Biochemistry 38:12665–12674
Ngo H, Kimmich N, Harris R, Niks D, Blumenstein L, Kulik V, Barends TR, Schlichting I, Dunn MF (2007) Allosteric regulation of substrate channeling in tryptophan synthase: modulation of the l-serine reaction in stage I of the β-reaction by α-site ligands. Biochemistry 46:7740–7753
Anderson KS, Kim AY, Quillen JM, Sayers E, Yang XJ, Miles EW (1995) Kinetic characterization of channel impaired mutants of tryptophan synthase. J Biol Chem 270:29936–29944
Brzovic PS, Ngo K, Dunn MF (1992) Allosteric interactions coordinate catalytic activity between successive metabolic enzymes in the tryptophan synthase bienzyme complex. Biochemistry 31:3831–3839
Lane AN, Kirschner K (1991) Mechanism of the physiological reaction catalyzed by tryptophan synthase from Escherichia coli. Biochemistry 30:479–484
Schleicher E, Mascaro K, Potts R, Mann DR, Floss HB (1976) Letter: stereochemistry and mechanism of reactions catalyzed by tryptophanase and tryptophan synthetase. J Am Chem Soc 98:1043–1044
Skye GE, Potts R, Floss HG (1974) Stereochemistry of the tryptophan synthetase reaction. J Am Chem Soc 96:1593–1595
Tai CH, Cook PF (2001) Pyridoxal 5′-phosphate-dependent α,β-elimination reactions: mechanism of O-acetylserine sulfhydrylase. Acc Chem Res 34:49–59
Dunn MF, Agular V, Drewe WF Jr, Houben K, Robustell B, Roy M (1987) The interconversion of E. coli tryptophan synthase intermediates is modulated by allosteric interactions. Ind J Biochem Biophys 24(Suppl 4):4–51
Roy M, Keblawi S, Dunn MF (1988) Stereoelectronic control of bond formation in Escherichia coli tryptophan synthase: substrate specificity and enzymatic synthesis of the novel amino acid dihydroisotryptophan. Biochemistry 27:6698–6704
Faeder EJ, Hammes GG (1970) Kinetic studies of tryptophan synthetase: interaction of substrates with the β subunit. Biochemistry 9:4043–4049
Peracchi A, Bettati S, Mozzarelli A, Rossi GL, Miles EW, Dunn MF (1996) Allosteric regulation of tryptophan synthase: effects of pH, temperature, and α-subunit ligands on the equilibrium distribution of pyridoxal 5′-phosphate-l-serine intermediates. Biochemistry 35:1872–1880
Peracchi A, Mozzarelli A, Rossi GL (1995) Monovalent cations affect dynamic and functional properties of the tryptophan synthase α2β2 complex. Biochemistry 34:9459–9465
Woehl E, Dunn MF (1999) Mechanisms of monovalent cation action in enzyme catalysis: the first stage of the tryptophan synthase β-reaction. Biochemistry 38:7118–7130
Woehl EU, Dunn MF (1995) Monovalent metal ions play an essential role in catalysis and intersubunit communication in the tryptophan synthase bienzyme complex. Biochemistry 34:9466–9476
Mozzarelli A, Peracchi A, Rossi GL, Ahmed SA, Miles EW (1989) Microspectrophotometric studies on single crystals of the tryptophan synthase α2β2 complex demonstrate formation of enzyme-substrate intermediates. J Biol Chem 264:15774–15780
Fan YX, McPhie P, Miles EW (2000) Regulation of tryptophan synthase by temperature, monovalent cations, and an allosteric ligand: evidence from Arrhenius plots, absorption spectra, and primary kinetic isotope effects. Biochemistry 39:4692–4703
Ahmed SA, McPhie P, Miles EW (1996) Mechanism of activation of the tryptophan synthase α2β2 complex: solvent effects of the co-substrate β-mercaptoethanol. J Biol Chem 271:29100–29106
Ahmed SA, Miles EW (1994) Aliphatic alcohols stabilize an alternative conformation of the tryptophan synthase α2β2 complex from Salmonella typhimurium. J Biol Chem 269:16486–16492
