Small-Angle X-ray Solution-Scattering Studies on Ligand-Induced Subunit Interactions of the Thiamine Diphosphate Dependent Enzyme Pyruvate Decarboxylase from Different Organisms

König, Stephan; Svergun, Dmitri I.; Волков, В. В.; Feĭgin, L. A.; Koch, Michel H. J.

doi:10.1021/bi972125v

Cited by 21 publications

(18 citation statements)

References 27 publications

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“…Evaluation of the scattering experiments with ThDP-free EcIPDC demonstrates a pHdependent equilibrium between tetramers, dimers and even monomers. A similar behaviour (without occurrence of a monomer fraction) was described for PDCs from various organisms, but not for ZmPDC, where the tetramer is stable from pH 5 to pH 9 [43]. The cofactors ThDP and Mg 2+ stabilize the tetrameric state of EcIPDC up to pH 7.5 (Fig.…”

Section: Discussionsupporting

confidence: 71%

Studies on structure–function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway

Schütz

Golbik

Tittmann

et al. 2003

European Journal of Biochemistry

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Enterobacter cloacae, isolated from the rhizosphere of cucumbers, produces large amounts of indole‐3‐acetic acid. Indolepyruvate decarboxylase, the key enzyme in the biosynthetic pathway of indole‐3‐acetic acid, catalyses the formation of indole‐3‐acetaldehyde and carbon dioxide from indole‐3‐pyruvic acid. The enzyme requires the cofactors thiamine diphosphate and magnesium ions for catalytic activity. Recombinant indolepyruvate decarboxylase was purified from the host Escherichia coli strain JM109. Specificity of the enzyme for the substrates indole‐3‐pyruvic acid, pyruvic acid, benzoylformic acid, and seven benzoylformic acid analogues was investigated using a continuous optical assay. Stopped‐flow kinetic data showed no indication for substrate activation in the decarboxylation reaction of indole‐3‐pyruvic acid, pyruvic acid or benzoylformic acid. Size exclusion chromatography and small angle X‐ray solution scattering experiments suggested the tetramer as the catalytically active state and a pH‐dependent subunit association equilibrium. Analysis of the kinetic constants of the benzoylformic acid analogues according to Hansch et al. [Hansch, C., Leo, A., Unger, S.H., Kim, K.H., Nikaitani, D & Lien, E.J. (1973) J. Med. Chem.16, 1207–1216] and comparison with indole‐3‐pyruvic acid conversion by pyruvate decarboxylases from Saccharomyces cerevisiae and Zymomonas mobilis provided some insight into the catalytic mechanism of indolepyruvate decarboxylase.

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Section: Discussionsupporting

confidence: 71%

Studies on structure–function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway

Schütz

Golbik

Tittmann

et al. 2003

European Journal of Biochemistry

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“…6. This method is being used successfully (Kö nig et al, 1998;Macheroux et al, 1998). The envelope representation has intrinsic limitations, e.g.…”

Section: Figurementioning

confidence: 99%

Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS

Stuhrmann

2007

Acta Cryst Sect A

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Methods of contrast variation are tools that are essential in macromolecular structure research. Anomalous dispersion of X-ray diffraction is widely used in protein crystallography. Recent attempts to extend this method to native resonant labels like sulfur and phosphorus are promising. Substitution of hydrogen isotopes is central to biological applications of neutron scattering. Proton spin polarization considerably enhances an existing contrast prepared by isotopic substitution. Concepts and methods of nuclear magnetic resonance (NMR) become an important ingredient in neutron scattering from dynamically polarized targets.

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“…The pyruvate decarboxylase enzyme (PDC, EC 4.1.1.1) can be found in plants and fungi, but is very rare in prokaryotes and absent in animals [1]. This enzyme requires thiamine diphosphate (ThDP) and Mg 2+ cofactors for its function in catalyzing the non-oxidative decarboxylation of 2-keto-acids, of which its preferred substrate is pyruvate.…”

Section: Introductionmentioning

confidence: 99%

Modeling of pyruvate decarboxylases from ethanol producing bacteria

Shrestha¹,

Dhamwichukorn²,

Jenwitheesuk³

2010

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Pyruvate decarboxylase (PDC) is a key enzyme in homoethanol fermentation process, which decarboxylates 2-keto acid pyruvate into acetaldehyde and carbon dioxide. PDC enzymes from potential ethanol-producing bacteria such as Zymomonas mobilis, Zymobacter palmae and Sarcina ventriculi have different Km and kcat values for the substrate pyruvate at their respective optimum pH. In this study, the putative three-dimensional structures of PDC dimer of Z. palmae PDC and S. ventriculi PDC were generated based on the X-ray crystal structures of Z. mobilis PDC, Saccharomyces cerevisiae PDC form-A and Enterobacter cloacae indolepyruvate decarboxylase in order to compare the quaternary structures of these bacterial PDCs with respect to enzyme-substrate interactions, and subunit-subunit interfaces that might be related to the different biochemical characteristics. The PROCHECK scores for both models were within recommended intervals. The generated models are similar to the X-ray crystal structure of Z. mobilis PDC in terms of binding modes of the cofactor, the position of Mg2+, and the amino acids that form the active sites. However, subunit-subunit interface analysis showed lower H-bonding in both models compared with X-ray crystal structure of Z. mobilis PDC, suggesting a smaller interface area and the possibility of conformational change upon substrate binding in both models. Both models have predicted lower affinity towards branched and aromatic 2-keto acids, which correlated with the molecular volumes of the ligands. The models shed valuable information necessary for further improvement of PDC enzymes for industrial production of ethanol and other products.

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Small-Angle X-ray Solution-Scattering Studies on Ligand-Induced Subunit Interactions of the Thiamine Diphosphate Dependent Enzyme Pyruvate Decarboxylase from Different Organisms

Cited by 21 publications

References 27 publications

Studies on structure–function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway

Studies on structure–function relationships of indolepyruvate decarboxylase from Enterobacter cloacae, a key enzyme of the indole acetic acid pathway

Small-angle scattering and its interplay with crystallography, contrast variation in SAXS and SANS

Modeling of pyruvate decarboxylases from ethanol producing bacteria

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