Conformational changes and loose packing promote E. coli Tryptophanase cold lability

BMC Structural Biology

Volumn 9, Issue , 2009, Pages

  Kogan, Anna ^a   Gdalevsky, Garik Y ^a   Cohen Luria, Rivka ^a   Goldgur, Yehuda ^a   Phillips, Robert S ^b   Parola, Abraham H ^a   Almog, Orna ^a  

^a BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

^b UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; APOENZYME; DIMER; HOLOENZYME; MONOMER; PYRIDOXAL 5 PHOSPHATE; TETRAMER; TRYPTOPHANASE; RECOMBINANT PROTEIN;

ARTICLE; CATALYSIS; COLD; COLD LABILITY; CONFORMATIONAL TRANSITION; CONTROLLED STUDY; COOLING; CRYSTAL STRUCTURE; DISSOCIATION; ENZYME ACTIVITY; ENZYME RELEASE; ESCHERICHIA COLI; HYDROPHOBICITY; HYDROSTATIC PRESSURE; NONHUMAN; POINT MUTATION; PRESSURE; PROTEIN FUNCTION; PROTEUS VULGARIS; TEMPERATURE; CHEMISTRY; ENZYMOLOGY; GENETICS; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SITE DIRECTED MUTAGENESIS; TIME; X RAY CRYSTALLOGRAPHY;

ESCHERICHIA COLI;

CRYSTALLOGRAPHY, X-RAY; ESCHERICHIA COLI; MUTAGENESIS, SITE-DIRECTED; PRESSURE; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; TEMPERATURE; TIME FACTORS; TRYPTOPHANASE;

EID: 70450174813     PISSN: None     EISSN: 14726807     Source Type: Journal    
DOI: 10.1186/1472-6807-9-65     Document Type: Article

References (55)