Phillips RS, Miles EW, McPhie P, Marchal S, Georges C, Dupont Y, Lange R (2008) Pressure and temperature jump relaxation kinetics of the conformational change in Salmonella typhimurium tryptophan synthase l-serine complex: large activation compressibility and heat capacity changes demonstrate the contribution of solvation. J Am Chem Soc 130:13580–13588
Phillips RS, Miles EW, Holtermann G, Goody RS (2005) Hydrostatic pressure affects the conformational equilibrium of Salmonella typhimurium tryptophan synthase. Biochemistry 44:7921–7928
Phillips RS, McPhie P, Miles EW, Marchal S, Lange R (2008) Quantitative effects of allosteric ligands and mutations on conformational equilibria in Salmonella typhimurium tryptophan synthase. Arch Biochem Biophys 470:8–19
Drewe WF Jr, Dunn MF (1985) Detection and identification of intermediates in the reaction of l-serine with Escherichia coli tryptophan synthase via rapid-scanning ultraviolet-visible spectroscopy. Biochemistry 24:3977–3987
Lane AN, Kirschner K (1983) The mechanism of binding of l-serine to tryptophan synthase from Escherichia coli. Eur J Biochem 129:561–570
Schiaretti F, Bettati S, Viappiani C, Mozzarelli A (2004) pH dependence of tryptophan synthase catalytic mechanism: I. The first stage, the β-elimination reaction. J Biol Chem 279:29572–29582
York SS (1972) Kinetic spectroscopic studies of substrate and subunit interactions of tryptophan synthetase. Biochemistry 11:2733–2740
Pan P, Dunn MF (1996) β-Site covalent reactions trigger transitions between open and closed conformations of the tryptophan synthase bienzyme complex. Biochemistry 35:5002–5013
Casino P, Niks D, Ngo H, Pan P, Brzovic P, Blumenstein L, Barends TR, Schlichting I, Dunn MF (2007) Allosteric regulation of tryptophan synthase channeling: the internal aldimine probed by trans-3-indole-3′-acrylate binding. Biochemistry 46:7728–7739
Brzovic PS, Kayastha AM, Miles EW, Dunn MF (1992) Substitution of glutamic acid 109 by aspartic acid alters the substrate specificity and catalytic activity of the β-subunit in the tryptophan synthase bienzyme complex from Salmonella typhimurium. Biochemistry 31:1180–1190
Lu Z, Nagata S, McPhie P, Miles EW (1993) Lysine 87 in the β-subunit of tryptophan synthase that forms an internal aldimine with pyridoxal phosphate serves critical roles in transimination, catalysis, and product release. J Biol Chem 268:8727–8734
Osborne A, Teng Q, Miles EW, Phillips RS (2003) Detection of open and closed conformations of tryptophan synthase by 15N-heteronuclear single-quantum coherence nuclear magnetic resonance of bound 1-15N-l-tryptophan. J Biol Chem 278:44083–44090
Ferrari D, Niks D, Yang LH, Miles EW, Dunn MF (2003) Allosteric communication in the tryptophan synthase bienzyme complex: roles of the β-subunit aspartate 305-arginine 141 salt bridge. Biochemistry 42:7807–7818
Ferrari D, Yang LH, Miles EW, Dunn MF (2001) βD305A mutant of tryptophan synthase shows strongly perturbed allosteric regulation and substrate specificity. Biochemistry 40:7421–7432
Drewe WF Jr, Dunn MF (1986) Characterization of the reaction of l-serine and indole with Escherichia coli tryptophan synthase via rapid-scanning ultraviolet-visible spectroscopy. Biochemistry 25:2494–2501
Woehl E, Dunn MF (1999) Mechanisms of monovalent cation action in enzyme catalysis: the tryptophan synthase α-, β-, and α, β-reactions. Biochemistry 38:7131–7141
Weber-Ban E, Hur O, Bagwell C, Banik U, Yang LH, Miles EW, Dunn MF (2001) Investigation of allosteric linkages in the regulation of tryptophan synthase: the roles of salt bridges and monovalent cations probed by site-directed mutation, optical spectroscopy, and kinetics. Biochemistry 40:3497–3511
