• 1
    Okon Y (1985) Azospirillum as a potential inoculant for agriculture. Trends Biotechnol 3, 223228.
  • 2
    Steenhoudt O & Vanderleyden J (2000) Azospirillum, a free-living nitrogen-fixing bacterium closely associated with grasses: genetic, biochemical and ecological aspects. FEMS Microbiol Rev 24, 487506.
  • 3
    Dobbelaere S, Croonenborghs A, Thys A, Vande Broek A & Vanderleyden J (1999) Phytostimulatory effect of Azospirillum brasilense wild-type and mutant strains altered in IAA production on wheat. Plant Soil 212, 155164.
  • 4
    Costacurta A, Keijers V & Vanderleyden J (1994) Molecular cloning and sequence analysis of an Azospirillum brasilense indole-3-pyruvate decarboxylase gene. Mol Gen Genet 243, 463472.
  • 5
    Prinsen E, Costacurta A, Michiels K, Vanderleyden J & Vanonckelen H (1993) Azospirillum brasilense indole-3-acetic acid biosynthesis: evidence for a non-tryptophan dependent pathway. Mol Plant Microbe Interact 6, 609615.
  • 6
    Vande Broek A, Gysegom P, Ona O, Hendrickx N, Prinsen E, Van Impe J & Vanderleyden J (2005) Transcriptional analysis of the Azospirillum brasilense indole-3-pyruvate decarboxylase gene and identification of a cis-acting sequence involved in auxin responsive expression. Mol Plant Microbe Interact 18, 311323.
  • 7
    Somers E, Ptacek D, Gysegom P, Srinivasan M & Vanderleyden J (2005) Azospirillum brasilense produces the auxin-like phenylacetic acid by using the key enzyme for indole-3-acetic acid biosynthesis. Appl Environ Microbiol 71, 18031810.
  • 8
    Woodward AW & Bartel B (2005) Auxin: regulation, action, and interaction. Ann Bot 95, 707735.
  • 9
    Soto-Urzua L, Xochinua-Corona YG, Flores-Encarnacion M & Baca BE (1996) Purification and properties of aromatic amino acid aminotransferases from Azospirillum brasilense UAP 14 strain. Can J Microbiol 42, 294298.
  • 10
    Vuralhan Z, Morais MA, Tai SL, Piper MD & Pronk JT (2003) Identification and characterization of phenylpyruvate decarboxylase genes in Saccharomyces cerevisiae. Appl Environ Microbiol 69, 45344541.
  • 11
    Guo Z, Goswami A, Nanduri VB & Patel RN (2001) Asymmetric acyloin condensation catalysed by phenylpyruvate decarboxylase. Part 2: Substrate specificity and purification of the enzyme. Tetrahedron Asymmetry 12, 571577.
  • 12
    Koga J, Adachi T & Hidaka H (1992) Purification and characterization of indolepyruvate decarboxylase. A novel enzyme for indole-3-acetic acid biosynthesis in Enterobacter cloacae. J Biol Chem 267, 1582315828.
  • 13
    Schütz A, Golbik R, Tittmann K, Svergun DI, Koch MH, Hübner G & König S (2003) Studies on structure-function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway. Eur J Biochem 270, 23222332.
  • 14
    Schowen RL (1998) Thiamin-dependent enzymes. In Comprehensive Biological Catalysis. A Mechanistic Reference. Reactions of Nucleophilic/Carbanionoid Carbon. Vol. II. (Sinnott M, ed), pp. 217266. Academic Press, San Diego, CA.
  • 15
    Hübner G, Weidhase R & Schellenberger A (1978) The mechanism of substrate activation of pyruvate decarboxylase: a first approach. Eur J Biochem 92, 175181.
  • 16
    Sergienko EA & Jordan F (2002) New model for activation of yeast pyruvate decarboxylase by substrate consistent with the alternating sites mechanism: demonstration of the existence of two active forms of the enzyme. Biochemistry 41, 39523967.
  • 17
    Krieger F, Spinka M, Golbik R, Hübner G & König S (2002) Pyruvate decarboxylase from Kluyveromyces lactis. An enzyme with an extraordinary substrate activation behaviour. Eur J Biochem 269, 32563263.
  • 18
    Raj KC, Talarico LA, Ingram LO & Maupin-Furlow JA (2002) Cloning and characterization of the Zymobacter palmae pyruvate decarboxylase gene (PDC) and comparison to bacterial homologues. Appl Environ Microbiol 68, 28692876.
  • 19
    Duggleby RG (2006) Domain relationships in thiamine diphosphate-dependent enzymes. Acc Chem Res 39, 550557.
  • 20
    Furey W, Arjunan P, Chen L, Sax M, Guo F & Jordan F (1998) Structure-function relationships and flexible tetramer assembly in pyruvate decarboxylase revealed by analysis of crystal structures. Biochim Biophys Acta 1385, 253270.