1. Another Look at Cold Lability of Enzymes. PE Bock C Frieden, Trends in Biochemical Sciences 1978 3 5 100 103 10.1016/S0968-0004(78)80013-9
2. Analysis of the cold lability behavior of rabbit muscle phosphofructokinase. PE Bock HR Gilbert C Frieden, Biochem Biophys Res Commun 1975 66 2 564 569 10.1016/0006-291X(75)90547-1 241341
3. Cold Lability of the Mutant Forms of Escherichia-Coli Inorganic Pyrophosphatase. IV Velichko SE Volk VY Dudarenkov NN Magretova VY Chernyak A Goldman BS Cooperman R Lahti AA Baykov, FEBS Lett 1995 359 1 20 22 10.1016/0014-5793(95)00003-R 7851523
4. Pyruvate Carboxylase. Reversible Inactivation by Cold. JJ Irias MR Olmsted MF Utter, Biochemistry 1969 8 12 5136 5148 10.1021/bi00840a068 5391871
5. Invitro Dissociation and Reassociation of Human Alcohol-Dehydrogenase Class-I Isozymes. F Briganti WP Fong DS Auld BL Vallee, Biochemistry 1989 28 13 5374 5379 10.1021/bi00439a009 2775712
6. Glutamic acid decarboxylase. III. The inactivation of the enzyme at low temperatures. R Shukuya GW Schwert, J Biol Chem 1960 235 1658 1661 14446292
7. Properties of tryptophanase from Escherichia coli. RO Burns RD Demoss, Biochim Biophys Acta 1962 65 233 244 10.1016/0006-3002(62)91042-9 14017164
8. Studies on the mechanism of the tryptophan synthetase reaction. JA Demoss, Biochim Biophys Acta 1962 62 279 293 10.1016/0006-3002(62)90041-0 13885361
9. Structural insights into cold inactivation of tryptophanase and cold adaptation of subtilisin S41. O Almog A Kogan M Leeuw GY Gdalevsky R Cohen-Luria AH Parola, Biopolymers 2008 89 5 354 359 10.1002/bip.20866 17937401
10. Heat capacity of proteins. II. Partial molar heat capacity of the unfolded polypeptide chain of proteins: protein unfolding effects. PL Privalov GI Makhatadze, J Mol Biol 1990 213 2 385 391 10.1016/S0022-2836(05)80198-6 2160545
11. Cold inactivation and dissociation into dimers of Escherichia coli tryptophanase and its W330F mutant form. T Erez G Gdalevsky YM Torchinsky RS Phillips AH Parola, Biochim Biophys Acta 1998 1384 2 365 372 9659398
12. Pyridoxal phosphate binding to wild type, W330F, and C298S mutants of Escherichia coli apotryptophanase: unraveling the cold inactivation. T Erez RS Phillips AH Parola, FEBS Lett 1998 433 3 279 282 10.1016/S0014-5793(98)00931-4 9744811
13. Cold denaturation of proteins under high pressure. S Kunugi N Tanaka, Biochim Biophys Acta 2002 1595 1-2 329 344 11983406
14. Conformational drift of dissociated lactate dehydrogenases. L King G Weber, Biochemistry 1986 25 12 3632 3637 10.1021/bi00360a023 3718949
15. Conformational drift and cryoinactivation of lactate dehydrogenase. L King G Weber, Biochemistry 1986 25 12 3637 3640 10.1021/bi00360a024 3718950
16. Navigating the folding routes. PG Wolynes JN Onuchic D Thirumalai, Science 1995 267 5204 1619 1620 10.1126/science.7886447 7886447
17. Protein destabilization at low temperatures. F Franks, Adv Protein Chem 1995 46 105 139 full-text 7771316
18. Crystal structure of tryptophanase. MN Isupov AA Antson EJ Dodson GG Dodson IS Dementieva LN Zakomirdina KS Wilson Z Dauter AA Lebedev EH Harutyunyan, J Mol Biol 1998 276 3 603 623 10.1006/jmbi.1997.1561 9551100
19. Kinetic and equilibrium studies on the activation of Escherichia coli K12 tryptophanase by pyridoxal 5'-phosphate and monovalent cations. A Hogberg-Raibaud O Raibaud ME Goldberg, J Biol Chem 1975 250 9 3352 3358 1091651
20. Monovalent cation activation of tryptophanase. CH Suelter EE Snell, J Biol Chem 1977 252 6 1852 1857 321445
21. Application of a direct spectrophotometric assay employing a chromogenic substrate for tryptophanase to the determination of pyridoxal and pyridoxamine 5'-phosphates. CH Suelter J Wang EE Snell, Anal Biochem 1976 76 l 221 232 10.1016/0003-2697(76)90280-3 11704
22. Essential Role of Monovalent Cations in the Firm Binding of Pyridoxal 5'-Phosphate to Tryptophanase and P-Tyrosinase. T Toraya T Nihira S Fukui, Eur J Biochem 1976 69 411 419 10.1111/j.1432-1033.1976.tb10925.x
23. The Mechanism of Tryptophan Indole-lyase: Insights from Pre-steady-state Kinetics and Substrate and Solvent Isotope Effects. RS Phillips, J Am Chem Soc 1989 111 727 730 10.1021/ja00184a051
24. Mechanism of binding of substrate analogues to tryptophan indole-lyase: studies using rapid-scanning and single-wavelength stopped-flow spectrophotometry. RS Phillips SL Bender P Brzovic MF Dunn, Biochemistry 1990 29 37 8608 8614 10.1021/bi00489a016 2271544
25. Structure and mechanism of tryptophan indole-lyase and tyrosine phenol-lyase. RS Phillips TV Demidkina NG Faleev, Biochim Biophys Acta 2003 1647 1-2 167 172 12686128
26. Crystals of tryptophan indole-lyase and tyrosine phenol-lyase form stable quinonoid complexes. RS Phillips TV Demidkina LN Zakomirdina S Bruno L Ronda A Mozzarelli, J Biol Chem 2002 277 24 21592 21597 10.1074/jbc.M200216200 11934889
27. Cold-induced enzyme inactivation: how does cooling lead to pyridoxal phosphate-aldimine bond cleavage in tryptophanase? T Erez GY Gdalevsky C Hariharan D Pines E Pines RS Phillips R Cohen-Luria AH Parola, Biochim Biophys Acta 2002 1594 2 335 340 11904229
28. Structure of Escherichia coli tryptophanase. SY Ku P Yip PL Howell, Acta Crystallogr D Biol Crystallogr 2006 62 Pt 7 814 823 10.1107/S0907444906019895 16790938
29. The structure of apo tryptophanase from Escherichia coli reveals a wide-open conformation. N Tsesin A Kogan GY Gdalevsky JP Himanen R Cohen-Luria AH Parola Y Goldgur O Almog, Acta Crystallogr D Biol Crystallogr 2007 63 Pt 9 969 974 10.1107/S0907444907036396 17704565
