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

Schütz, Anja; Golbik, Ralph; Tittmann, Kai; Svergun, Dmitri I.; Koch, Michel H. J.; Hübner, Gerhard; König, Stephan

doi:10.1046/j.1432-1033.2003.03602.x

Cited by 75 publications

(85 citation statements)

References 49 publications

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“…The amino acid sequences of the ipd gene product and KdcA were aligned with the sequences of two well-characterized and homologous keto acid decarboxylating enzymes, yeast pyruvate decarboxylase (Pdc1p_SacCe) and indolepyruvate decarboxylase of Enterobacter cloacae (IpdC_EntCl) (11,31). KdcA, pyruvate decarboxylases, and indolepyruvate decarboxylases all depend on TPP and Mg 2ϩ as cofactors.…”

Section: Homology Of Kdca To Other Tpp-dependent Decarboxylasesmentioning

confidence: 99%

“…Several regions were highly conserved, including the regions containing residues catalyzing the transition state intermediate during catalysis ( Fig. 2) (21) and residues involved in binding of the substrate and cofactors (31). The alignment in Fig.…”

Section: Homology Of Kdca To Other Tpp-dependent Decarboxylasesmentioning

confidence: 99%

“…base catalyst and Asp29, His112, His113, and Glu462 are involved in stabilization of the transition state intermediate (21,31).…”

Section: Isobutanoic Acidmentioning

confidence: 99%

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Identification, Cloning, and Characterization of a Lactococcus lactis Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation

Smit

Vlieg

Engels

et al. 2005

Appl Environ Microbiol

119

139

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The biochemical pathway for formation of branched-chain aldehydes, which are important flavor compounds derived from proteins in fermented dairy products, consists of a protease, peptidases, a transaminase, and a branched-chain ␣-keto acid decarboxylase (KdcA). The activity of the latter enzyme has been found only in a limited number of Lactococcus lactis strains. By using a random mutagenesis approach, the gene encoding KdcA in L. lactis B1157 was identified. The gene for this enzyme is highly homologous to the gene annotated ipd, which encodes a putative indole pyruvate decarboxylase, in L. lactis IL1403. Strain IL1403 does not produce KdcA, which could be explained by a 270-nucleotide deletion at the 3 terminus of the ipd gene encoding a truncated nonfunctional decarboxylase. The kdcA gene was overexpressed in L. lactis for further characterization of the decarboxylase enzyme. Of all of the potential substrates tested, the highest activity was observed with branchedchain ␣-keto acids. Moreover, the enzyme activity was hardly affected by high salinity, and optimal activity was found at pH 6.3, indicating that the enzyme might be active under cheese ripening conditions.Flavor formation in cheeses is mainly the result of catabolism of milk proteins, sugar, and lipids. Degradation of proteins into amino acids followed by conversion of these amino acids by Lactococcus spp. is very important for flavor formation in semihard types of cheese, like Gouda (for reviews see references 12, 25, 38, and 43). One of the predominant amino acid conversion routes is initiated by transaminases. Transamination of amino acids yields the corresponding ␣-keto acids, which do not have strong flavor properties (12, 13) but are the precursors of various aldehydes, alcohols, acids, and (thio-)esters. The latter compounds generally have much lower odor thresholds and strongly contribute to cheese flavor. This is exemplified by the production of flavor compounds from leucine. Transamination of leucine results in the production of ␣-isocaproic acid (KICA). Interestingly, only a limited number of Lactococcus lactis strains are capable of decarboxylating this ␣-keto acid to 3-methylbutanal (36, 37). The decarboxylating activity is observed mainly in L. lactis strains with nondairy origins, whereas the industrial strains tested hardly showed this activity (36). Subsequently, (de)hydrogenation of 3-methylbutanal results in 3-methylbutanol or 3-methylbutyric acid, which also contributes to the flavor of cheese, but the odor thresholds for these compounds are higher than the odor threshold for 3-methylbutanal (24, 29). The rate-determining step in this route is the decarboxylation of KICA, and therefore, control of this enzyme offers good prospects for the design of starter cultures with tailored flavor production (37, 43).The enzyme performing this reaction has not been identified. A number of thiamine pyrophosphate (TPP)-dependent

