Structure and mechanism of the ThDP-dependent benzaldehyde lyase from Pseudomonas fluorescens

FEBS Journal

Volumn 272, Issue 23, 2005, Pages 6067-6076

  Mosbacher, Tanja G ^a   Mueller, Michael ^a   Schulz, Georg E ^a  

^a UNIVERSITY OF FREIBURG   (Germany)

Author keywords

Acyloin condensation; Carbon carbon ligation; Crystal structure; Seleno methionine MAD

Indexed keywords

BENZALDEHYDE LYASE; CARBON; LYASE; THIAMINE PYROPHOSPHATASE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GROWTH; CARBON SOURCE; CATALYSIS; ENERGY RESOURCE; ENZYME ACTIVE SITE; ENZYME BINDING; ENZYME MECHANISM; ENZYME STRUCTURE; ENZYME SUBSTRATE; ENZYME SYNTHESIS; PRIORITY JOURNAL; PROTEIN DOMAIN; PSEUDOMONAS FLUORESCENS; STEREOSPECIFICITY; STRUCTURE ANALYSIS;

ALDEHYDE-LYASES; AMINO ACID SEQUENCE; BACTERIAL PROTEINS; BINDING SITES; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; PSEUDOMONAS FLUORESCENS; SEQUENCE ALIGNMENT; SUBSTRATE SPECIFICITY; THIAMINE PYROPHOSPHATE;

BACTERIA (MICROORGANISMS); PSEUDOMONAS FLUORESCENS;

EID: 28244449299     PISSN: 1742464X     EISSN: 17424658     Source Type: Journal    
DOI: 10.1111/j.1742-4658.2005.04998.x     Document Type: Article

References (44)