30. Development of hydrophobicity parameters to analyze proteins which bear post- or cotranslational modifications. SD Black DR Mould, Anal Biochem 1991 193 1 72 82 10.1016/0003-2697(91)90045-U 2042744
31. A large compressibility change of protein induced by a single amino acid substitution. K Gekko Y Tamura E Ohmae H Hayashi H Kagamiyama H Ueno, Protein Science 1996 5 3 542 545 8868493
32. Cavity-filling mutations enhance protein stability by lowering the free energy of native state. M Saito H Kono H Morii H Uedaira TH Tahirov K Ogata A Sarai, Journal of Physical Chemistry B 2000 104 15 3705 3711 10.1021/jp991717f (Pubitemid 30858502)
33. Size of the amino acid side chain at position 158 of cytochrome b is critical for an active cytochrome bc1 complex and for photosynthetic growth of Rhodobacter capsulatus. E Atta-Asafo-Adjei F Daldal, Proc Natl Acad Sci USA 1991 88 2 492 496 10.1073/pnas.88.2.492 1846443
34. Tryptophanase from Proteus vulgaris: the conformational rearrangement in the active site, induced by the mutation of Tyrosine 72 to phenylalanine, and its mechanistic consequences. VV Kulikova LN Zakomirdina IS Dementieva RS Phillips PD Gollnick TV Demidkina NG Faleev, Biochim Biophys Acta 2006 1764 4 750 757 16455316
35. Quantitative effects of allosteric ligands and mutations on conformational equilibria in Salmonella typhimurium tryptophan synthase. RS Phillips P McPhie EW Miles S Marchal R Lange, Arch Biochem Biophys 2008 470 1 8 19 10.1016/j.abb.2007.11.003 18047826
36. Hydrostatic pressure affects the conformational equilibrium of Salmonella typhimurium tryptophan synthase. RS Phillips EW Miles G Holtermann RS Goody, Biochemistry 2005 44 21 7921 7928 10.1021/bi050056b 15910007
37. Probing the contribution of internal cavities to the volume change of protein unfolding under pressure. KJ Frye CA Royer, Protein Sci 1998 7 10 2217 2222 10.1002/pro.5560071020 9792110
38. Solubility of alpha-amino acids in water under high pressure: glycine, L-alanine, L-valine, L-leucine, and L-isoleucine. H Matsuo Y Suzuki S Sawamura, Fluid Phase Equilibria 2002 200 2 227 237 10.1016/S0378-3812(02)00029-8 (Pubitemid 34669878)
39. Inhomogeneous molecular density: reference packing densities and distribution of cavities within proteins. K Rother R Preissner A Goede C Frommel, Bioinformatics 2003 19 16 2112 2121 10.1093/bioinformatics/btg292 14594717
40. Processing of X-ray diffraction data collected in oscillation mode. Z Otwinowski W Minor, Methods in Enzymology 1997 276 307 326 full-text
41. Characterization of the tryptophanase operon of Proteus vulgaris. Cloning, nucleotide sequence, amino acid homology, and in vitro synthesis of the leader peptide and regulatory analysis. AV Kamath C Yanofsky, J Biol Chem 1992 267 28 19978 19985 1400314
42. Mechanism of action of aspartate aminotransferase proposed on the basis of its spatial structure. JF Kirsch G Eichele GC Ford MG Vincent JN Jansonius H Gehring P Christen, J Mol Biol 1984 174 3 497 525 10.1016/0022-2836(84)90333-4 6143829
43. Synthesis of L-Tyrosine from Phenol and S-(Ortho-Nitrophenyl)-L-Cysteine Catalyzed by Tyrosine Phenol-Lyase. RS Phillips K Ravichandran RL Vontersch, Enzyme and Microbial Technology 1989 11 2 80 83 10.1016/0141-0229(89)90064-1
44. Evidence that cysteine 298 is in the active site of tryptophan indole-lyase. RS Phillips PD Gollnick, J Biol Chem 1989 264 18 10627 10632 2659590
45. Crystallization and preliminary X-ray analysis of the apo form of Escherichia coli tryptophanase. A Kogan GY Gdalevsky R Cohen-Luria AH Parola Y Goldgur, Acta Crystallogr D Biol Crystallogr 2004 60 Pt 11 2073 2075 10.1107/S0907444904022425 15502331
46. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. MM Bradford, Anal Biochem 1976 72 248 254 10.1016/0003-2697(76)90527-3 942051
47. The environments of Trp-248 and Trp-330 in tryptophan indole-lyase from Escherichia coli. RS Phillips P Gollnick, FEBS Lett 1990 268 1 213 216 10.1016/0014-5793(90)81011-C 2200710
48. Direct spectrophotometric assay of tryptophanase. CH Suelter J Wang EE Snell, FEBS Lett 1976 66 2 230 232 10.1016/0014-5793(76)80510-8 955084
49. The light-induced reactions of tryptophan with halocompounds. RA Edwards G Jickling RJ Turner, Photochem Photobiol 2002 75 4 362 368 10.1562/0031- 8655(2002)075<0362:TLIROT7gt;2.0.CO;2 12003125
50. The tryptophanase from Escherichia coli K-12. II. Comparison of the thermal stabilities of apo-, holo-, and hybrid enzymes. O Raibaud ME Goldberg, J Biol Chem 1973 248 10 3451 3455 4573978
51. Differential effects of temperature and hydrostatic pressure on the formation of quinonoid intermediates from L-Trp and L-Met by H463F mutant Escherichia coli tryptophan indole-lyase. RS Phillips G Holtermann, Biochemistry 2005 44 43 14289 14297 10.1021/bi051062a 16245945
52. Robust Multivariate-Analysis Applied to Separation of Components in Absorption-Spectra. IBC Matheson RJ Desa, Computers & Chemistry 1990 14 2 157 164 10.1016/0097-8485(90)80019-X (Pubitemid 20661266)
53. Recent developments for the efficient crystallographic refinement of macromolecular structures. AT Brunger PD Adams LM Rice, Curr Opin Struct Biol 1998 8 5 606 611 10.1016/S0959-440X(98)80152-8 9818265
54. A graphics model building and refinement system for macromolecules. TA Jones, J Appl Crystallogr 1978 11 268 272 10.1107/S0021889878013308
55. A simple method for displaying the hydropathic character of a protein. J Kyte RF Doolittle, J Mol Biol 1982 157 1 105 132 10.1016/0022-2836(82)90515-0 7108955