Purification and crystallization of benzoylformate decarboxylase

A new large‐scale purification method for benzoylformate decarboxylase from Pseudomonas putida has allowed us to undertake an X‐ray crystallographic study of the enzyme. The previously observed instability of the enzyme was overcome by addition of 100 μM thiamine pyrophosphate to buffers used in the purification. The final enzyme preparation was more than 97% pure, as determined by denaturing gel electrophoresis and densitometry. The mobility of the enzyme on a gel filtration column indicates that it is a tetramer of 57‐kDa subunits. Large, single crystals of benzoylformate decarboxylase were grown from solutions of buffered polyethylene glycol 400, pH 8.5. The crystals diffract to beyond 1.6 Å resolution and are stable for days to X‐ray radiation. Analysis of X‐ray data from the crystals, along with the newly determined quaternary structure, identifies the space group as 1222. The unit cell dimensions are a = 82 Å, b = 97 Å, c = 138 Å. An average Vm value for the crystals is consistent with one subunit per asymmetric unit. The subunits of the tetramer must be arranged with tetrahedral 222 symmetry.

[1]  R. Stanier Simultaneous Adaptation: A New Technique for the Study of Metabolic Pathways , 1947, Journal of bacteriology.

[2]  T. Spector Refinement of the Coomassie blue method of protein quantitation: A simple and linear spectrophotometric assay for ≤0.5 to 50 μg of protein , 1978 .

[3]  B. Robinson,et al.  The relationships between transketolase, yeast pyruvate decarboxylase and pyruvate dehydrogenase of the pyruvate dehydrogenase complex , 1993, FEBS letters.

[4]  G. Hegeman [89] Benzoylformate decarboxylase (Pseudomonas putida)☆ , 1970 .

[5]  L. Ingraham,et al.  ON THE MECHANISM OF THIAMINE ACTION , 1960 .

[6]  G. Schneider,et al.  Refined structure of transketolase from Saccharomyces cerevisiae at 2.0 A resolution. , 1994, Journal of molecular biology.

[7]  G L Kenyon,et al.  Differential reactivity in the processing of [p-(halomethyl)benzoyl] formates by benzoylformate decarboxylase, a thiamin pyrophosphate dependent enzyme. , 1988, Biochemistry.

[8]  H. Z. Sable,et al.  Thiamin: twenty years of progress. , 1982, Annals of the New York Academy of Sciences.

[9]  G. L. Kenyon,et al.  Carbon-13 nuclear magnetic resonance studies of mandelate metabolism in whole bacterial cells and in isolated, in vivo cross-linked enzyme complexes. , 1981, Biochemistry.

[10]  B. Matthews Solvent content of protein crystals. , 1968, Journal of molecular biology.

[11]  Frank Jordan,et al.  N1'-Methylthiaminium diiodide. Model study on the effect of a coenzyme bound positive charge on reaction mechanisms requiring thiamin pyrophosphate , 1978 .

[12]  P. Babbitt,et al.  Mandelate pathway of Pseudomonas putida: sequence relationships involving mandelate racemase, (S)-mandelate dehydrogenase, and benzoylformate decarboxylase and expression of benzoylformate decarboxylase in Escherichia coli. , 1990, Biochemistry.

[13]  Wolfgang Kabsch,et al.  Evaluation of Single-Crystal X-ray Diffraction Data from a Position-Sensitive Detector , 1988 .

[14]  G. Petsko,et al.  Mechanism of the reaction catalyzed by mandelate racemase. 2. Crystal structure of mandelate racemase at 2.5-A resolution: identification of the active site and possible catalytic residues. , 1991, Biochemistry.

[15]  R. Wilcocks,et al.  Acyloin formation by benzoylformate decarboxylase from Pseudomonas putida , 1992, Applied and environmental microbiology.

[16]  G. Schneider,et al.  Crystal structure of transketolase in complex with thiamine thiazolone diphosphate, an analogue of the reaction intermediate, at 2.3 Å resolution , 1993, FEBS letters.

[17]  W Furey,et al.  Catalytic centers in the thiamin diphosphate dependent enzyme pyruvate decarboxylase at 2.4-A resolution. , 1993, Biochemistry.

[18]  S. König,et al.  Correlation of cofactor binding and the quaternary structure of pyruvate decarboxylase as revealed by 31P NMR spectroscopy , 1992, FEBS letters.

[19]  S. Shigeoka,et al.  Characterization and molecular properties of 2-oxoglutarate decarboxylase from Euglena gracilis. , 1991, Archives of biochemistry and biophysics.

[20]  R. Duggleby,et al.  Pyruvate decarboxylase from Zymomonas mobilis. Structure and re-activation of apoenzyme by the cofactors thiamin diphosphate and magnesium ion. , 1991, The Biochemical journal.

[21]  A novel structural basis for membrane association of a protein: construction of a chimeric soluble mutant of (S)-mandelate dehydrogenase from Pseudomonas putida. , 1993, Biochemistry.

[22]  S. Nishikawa,et al.  NTIAL ROLES OF THE AMINOPYRIMIDINE RING IN THIAMIN CATALYZED REACTIONS * , 1982, Annals of the New York Academy of Sciences.

[23]  R. Yount The mechanism of thiamine action , 1958 .

[24]  G. L. Kenyon,et al.  Kinetics and mechanism of benzoylformate decarboxylase using 13C and solvent deuterium isotope effects on benzoylformate and benzoylformate analogues. , 1988, Biochemistry.

[25]  G. Schulz,et al.  Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase , 1993, Science.

[26]  G. Schneider,et al.  Three‐dimensional structure of transketolase, a thiamine diphosphate dependent enzyme, at 2.5 A resolution. , 1992, The EMBO journal.

[27]  Gregory A. Petsko,et al.  Mandelate racemase and muconate lactonizing enzyme are mechanistically distinct and structurally homologous , 1990, Nature.

[28]  M. M. Bradford A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. , 1976, Analytical biochemistry.

[29]  Ronald Breslow,et al.  On the Mechanism of Thiamine Action. IV.1 Evidence from Studies on Model Systems , 1958 .