1. Müller M & Sprenger GA (2004) Thiamine-dependent enzymes as catalysts of C-C bonding reactions: the role of 'orphan' enzymes. In Thiamine: Catalytic Mechanisms in Normal and Disease States (Jordan, F & Patel, MS, eds), pp. 77-92. Marcel Dekker, London.
2. Jordan F (2003) Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions. Nat Prod Rep 20, 184-201.
3. Gonzalez B & Vicuña R (1989) Benzaldehyde lyase, a novel thiamine PPI-requiring enzyme, from Pseudomonas fluorescens BiovaR-I. J Bacteriol 171, 2401-2405.
4. Hinrichsen P, Gomez I & Vicuña R (1994) Cloning and sequencing of the gene encoding benzaldehyde lyase from Pseudomonas fluorescens BiovaR-I. Gene 144, 137-138.
5. Demir S, Pohl M, Janzen E & Müller M (2001) Enantioselective synthesis of hydroxy ketones through cleavage and formation of acyloin linkage. Enzymatic kinetic resolution via C-C bond cleavage. J Chem Soc Perkin Trans 1, 633-635.
6. Demir S, Şeşenoglu Ö, Eren E, Hosrik B, Pohl M, Janzen E, Kolter D, Feldmann R, Dünkelmann P & Müller M (2002) Adv Synth Catal 344, 96-103.
7. Sanches-Gonzalez M & Rosazza JPN (2003) Mixed aromatic acyloin condensations with recombinant benzaldehyde lyase: synthesis of alpha-hydroxydihydrochalcones and related alpha-hydroxy ketones. Adv Synth Catal 345, 819-824.
8. Lingen B, Pohl M, Liese A, Demir AS & Müller M (2004) Enantioselective synthesis of hydroxyketones via benzaldehyde lyase and benzoylformate decarboxylase catalyzed C-C bond formation. In Thiamine: Catalytic Mechanisms in Normal and Disease States (Jordan, F & Patel, MS, eds), pp. 113-130. Marcel Dekker, London.
9. Pohl M, Sprenger GA & Müller M (2004) A new perspective on thiamine catalysis. Current Opinion Biotechnol 15, 335-342.
10. Demir AS, Şeşenoglu Ö, Dünkelmann P & Müller M (2003) Benzaldehyde lyase-catalyzed enantioselective carboligation of aromatic aldehydes with mono- and dimethoxy acetaldehyde. Org Lett 5, 2047-2050.
11. Dünkelmann P, Kolte-Jung D, Nitsche A, Demir AS, Siegert P, Lingen B, Baumann M, Pohl M & Müller M (2002) Development of a donor-acceptor concept for enzymatic cross-coupling reactions of aldehydes: the first asymmetric cross-benzoin condensation. J Am Chem Soc 124, 12084-12085.
12. Hasson MS, Muscate A, McLeish MJ, Polovnikova LS, Gerlt JA, Kenyon GL, Petsko GA & Ringe D (1998) The crystal structure of benzoylformate decarboxylase at 1.6 A resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry 37, 9918-9930.
13. Polovnikova ES, McLeish MJ, Sergienko EA, Burgner JT, Anderson NL, Bera AK, Jordan F, Kenyon GL & Hasson MS (2003) Structural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase. Biochemistry 42, 1820-1830.
14. Arjunan P, Umland T, Dyda F, Swaminathan S, Furey W, Sax M, Farrenkopf B, Gao Y, Zhang D & Jordan F (1996) Crystal structure of the thiamin diphosphate-dependent enzyme pyruvate decarboxylase from the yeast Saccharomyces cerevisiae at 2.3 Å resolution. J Mol Biol 3, 590-600.
15. Dobritzsch D, König S, Schneider G & Lu G (1998) High resolution crystal structure of pyruvate decarboxylase from Zymomonas mobilis. Implications for substrate activation in pyruvate decarboxylases. J Biol Chem 273, 20196-20204.
16. Lu G, Dobritzsch D, Baumann S, Schneider G & König S (2000) The structural basis of substrate activation in yeast pyruvate decarboxylase. A crystallographic and kinetic study. Eur J Biochem 267, 861-868.
17. Holm L & Sander C (1993) Protein structure comparison by alignment of distance matrices. J Mol Biol 233, 123-138.
18. Pang SS, Duggleby RG, Schowen RL & Guddat LW (2004) The crystal structures of Klebsiella pneumoniae acetolactate synthase with enzyme-bound cofactor and with an unusual intermediate. J Biol Chem 279, 2242-2253.
19. Pang SS, Duggleby RG & Guddat LW (2002) Crystal structure of yeast acetohydroxyacid synthase: a target for herbicidal inhibitors. J Mol Biol 317, 249-262.
20. Schütz A, Sandalova T, Ricagno S, Hübner G, König S & Schneider G (2003) Crystal structure of thiamindiphosphate-dependent indolepyruvate decarboxylase from Enterobacter cloacae, an enzyme involved in the biosynthesis of the plant hormone indole-3-acetic acid. Eur J Biochem 270, 2312-2321.
21. Gaines ME, Elkins JM, Hewitson KS & Schofield CJ (2004) Crystal structure and mechanistic implications of N2-(2-carboxyethyl) arginine synthase, the first enzyme in the clavulanic acid biosynthesis pathway. J Biol Chem 279, 5685-5692.
22. Muller YA & Schulz GE (1994) Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase. Science 259, 965-967.
23. Lindqvist Y, Schneider G, Ermler U & Sundström M (1992) Three-dimensional structure of transketolase, a thiamine diphosphate-dependent enzyme, at 2.5 A resolution. EMBO J 11, 2373-2379.
24. Hawkins CF, Borges A & Perham RN (1989) A common structural motif in thiamine pyrophosphate-binding enzymes. FEBS Lett 255, 77-82.
25. Siegert P, Pohl M, Kneen MM, Pogozheva ID, Kenyon GL & McLeish MJ (2004) Exploring the substrate specificity of benzoylformate decarboxylase, pyruvate decarboxylase, and benzaldehyde lyase. In Thiamine: Catalytic Mechanisms in Normal and Disease States (Jordan, F & Patel, MS, eds), pp. 275-290. Marcel Dekker, London.
26. Jordan F, Nemeria NS, Zhang S, Yan Y, Arjunan P & Furey W (2003) Dual catalytic apparatus of the thiamin diphosphate coenzyme: acid-base via the 1′,4′-iminopyrimidine tautomer along with its electrophilic role. J Am Chem Soc 125, 12732-12738.
27. Nemeria N, Baykal A, Joseph E, Zhang S, Yan Y, Furey W & Jordan F (2004) Tetrahedral intermediates in thiamin diphosphate-dependent decarboxylations exist as a 1′,4′-imino tautomeric form of the coenzyme, unlike the Michaelis complex or the free coenzyme. Biochemistry 43, 6565-6575.
28. Pohl M, Lingen B & Müller M (2002) Thiamin-diphosphate-dependent enzymes: new aspects of asymmetric C-C bond formation. Chem Eur J 8, 5288-5295.
29. Iding H, Dünnwald T, Greiner L, Liese A, Müller M, Siegert P, Grötzinger J, Demir AS & Pohl M (2000) Benzoylformate decarboxylase from Pseudomonas putida as stable catalyst for the synthesis of chiral 2-hydroxy ketones. Chem Eur J 6, 1483-1495.
30. Bürgi HB & Dunitz JD (1983) From crystal statics to chemical dynamics. Acc Chem Res 16, 153-161.
31. Janzen E (2002) Die Benzaldehydlyase aus Pseudomonas fluoreszens. Biochemische Charakterisierung und die Untersuchung von Struktur- Funktionsbeziehungen. PhD Thesis, University of Duesseldorf.
32. Hendrickson WA, Horton JR & LeMaster DM (1990) Selenomethionyl proteins produced for analysis by multiwavelength anomalous diffraction (MAD): a vehicle for direct determination of three-dimensional structure. EMBO J 9, 1665-1672.
33. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Cryst 26, 795-800.
34. Terwilliger TC & Berendzen J (1999) Automated MAD and MIR structure solution. Acta Crystallogr D55, 849-861.
35. de la Fortelle E & Bricogne G (1997) Maximum-likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol 276, 472-494.
36. Terwilliger TC (2003) Automated main-chain model building by template matching and iterative fragment extension. Acta Crystallogr D59, 38-44.
37. McRee DE (1999) XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density. J Struct Biol 125, 156-165.
38. Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang JS, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T & Warren GL (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr D54, 905-921.
39. Collaborative Computational Project, Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D50, 760-763.
40. Perrakis A, Sixma TK, Wilson KS & Lamzin VS (1997) wARP: improvement and extension of crystallographic phases by weighted averaging of multiple refined dummy atomic models. Acta Crystallogr D53, 448-455.
41. Winn MD, Isupov MN & Murshudov GN (2001) Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D57, 122-133.
42. Laskowski RA, MacArthur MW, Moss DS & Thornton JM (1993) PROCHECK - a program to check the stereochemical quality of protein structures. J Appl Cryst 26, 283-291.
43. Lovell SC, Davis IW, Arendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS & Richardson DC (2002) Structure validation by Calpha geometry: phi, psi and Cbeta deviation. Proteins: Struct Funct Genet 50, 437-450.
44. Fenn TD, Ringe D & Petsko GA (2003) POV-Script+: a program for model and data visualization using persistence of vision ray-tracing. J Appl Cryst 36, 944-947.