Saturation mutagenesis of putative catalytic residues of benzoylformate decarboxylase provides a challenge to the accepted mechanism

Proceedings of the National Academy of Sciences of the United States of America

Volumn 105, Issue 15, 2008, Pages 5733-5738

  Yep, Alejandra ^a   Kenyon, George L ^a   McLeish, Michael J ^a  

^a UNIVERSITY OF MICHIGAN   (United States)

Author keywords

Catalytic mechanism; Thiamin diphosphate

Indexed keywords

ALANINE; BENZOYLFORMATE DECARBOXYLASE; CARBOXYLIC ACID; CARBOXYLYASE; ENAMINE; HISTIDINE; LEUCINE; METHIONINE; PHENYLALANINE; SERINE; THREONINE;

ARTICLE; CATALYST; CONTROLLED STUDY; ENZYME ACTIVITY; ENZYME ASSAY; ENZYME SPECIFICITY; HYDROGEN BOND; MUTAGENESIS; MUTANT; NONHUMAN; PRIORITY JOURNAL; PROTEIN VARIANT; PROTON TRANSPORT;

AMINO ACIDS; CARBOXY-LYASES; CATALYSIS; CATALYTIC DOMAIN; KINETICS; MUTAGENESIS, SITE-DIRECTED; PSEUDOMONAS PUTIDA;

PSEUDOMONAS PUTIDA;

EID: 44449095046     PISSN: 00278424     EISSN: 10916490     Source Type: Journal    
DOI: 10.1073/pnas.0709657105     Document Type: Article

References (27)

1. Gunsalus CF, Stanier RY, Gunsalus IC (1953) The enzymatic conversion of mandelic acid to benzoic acid. III. Fractionation and properties of the soluble enzymes. J Bacteriol 66:548-553.
2. +-dependent benzaldehyde dehydrogenase involved in D-phenylglycine metabolism in Pseudomonas stutzeri ST-201. Biochim Biophys Acta 1770:1585-1592.
3. Hasson MS, et al. (1998) The crystal structure of benzoylformate decarboxylase at 1.6 Å resolution: Diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry 37:9918-9930.
4. Polovnikova ES, et al. (2003) Structural and kinetic analysis of catalysis by a thiamin diphosphate-dependent enzyme, benzoylformate decarboxylase. Biochemistry 42:1820-1830.
5. Sergienko EA, et al. (2000) Spectroscopic detection of transient thiamin diphosphate-bound intermediates on benzoylformate decarboxylase. Biochemistry 39:13862-13869.
6. Huang CY, Chang AK, Nixon PF, Duggleby RG (2001) Site-directed mutagenesis of the ionizable groups in the active site of Zymomonas mobilis pyruvate decarboxylase: Effect on activity and pH dependence. Eur J Biochem 268:3558-3565.
7. Siegert P, et al. (2005) Exchanging the substrate specificities of pyruvate decarboxylase from Zymomonas mobilis and benzoylformate decarboxylase from Pseudomonas putida. Prot Eng Des Sel 18:345-357.
8. Yep A, Kenyon GL, McLeish MJ (2006) Determinants of substrate specificity in KdcA, a thiamin diphosphate-dependent decarboxylase. Bioorg Chem 34:325-336.
9. Kaur J, Sharma R (2006) Directed evolution: An approach to engineer enzymes. Crit Rev Biotechnol 16:165-199.
10. Hancock SM, Vaughan MD, Withers SG (2006) Engineering of glycosidases and glycosyltransferases. Curr Opin Chem Biol 10:509-519.
11. Ullrich J (1970) Yeast pyruvate decarboxylase (2-oxoacid carboxylase, EC 4.1.1.1) Assay of thiamine pyrophosphate. Methods Enzymol 18:109-115.
12. Jones DT (1999) GenTHREADER: An efficient and reliable protein fold recognition method for genomic sequences. J Mol Biol 287:797-815.
13. McGuffin LJ, Jones DT (2003) Improvement of the GenTHREADER method for genomic fold recognition. Bioinformatics 19:874-881.
14. Ramakrishna Rao DN, Vaidyanathan CS (1977) Metabolism of mandelic acid by Neurospora crassa. Can J Microbiol 23:1496-1499.
15. Schütz A, Golbik R, König S, Hübner G, Tittmann K (2005) Intermediates and transition states in thiamin diphosphate-dependent decarboxylases. A kinetic and NMR study on WT indolepyruvate decarboxylase and variants using indolepyruvate, benzoylformate, and pyruvate as substrates. Biochemistry 44:6164-6179.
16. Tittmann K, et al. (2003) NMR analysis of covalent intermediates in thiamin diphosphate enzymes. Biochemistry 42:7885-7891.
17. Jordan F, Li H, Brown A (1999) Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases. Biochemistry 38:6369-6373.
18. Zhang S, et al. (2005) Evidence for dramatic acceleration of a C-H bond ionization rate in thiamin diphosphate enzymes by the protein environment. Biochemistry 44:2237-2243.
19. Nemeria N, et al. (2007) Elucidation of the chemistry of enzyme-bound thiamin diphosphate prior to substrate binding: Defining internal equilibria among tautomeric and ionization states. Biochemistry 46:10739-10744.
20. Fiedler E, et al. (2002) Snapshot of a key intermediate in enzymatic thiamin catalysis: Crystal structure of the α-carbanion of (α,β-dihydroxyethyl)-thiamin diphosphate in the active site of transketolase from Saccharomyces cerevisiae. Proc Natl Acad Sci USA 99:591-595.
21. Wille G, et al. (2006) The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat Chem Biol 2:324-328.
22. Sergienko EA, Jordan F (2001) Catalytic acid-base groups in yeast pyruvate decarboxylase. 2. Insights into the specific roles of D28 and E477 from the rates and stereospecificity of formation of carboligase side products. Biochemistry 40:7369-7381.
23. Davis JP, Copeland RA (1997) Histidine to alanine mutants of human dihydroorotate dehydrogenase. Identification of a brequinar-resistant mutant enzyme. Biochem Pharmacol 54:459-465.
24. 13C and solvent deuterium isotope effects on benzoylformate and benzoylformate analogues. Biochemistry 27:2197-2205.
25. Morrison KL, Weiss GA (2001) Combinatorial alanine scanning. Curr Opin Chem Biol 5:302-307.
26. Peracchi A (2001) Enzyme catalysis: Removing chemically "essential" residues by site-directed mutagenesis. Trends Biochem Sci 26:497-503.
27. Kneen MM, Pogozheva ID, Kenyon GL, McLeish MJ (2005) Exploring the active site of benzaldehyde lyase by modeling and mutagenesis. BBA-Proteins Proteom 1753:263-271.