Cash MT, Miles EW, Phillips RS (2004) The reaction of indole with the aminoacrylate intermediate of Salmonella typhimurium tryptophan synthase: observation of a primary kinetic isotope effect with 3-[2H]indole. Arch Biochem Biophys 432:233–243
Brzovic PS, Hyde CC, Miles EW, Dunn MF (1993) Characterization of the functional role of a flexible loop in the α-subunit of tryptophan synthase from Salmonella typhimurium by rapid-scanning, stopped-flow spectroscopy and site-directed mutagenesis. Biochemistry 32:10404–10413
Brzovic PS, Sawa Y, Hyde CC, Miles EW, Dunn MF (1992) Evidence that mutations in a loop region of the α-subunit inhibit the transition from an open to a closed conformation in the tryptophan synthase bienzyme complex. J Biol Chem 267:13028–13038
Mozzarelli A, Peracchi A, Rovegno B, Dale G, Rossi GL, Dunn MF (2000) Effect of pH and monovalent cations on the formation of quinonoid intermediates of the tryptophan synthase α2β2 complex in solution and in the crystal. J Biol Chem 275:6956–6962
Strambini GB, Cioni P, Peracchi A, Mozzarelli A (1992) Conformational changes and subunit communication in tryptophan synthase: effect of substrates and substrate analogs. Biochemistry 31:7535–7542
Strambini GB, Cioni P, Peracchi A, Mozzarelli A (1992) Characterization of tryptophan and coenzyme luminescence in tryptophan synthase from Salmonella typhimurium. Biochemistry 31:7527–7534
Vaccari S, Benci S, Peracchi A, Mozzarelli A (1996) Time-resolved fluorescence of tryptophan synthase. Biophys Chem 61:9–22
Bettati S, Benci S, Campanini B, Raboni S, Chirico G, Beretta S, Schnackerz KD, Hazlett TL, Gratton E, Mozzarelli A (2000) Role of pyridoxal 5′-phosphate in the structural stabilization of O-acetylserine sulfhydrylase. J Biol Chem 275:40244–40251
Bettati S, Campanini B, Vaccari S, Mozzarelli A, Schianchi G, Hazlett TL, Gratton E, Benci S (2002) Unfolding of pyridoxal 5′-phosphate-dependent O-acetylserine sulfhydrylase probed by time-resolved tryptophan fluorescence. Biochim Biophys Acta 1596:47–54
Schnackerz KD, Mozzarelli A (1998) Plasticity of the tryptophan synthase active site probed by 31P NMR spectroscopy. J Biol Chem 273:33247–33253
Rhee S, Miles EW, Mozzarelli A, Davies DR (1998) Cryocrystallography and microspectrophotometry of a mutant (αD60N) tryptophan synthase α2β2 complex reveals allosteric roles of αAsp60. Biochemistry 37:10653–10659
Kulik V, Weyand M, Seidel R, Niks D, Arac D, Dunn MF, Schlichting I (2002) On the role of αThr183 in the allosteric regulation and catalytic mechanism of tryptophan synthase. J Mol Biol 324:677–690
Ahmed SA, Hyde CC, Thomas G, Miles EW (1987) Microcrystals of tryptophan synthase α2β2 complex from Salmonella typhimurium are catalytically active. Biochemistry 26:5492–5498
Pioselli B, Bettati S, Mozzarelli A (2005) Confinement and crowding effects on tryptophan synthase α2β2 complex. FEBS Lett 579:2197–2202
Leja CA, Woehl EU, Dunn MF (1995) Allosteric linkages between β-site covalent transformations and α-site activation and deactivation in the tryptophan synthase bienzyme complex. Biochemistry 34:6552–6561
Ogasahara K, Hiraga K, Ito W, Miles EW, Yutani K (1992) Origin of the mutual activation of the α and β2 subunits in the α2β2 complex of tryptophan synthase. Effect of alanine or glycine substitutions at proline residues in the α-subunit. J Biol Chem 267:5222–5228