  • 21
    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, 23122321.
  • 22
    Muller YA & Schulz GE (1993) Structure of the thiamine- and flavin-dependent enzyme pyruvate oxidase. Science 259, 965967.
  • 23
    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 256, 590600.
  • 24
    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, 2019620204.
  • 25
    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 Å resolution: diversity of catalytic residues in thiamin diphosphate-dependent enzymes. Biochemistry 37, 99189930.
  • 26
    Berthold CL, Moussatche P, Richards NG & Lindqvist Y (2005) Structural basis for activation of the thiamin diphosphate-dependent enzyme oxalyl-CoA decarboxylase by adenosine diphosphate. J Biol Chem 280, 4164541654.
  • 27
    Mosbacher TG, Mueller M & Schulz GE (2005) Structure and mechanism of the ThDP-dependent benzaldehyde lyase from Pseudomonas fluorescens. FEBS J 272, 60676076.
  • 28
    Lu G, Dobritzsch D, König S & Schneider G (1997) Novel tetramer assembly of pyruvate decarboxylase from brewer's yeast observed in a new crystal form. FEBS Lett 403, 249253.
  • 29
    Kutter S, Wille G, Relle S, Weiss MS, Hübner G & König S (2006) The crystal structure of pyruvate decarboxylase from Kluyveromyces lactis. Implications for the substrate activation mechanism of this enzyme. FEBS J 273, 41994209.
  • 30
    Bringer-Meyer S, Schimz KL & Sahm H (1986) Pyruvate decarboxylase from Zymomonas mobilis. Isolation and partial characterization. Arch Microbiol 146, 105110.
  • 31
    Candy JM & Duggleby RG (1998) Structure and properties of pyruvate decarboxylase and site-directed mutagenesis of the Zymomonas mobilis enzyme. Biochim Biophys Acta 1385, 323338.
  • 32
    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, 18201830.
  • 33
    Davies DD (1967) Glyoxylate as a substrate for pyruvic decarboxylase. Biochem J 104, 50P.
  • 34
    Baburina I, Gao Y, Hu Z, Jordan F, Hohmann S & Furey W (1994) Substrate activation of brewers' yeast pyruvate decarboxylase is abolished by mutation of cysteine 221 to serine. Biochemistry 33, 56305635.
  • 35
    Baburina I, Li H, Bennion B, Furey W & Jordan F (1998) Interdomain information transfer during substrate activation of yeast pyruvate decarboxylase: the interaction between cysteine 221 and histidine 92. Biochemistry 37, 12351244.
  • 36
    Li H, Furey W & Jordan F (1999) Role of glutamate 91 in information transfer during substrate activation of yeast pyruvate decarboxylase. Biochemistry 38, 999210003.
  • 37
    Li H & Jordan F (1999) Effects of substitution of tryptophan 412 in the substrate activation pathway of yeast pyruvate decarboxylase. Biochemistry 38, 1000410012.
  • 38
    Wang J, Golbik R, Seliger B, Spinka M, Tittmann K, Hübner G & Jordan F (2001) Consequences of a modified putative substrate-activation site on catalysis by yeast pyruvate decarboxylase. Biochemistry 40, 17551763.
  • 39
    Kern D, Kern G, Neef H, Tittmann K, Killenberg-Jabs M, Wikner C, Schneider G & Hübner G (1997) How thiamine diphosphate is activated in enzymes. Science 275, 6770.
  • 40
    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, 861868.
  • 41
    Joseph E, Wei W, Tittmann K & Jordan F (2006) Function of a conserved loop of the beta-domain, not involved in thiamin diphosphate binding, in catalysis and substrate activation in yeast pyruvate decarboxylase. Biochemistry 45, 1351713527.
  • 42
    Jordan F, Nemeria N, Guo FS, Baburina I, Gao YH, Kahyaoglu A, Li HJ, Wang J, Yi JZ, Guest JR & Furey W (1998) Regulation of thiamin diphosphate-dependent 2-oxo acid decarboxylases by substrate and thiamin diphosphate. Mg(II) – evidence for tertiary and quaternary interactions. Biochim Biophys Acta 1385, 287306.
  • 43
    Jordan F, Nemeria N & Sergienko EA (2005) Multiple modes of active center communication in thiamin diphosphate-dependent enzymes. Acc Chem Res 38, 755763.
  • 44
    Seifert F, Golbik R, Brauer J, Lilie H, Schroder-Tittmann K, Hinze E, Korotchkina LG, Patel MS & Tittmann K (2006) Direct kinetic evidence for half-of-the-sites reactivity in the E1 component of the human pyruvate dehydrogenase multienzyme complex through alternating sites cofactor activation. Biochemistry 45, 1277512785.
  • 45
    Khailova LS & Korochkina LG (1985) Half-of-The-Site Reactivity of the Decarboxylating Component of the Pyruvate-Dehydrogenase Complex from Pigeon Breast Muscle with Respect to 2-Hydroxyethyl Thiamine Pyrophosphate. Biochem Int 11, 509516.