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Section: Homology Of Kdca To Other Tpp-dependent Decarboxylasesmentioning

confidence: 99%

Section: Homology Of Kdca To Other Tpp-dependent Decarboxylasesmentioning

confidence: 99%

See 1 more Smart Citation

Identification, Cloning, and Characterization of a Lactococcus lactis Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation

Smit

Vlieg

Engels

et al. 2005

Appl Environ Microbiol

119

139

View full text Add to dashboard Cite

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“…Significant amounts of trimeric or tetrameric oligomers were not observed by gel filtration, dynamic light scattering, or analytic ultracentrifugation at higher concentrations of enzyme, including the conditions of crystallization (17; A. K. Steinbach et al, submitted for publication). Most ThDP-dependent enzymes are arranged as homotetramers, such as POX from Lactobacillus plantarum (56), benzoylformate decarboxylase from Pseudomonas putida (23), indolepyruvate decarboxylase from Enterobacter cloacae (54), or pyruvate decarboxylase from Zymomonas mobilis (41). Bacterial AHAS reveals a common ␣ 2 ␤ 2 tetrameric structure (21, 51), whereas AHAS from Arabidopsis thaliana (9) and transketolase from Saccharomyces cerevisiae (59) represent examples of dimeric ThDP enzymes.…”

Section: Discussionmentioning

confidence: 99%

Cyclohexane-1,2-Dione Hydrolase from Denitrifying Azoarcus sp. Strain 22Lin, a Novel Member of the Thiamine Diphosphate Enzyme Family

et al. 2011

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Alicyclic compounds with hydroxyl groups represent common structures in numerous natural compounds, such as terpenes and steroids. Their degradation by microorganisms in the absence of dioxygen may involve a COC bond ring cleavage to form an aliphatic intermediate that can be further oxidized. The cyclohexane-1,2-dione hydrolase (CDH) (EC 3.7.1.11) from denitrifying Azoarcus sp. strain 22Lin, grown on cyclohexane-1,2-diol as a sole electron donor and carbon source, is the first thiamine diphosphate (ThDP)-dependent enzyme characterized to date that cleaves a cyclic aliphatic compound. The degradation of cyclohexane-1,2-dione (CDO) to 6-oxohexanoate comprises the cleavage of a COC bond adjacent to a carbonyl group, a typical feature of reactions catalyzed by ThDP-dependent enzymes. In the subsequent NAD ؉ -dependent reaction, 6-oxohexanoate is oxidized to adipate. CDH has been purified to homogeneity by the criteria of gel electrophoresis (a single band at ϳ59 kDa; calculated molecular mass, 64.5 kDa); in solution, the enzyme is a homodimer (ϳ105 kDa; gel filtration). As isolated, CDH contains 0.8 ؎ 0.05 ThDP, 1.0 ؎ 0.02 Mg 2؉ , and 1.0 ؎ 0.015 flavin adenine dinucleotide (FAD) per monomer as a second organic cofactor, the role of which remains unclear. Strong reductants, Ti(III)-citrate, Na ؉ -dithionite, and the photochemical 5-deazaflavin/oxalate system, led to a partial reduction of the FAD chromophore. The cleavage product of CDO, 6-oxohexanoate, was also a substrate; the corresponding cyclic 1,3-and 1,4-diones did not react with CDH, nor did the cis-and trans-cyclohexane diols. The enzymes acetohydroxyacid synthase (AHAS) from Saccharomyces cerevisiae, pyruvate oxidase (POX) from Lactobacillus plantarum, benzoylformate decarboxylase from Pseudomonas putida, and pyruvate decarboxylase from Zymomonas mobilis were identified as the closest relatives of CDH by comparative amino acid sequence analysis, and a ThDP binding motif and a 2-fold Rossmann fold for FAD binding could be localized at the C-terminal end and central region of CDH, respectively. A first mechanism for the ring cleavage of CDO is presented, and it is suggested that the FAD cofactor in CDH is an evolutionary relict.Alicyclic compounds, such as steroids and terpenes, are widespread in nature. They are produced by plant cells as secondary metabolites and occur in fossil fuels. Microorganisms can convert these compounds to cellular metabolites under oxic and anoxic conditions. Their biodegradation proceeds via COC bond ring cleavage to form an aliphatic intermediate, which can be further degraded by ␤-oxidation. In aerobic bacteria, the cleavage of the cyclic compound is catalyzed by a NADPH-dependent, flavin-containing monooxygenase. For example, cyclohexanone is converted to ε-caprolactone in a Bayer-Villiger-type reaction (14). Subsequently, the lactone is hydrolyzed to 6-hydroxyhexanoate (63), followed by two NAD ϩ /NADP ϩ -dependent oxidation steps with adipate as the final product. In anaerobes, such as Pseudomonas sp. strain K601, cyclohexa...