Rowlett R, Yang LH, Ahmed SA, McPhie P, Jhee KH, Miles EW (1998) Mutations in the contact region between the α and β subunits of tryptophan synthase alter subunit interaction and intersubunit communication. Biochemistry 37:2961–2968
Marabotti A, De Biase D, Tramonti A, Bettati S, Mozzarelli A (2001) Allosteric communication of tryptophan synthase: functional and regulatory properties of the βS178P mutant. J Biol Chem 276:17747–17753
Raboni S, Bettati S, Mozzarelli A (2005) Identification of the geometric requirements for allosteric communication between the α- and β-subunits of tryptophan synthase. J Biol Chem 280:13450–13456
Raboni S, Pioselli B, Bettati S, Mozzarelli A (2003) The molecular pathway for the allosteric regulation of tryptophan synthase. Biochim Biophys Acta 1647:157–160
Spyrakis F, Raboni S, Cozzini P, Bettati S, Mozzarelli A (2006) Allosteric communication between α- and β-subunits of tryptophan synthase: modelling the open-closed transition of the α-subunit. Biochim Biophys Acta 1764:1102–1109
Amadasi A, Bertoldi M, Contestabile R, Bettati S, Cellini B, di Salvo ML, Borri-Voltattorni C, Bossa F, Mozzarelli A (2007) Pyridoxal 5′-phosphate enzymes as targets for therapeutic agents. Curr Med Chem 14:1291–1324
Greenville-Briggs LJ, Avreva AO, Bruce CR, Williams A, Whisson SC, Birch PR, van West P (2005) Elevated amino acid biosynthesis in Phytophthora infestans during appressorium formation and potato infection. Fungal Genet Biol 42:244–256
Caldwell HD, Wood H, Crane D, Bailey R, Jones RB, Mabey D, Maclean I, Mohammed Z, Peeling R, Roshick C, Schachter J, Solomon AW, Stamm WE, Suchland RJ, Taylor L, West SK, Quinn TC, Belland RJ, McClarty G (2003) Polymorphisms in Chlamydia trachomatis tryptophan synthase genes differentiate between genital and ocular isolates. J Clin Invest 111:1757–1769
Fehlner-Gardiner C, Roshick C, Carlson JH, Hughes S, Belland RJ, Caldwell HD, McClarty G (2002) Molecular basis defining human Chlamydia trachomatis tissue tropism: a possible role for tryptophan synthase. J Biol Chem 277:26893–26903
Chaudhary K, Roos DS (2005) Protozoan genomics for drug discovery. Nat Biotechnol 23:1089–1091
Finn J, Langevine C, Birk I, Birk J, Nickerson K, Rodaway S (1999) Rational herbicide design by inhibition of tryptophan biosynthesis. Bioorg Med Chem Lett 9:2297–2302
Dias MV, Canduri F, da Silveira NJ, Czekster CM, Basso LA, Palma MS, Santos DS, de Azevedo WF Jr (2006) Molecular models of tryptophan synthase from Mycobacterium tuberculosis complexed with inhibitors. Cell Biochem Biophys 44:375–384
Becker D, Selbach M, Rollenhagen C, Ballmaier M, Meyer TF, Mann M, Bumann D (2006) Robust Salmonella metabolism limits possibilities for new antimicrobials. Nature 440:303–307
Blumenstein L, Domratcheva T, Niks D, Ngo H, Seidel R, Dunn MF, Schlichting I (2007) βQ114N and βT110V mutations reveal a critically important role of the substrate α-carboxylate site in the reaction specificity of tryptophan synthase. Biochemistry 46:14100–14116
Ngo H, Harris R, Kimmich N, Casino P, Niks D, Blumenstein L, Barends TR, Kulik V, Weyand M, Schlichting I, Dunn MF (2007) Synthesis and characterization of allosteric probes of substrate channeling in the tryptophan synthase bienzyme complex. Biochemistry 46:7713–7727
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Raboni, S., Bettati, S. & Mozzarelli, A. Tryptophan synthase: a mine for enzymologists. Cell. Mol. Life Sci. 66, 2391–2403 (2009). https://doi.org/10.1007/s00018-009-0028-0
Received:
Revised:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s00018-009-0028-0