Publications

• Formation of alpha-ketoglutaric semialdehyde from L-2-keto-3-deoxyarabonic acid and isolation of L-2-keto-3-deoxyarabonate dehydratase from Pseudomonas saccharophila.

  Stoolmiller A.C., Abeles R.H.

  J Biol Chem 241:5764-5771(1966) [PubMed] [EuropePMC]

• Identification and characterization of L-arabonate dehydratase, L-2-keto-3-deoxyarabonate dehydratase and L-arabinolactonase involved in an alternative pathway of L-arabinose metabolism: novel evolutionary insight into sugar metabolism.

  Watanabe S., Shimada N., Tajima K., Kodaki T., Makino K.

  Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the ... >> More

  Azospirillum brasiliense possesses an alternative pathway of L-arabinose metabolism, different from the known bacterial and fungal pathways. In the preceding articles, we identified and characterized L-arabinose-1-dehydrogenase and alpha-ketoglutaric semialdehyde dehydrogenase, which catalyzes the first and final reaction steps in this pathway, respectively (Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 2612-2623 and Watanabe, S., Kodaki, T., and Makino, K. (2006) J. Biol. Chem. 281, 28876-28888). We here report the remaining three enzymes, L-arabonate dehydratase, L-2-keto-3-deoxyarabonate (L-KDA) dehydratase, and L-arabinolactonase. N-terminal amino acid sequences of L-arabonate dehydratase and L-KDA dehydratase purified from A. brasiliense cells corresponded to those of AraC and AraD genes, which form a single transcriptional unit together with the L-arabinose-1-dehydrogenase gene. Furthermore, the L-arabinolactonase gene (AraB) was also identified as a component of the gene cluster. Genetic characterization of the alternative L-arabinose pathway suggested a significant evolutional relationship with the known sugar metabolic pathways, including the Entner-Doudoroff (ED) pathway and the several modified versions. L-arabonate dehydratase belongs to the ILVD/EDD family and spectrophotometric and electron paramagnetic resonance analysis revealed it to contain a [4Fe-4S](2+) cluster. Site-directed mutagenesis identified three cysteine ligands essential for cluster coordination. L-KDA dehydratase was sequentially similar to DHDPS/NAL family proteins. D-2-Keto-3-deoxygluconate aldolase, a member of the DHDPS/NAL family, catalyzes the equivalent reaction to L-KDA aldolase involved in another alternative L-arabinose pathway, probably associating a unique evolutional event between the two alternative L-arabinose pathways by mutation(s) of a common ancestral enzyme. Site-directed mutagenesis revealed a unique catalytic amino acid residue in L-KDA dehydratase, which may be a candidate for such a natural mutation. << Less

  J. Biol. Chem. 281:33521-33536(2006) [PubMed] [EuropePMC]

  This publication is cited by 2 other entries.

• Preliminary crystallographic analysis of L-2-keto-3-deoxyarabonate dehydratase, an enzyme involved in an alternative bacterial pathway of L-arabinose metabolism.

  Shimada N., Mikami B., Watanabe S., Makino K.

  L-2-Keto-3-deoxyarabonate (L-KDA) dehydratase is a novel member of the dihydrodipicolinate synthase (DHDPS)/N-acetylneuraminate lyase (NAL) protein family and catalyzes the hydration of L-KDA to alpha-ketoglutaric semialdehyde. L-KDA dehydratase was overexpressed, purified and crystallized at 291 ... >> More

  L-2-Keto-3-deoxyarabonate (L-KDA) dehydratase is a novel member of the dihydrodipicolinate synthase (DHDPS)/N-acetylneuraminate lyase (NAL) protein family and catalyzes the hydration of L-KDA to alpha-ketoglutaric semialdehyde. L-KDA dehydratase was overexpressed, purified and crystallized at 291 K using the hanging-drop vapour-diffusion method. The crystal diffracts to 2.0 A resolution using synchrotron radiation and belongs to the trigonal space group P3(1)21 or its enantiomorph P3(2)21, with unit-cell parameters a = b = 78.91, c = 207.71 A. << Less

  Acta Crystallogr. F 63:393-395(2007) [PubMed] [EuropePMC]

• Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1.

  Ghasempur S., Eswaramoorthy S., Hillerich B.S., Seidel R.D., Swaminathan S., Almo S.C., Gerlt J.A.