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“…Besides decarboxylation of indolepyruvate, IPDCs can decarboxylate a number of α-keto acids, including pyruvate, benzoylformate and phenylpyruvate with different catalytic efficiencies (Fedorov et al 2010). The direct involvement of these enzymes in IAA biosynthesis was shown for Azospirillum brasilense, Enterobacter cloacae, Pantoea agglomerans (Schütz et al 2003a;Spaepen et al 2007) and Methylobacterium extorquens (Fedorov et al 2010). In a previous study we have detected PDC activity in P. serpens cell extracts and suggested that this enzyme, that participates in the alcoholic fermentation, would reoxidize a portion of the NADH produced in the very active glycolytic pathway of the flagellate.…”

Section: Introductionmentioning

confidence: 99%

Auxin production by the plant trypanosomatidPhytomonas serpensand auxin homoeostasis in infected tomato fruits

et al. 2014

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S U M M A R YPreviously we have characterized the complete gene encoding a pyruvate decarboxylase (PDC)/indolepyruvate decarboxylase (IPDC) of Phytomonas serpens, a trypanosomatid highly abundant in tomato fruits. Phylogenetic analyses indicated that the clade that contains the trypanosomatid protein behaves as a sister group of IPDCs of γ-proteobacteria. Since IPDCs are key enzymes in the biosynthesis of the plant hormone indole-3-acetic acid (IAA), the ability for IAA production by P. serpens was investigated. Similar to many microorganisms, the production of IAA and related indolic compounds, quantified by high performance liquid chromatography, increased in P. serpens media in response to amounts of tryptophan. The auxin functionality was confirmed in the hypocotyl elongation assay. In tomato fruits inoculated with P. serpens the concentration of free IAA had no significant variation, whereas increased levels of IAA-amide and IAA-ester conjugates were observed. The data suggest that the auxin produced by the flagellate is converted to IAA conjugates, keeping unaltered the concentration of free IAA. Ethanol also accumulated in P. serpens-conditioned media, as the result of a PDC activity. In the article we discuss the hypothesis of the bifunctionality of P. serpens PDC/IPDC and provide a three-dimensional model of the enzyme.

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

Cited by 75 publications

References 49 publications

Identification, Cloning, and Characterization of a Lactococcus lactis Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation

Identification, Cloning, and Characterization of a Lactococcus lactis Branched-Chain α-Keto Acid Decarboxylase Involved in Flavor Formation

Cyclohexane-1,2-Dione Hydrolase from Denitrifying Azoarcus sp. Strain 22Lin, a Novel Member of the Thiamine Diphosphate Enzyme Family

Auxin production by the plant trypanosomatidPhytomonas serpensand auxin homoeostasis in infected tomato fruits

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