  • 46
    Frank RAW, Titman CM, Pratap JV, Luisi BF & Perham RN (2004) A molecular switch and proton wire synchronize the active sites in thiamine enzymes. Science 306, 872876.
  • 47
    Jordan F, Zhang Z & Sergienko EA (2002) Spectroscopic evidence for participation of the 1′,4′-imino tautomer of thiamin diphosphate in catalysis by yeast pyruvate decarboxylase. Bioorg Chem 30, 188198.
  • 48
    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, 1273212738.
  • 49
    Hawkins CF, Borges A & Perham RN (1989) A Common Structural Motif in Thiamin Pyrophosphate-Binding Enzymes. FEBS Lett 255, 7782.
  • 50
    Jordan F (2003) Current mechanistic understanding of thiamin diphosphate-dependent enzymatic reactions. Nat Prod Rep 20, 184201.
  • 51
    Wille G, Meyer D, Steinmetz A, Hinze E, Golbik R & Tittmann K (2006) The catalytic cycle of a thiamin diphosphate enzyme examined by cryocrystallography. Nat Chem Biol 2, 324328.
  • 52
    Arjunan P, Sax M, Brunskill A, Chandrasekhar K, Nemeria N, Zhang S, Jordan F & Furey W (2006) A thiamin-bound, pre-decarboxylation reaction intermediate analogue in the pyruvate dehydrogenase E1 subunit induces large scale disorder-to-order transformations in the enzyme and reveals novel structural features in the covalently bound adduct. J Biol Chem 281, 1529615303.
  • 53
    Jordan F & Nemeria N (2005) Experimental observation of thiamin diphosphate-bound intermediates on enzymes and mechanistic information derived from these observations. Bioorg Chem 33, 190215.
  • 54
    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 wild-type indolepyruvate decarboxylase and variants using indolepyruvate, benzoylformate, and pyruvate as substrates. Biochemistry 44, 61646179.
  • 55
    Zhang S, Zhou L, Nemeria N, Yan Y, Zhang Z, Zou Y & Jordan F (2005) Evidence for dramatic acceleration of a C-H bond ionization rate in thiamin diphosphate enzymes by the protein environment. Biochemistry 44, 22372243.
  • 56
    Jordan F, Li HJ & Brown A (1999) Remarkable stabilization of zwitterionic intermediates may account for a billion-fold rate acceleration by thiamin diphosphate-dependent decarboxylases. Biochemistry 38, 63696373.
  • 57
    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, 65656575.
  • 58
    Otwinowski Z & Minor W (1997) Processing of X-Ray Diffraction Data Collected in Oscillation Mode. In Methods in Enzymology, Macromolecular Crystallography Part A Vol. 276 (Carter CW & Sweet RM, eds), pp. 307326. Academic Press, New York, NY.
  • 59
    French S & Wilson K (1978) On the treatment of negative intensity observations. Acta Crystallogr A34, 517525.
  • 60
    McCoy AJ, Grosse-Kunstleve RW, Storoni LC & Read RJ (2005) Likelihood-enhanced fast translation functions. Acta Crystallogr D61, 458464.
  • 61
    Brünger AT, Krukowski A & Erickson JW (1990) Slow-cooling protocols for crystallographic refinement by simulated annealing. Acta Crystallogr A46, 585593.
  • 62
    Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grose-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges N, Pannu NS, Read RJ, Rice LM, Simonson T & Warren GL (1998) Crystallography and NMR system (CNS): a new software system for macromolecular structure determination. Acta Crystallogr D54, 905921.
  • 63
    Perrakis A, Morris RM & Lamzin VS (1999) Automated protein building combined with iterative structure refinement. Nat Struct Biol 6, 458463.
  • 64
    Emsley P & Cowtan K (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr D60, 21262132.
  • 65
    Lovell SC, Davis IW, Adrendall WB, de Bakker PIW, Word JM, Prisant MG, Richardson JS & Richardson DC (2003) Structure validation by C alpha geometry: phi,psi and C beta deviation. Proteins 50, 437450.
  • 66
    Holm L & Sander C (1998) Touring protein fold space with Dali/FSSP. Nucleic Acids Res 26, 316319.
  • 67
    Collaborative Computational Project Number 4 (1994) The CCP4 suite: programs for protein crystallography. Acta Crystallogr D50, 760763.
  • 68
    DeLano WL (2002) The PyMOL Molecular Graphics System. DeLano Scientific, San Carlos, CA.
  • 69
    Kraulis PJ (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J Appl Crystallogr 24, 946950.
  • 70
    Koga J, Adachi T & Hidaka H (1991) Molecular Cloning of the Gene for Indolepyruvate Decarboxylase from Enterobacter cloacae. Mol Gen Genet 226, 1016.