  The l-lyxonate dehydratase (LyxD) in vitro enzymatic activity and in vivo metabolic function were assigned to members of an isofunctional family within the mandelate racemase (MR) subgroup of the enolase superfamily. This study combined in vitro and in vivo data to confirm that the dehydration of ... >> More

  The l-lyxonate dehydratase (LyxD) in vitro enzymatic activity and in vivo metabolic function were assigned to members of an isofunctional family within the mandelate racemase (MR) subgroup of the enolase superfamily. This study combined in vitro and in vivo data to confirm that the dehydration of l-lyxonate is the biological role of the members of this family. In vitro kinetic experiments revealed catalytic efficiencies of ∼10(4) M(-1) s(-1) as previously observed for members of other families in the MR subgroup. Growth studies revealed that l-lyxonate is a carbon source for Pseudomonas aeruginosa PAO1; transcriptomics using qRT-PCR established that the gene encoding LyxD as well as several other conserved proximal genes were upregulated in cells grown on l-lyxonate. The proximal genes were shown to be involved in a pathway for the degradation of l-lyxonate, in which the first step is dehydration by LyxD followed by dehydration of the 2-keto-3-deoxy-l-lyxonate product by 2-keto-3-deoxy-l-lyxonate dehydratase to yield α-ketoglutarate semialdehyde. In the final step, α-ketoglutarate semialdehyde is oxidized by a dehydrogenase to α-ketoglutarate, an intermediate in the citric acid cycle. An X-ray structure for the LyxD from Labrenzia aggregata IAM 12614 with Mg(2+) in the active site was determined that confirmed the expectation based on sequence alignments that LyxDs possess a conserved catalytic His-Asp dyad at the end of seventh and sixth β-strands of the (β/α)7β-barrel domain as well as a conserved KxR motif at the end of second β-strand; substitutions for His 316 or Arg 179 inactivated the enzyme. This is the first example of both the LyxD function in the enolase superfamily and a pathway for the catabolism of l-lyxonate. << Less

  Biochemistry 53:3357-3366(2014) [PubMed] [EuropePMC]

  This publication is cited by 2 other entries.

• Studies on the mechanism of action of 2-keto-3-deoxy-L-arabonate dehydratase. The participation of an enzyme-substrate Schiff base in a dehydration.

  Portsmouth D., Stoolmiller A.C., Abeles R.H.

  J Biol Chem 242:2751-2759(1967) [PubMed] [EuropePMC]

• Characterization of an l-Ascorbate Catabolic Pathway with Unprecedented Enzymatic Transformations.

  Stack T.M.M., Morrison K.N., Dettmer T.M., Wille B., Kim C., Joyce R., Jermain M., Naing Y.T., Bhatti K., Francisco B.S., Carter M.S., Gerlt J.A.

  l-Ascorbate (vitamin C) is ubiquitous in both our diet and the environment. Here we report that <i>Ralstonia eutropha</i> H16 (<i>Cupriavidus necator</i> ATCC 17699) uses l-ascorbate as sole carbon source via a novel catabolic pathway. RNaseq identified eight candidate catabolic genes, sequence si ... >> More

  l-Ascorbate (vitamin C) is ubiquitous in both our diet and the environment. Here we report that <i>Ralstonia eutropha</i> H16 (<i>Cupriavidus necator</i> ATCC 17699) uses l-ascorbate as sole carbon source via a novel catabolic pathway. RNaseq identified eight candidate catabolic genes, sequence similarity networks, and genome neighborhood networks guided predictions for function of the encoded proteins, and the predictions were confirmed by <i>in vitro</i> assays and <i>in vivo</i> growth phenotypes of gene deletion mutants. l-Ascorbate, a lactone, is oxidized and ring-opened by enzymes in the cytochrome <i>b</i>₅₆₁ and gluconolactonase families, respectively, to form 2,3-diketo-l-gulonate. A protein predicted to have a WD40-like fold catalyzes an unprecedented benzilic acid rearrangement involving migration of a carboxylate group to form 2-carboxy-l-lyxonolactone; the lactone is hydrolyzed by a member of the amidohydrolase superfamily to yield 2-carboxy-l-lyxonate. A member of the PdxA family of oxidative decarboxylases catalyzes a novel decarboxylation that uses NAD⁺ catalytically. The product, l-lyxonate, is catabolized to α-ketoglutarate by a previously characterized pathway. The pathway is found in hundreds of bacteria, including the pathogens <i>Pseudomonas aeruginosa</i> and <i>Acinetobacter baumannii</i>. << Less

  J Am Chem Soc 142:1657-1661(2020) [PubMed] [EuropePMC]

  This publication is cited by 6 other entries.