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Robert H. White - One of the best experts on this subject based on the ideXlab platform.
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l aspartate semialdehyde and a 6 deoxy 5 ketohexose 1 phosphate are the precursors to the Aromatic Amino Acids in methanocaldococcus jannaschii
Biochemistry, 2004Co-Authors: Robert H. WhiteAbstract:No orthologs are present in the genomes of the archaea encoding genes for the first two steps in the biosynthesis of the Aromatic Amino Acids leading to 3-dehydroquinate (DHQ). The absence of these genes prompted me to examine the nature of the reactions involved in the archaeal pathway leading to DHQ in Methanocaldococcus jannaschii. Here I report that 6-deoxy-5-ketofructose 1-phosphate and l-aspartate semialdehyde are precursors to DHQ. The sugar, which is derived from glucose 6-P, supplies a “hydroxyacetone” fragment, which, via a transaldolase reaction, undergoes an aldol condensation with the l-aspartate semialdehyde to form 2-Amino-3,7-dideoxy-d-threo-hept-6-ulosonic acid. Despite the fact that both hydroxyacetone and hydroxyacetone-P were measured in the cell extracts and confirmed to arise from glucose 6-P, neither compound was found to serve as a precursor to DHQ. This Amino sugar then undergoes a NAD dependent oxidative deamination to produce 3,7-dideoxy-d-threo-hept-2,6-diulosonic acid which cy...
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l aspartate semialdehyde and a 6 deoxy 5 ketohexose 1 phosphate are the precursors to the Aromatic Amino Acids in methanocaldococcus jannaschii
Biochemistry, 2004Co-Authors: Robert H. WhiteAbstract:No orthologs are present in the genomes of the archaea encoding genes for the first two steps in the biosynthesis of the Aromatic Amino Acids leading to 3-dehydroquinate (DHQ). The absence of these genes prompted me to examine the nature of the reactions involved in the archaeal pathway leading to DHQ in Methanocaldococcus jannaschii. Here I report that 6-deoxy-5-ketofructose 1-phosphate and l-aspartate semialdehyde are precursors to DHQ. The sugar, which is derived from glucose 6-P, supplies a "hydroxyacetone" fragment, which, via a transaldolase reaction, undergoes an aldol condensation with the l-aspartate semialdehyde to form 2-Amino-3,7-dideoxy-D-threo-hept-6-ulosonic acid. Despite the fact that both hydroxyacetone and hydroxyacetone-P were measured in the cell extracts and confirmed to arise from glucose 6-P, neither compound was found to serve as a precursor to DHQ. This Amino sugar then undergoes a NAD dependent oxidative deamination to produce 3,7-dideoxy-d-threo-hept-2,6-diulosonic acid which cyclizes to 3-dehydroquinate. The protein product of the M. jannaschii MJ0400 gene catalyzes the transaldolase reaction and the protein product of the MJ1249 gene catalyzes the oxidative deamination and the cyclization reactions. The DHQ is readily converted into dehydroshikimate and shikimate in M. jannaschii cell extracts, consistent with the remaining steps and genes in the pathway being the same as in the established shikimate pathway.
Joseph M Jez - One of the best experts on this subject based on the ideXlab platform.
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brassicaceae specific gretchen hagen 3 acyl acid amido synthetases conjugate Amino Acids to chorismate a precursor of Aromatic Amino Acids and salicylic acid
Journal of Biological Chemistry, 2019Co-Authors: Cynthia K Holland, Corey S Westfall, Jason E Schaffer, Alejandro De Santiago, Chloe Zubieta, Sophie Alvarez, Joseph M JezAbstract:To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an Amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. The model plant Arabidopsis thaliana has 19 GH3 proteins, of which 8 have confirmed biochemical functions. One Brassicaceae-specific clade of GH3 proteins was predicted to use benzoate as a substrate and includes AtGH3.7 and AtGH3.12/PBS3. Previously identified as a 4-hydroxybenzoic acid-glutamate synthetase, AtGH3.12/PBS3 influences pathogen defense responses through salicylic acid. Recent work has shown that AtGH3.12/PBS3 uses isochorismate as a substrate, forming an isochorismate-glutamate conjugate that converts into salicylic acid. Here, we show that AtGH3.7 and AtGH3.12/PBS3 can also conjugate chorismate to cysteine and glutamate, which act as precursors to Aromatic Amino Acids and salicylic acid, respectively. The X-ray crystal structure of AtGH3.12/PBS3 in complex with AMP and chorismate at 1.94 A resolution, along with site-directed mutagenesis, revealed how the active site potentially accommodates this substrate. Examination of Arabidopsis knockout lines indicated that the gh3.7 mutants do not alter growth and showed no increased susceptibility to the pathogen Pseudomonas syringae, unlike gh3.12 mutants, which were more susceptible than WT plants, as was the gh3.7/gh3.12 double mutant. The findings of our study suggest that GH3 proteins can use metabolic precursors of Aromatic Amino Acids as substrates.
Jochen Autschbach - One of the best experts on this subject based on the ideXlab platform.
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time dependent density functional theory modeling of specific rotation and optical rotatory dispersion of the Aromatic Amino Acids in solution
Journal of Physical Chemistry A, 2006Co-Authors: Matthew D Kundrat, Jochen AutschbachAbstract:Time Dependent Density Functional Theory (TDDFT) along with the COnductor-like Screening MOdel (COSMO) has been applied to model the specific rotation at 589.3 nm and the optical rotatory dispersion (ORD) of the Aromatic Amino Acids phenylalanine, tyrosine, histidine, and tryptophan. Solution structures at low, neutral, and high pH were determined. Both the anomalous dispersion absorbing (resonance) region and the lower energy (transparent) region of the ORD of the compounds were modeled. Linear response calculation of the specific rotation and ORD as well as Kramers-Kronig transformations of calculated circular dichroism spectra to model resonant ORD were compared with experimental data from the literature.
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time dependent density functional theory modeling of specific rotation and optical rotatory dispersion of the Aromatic Amino Acids in solution
Journal of Physical Chemistry A, 2006Co-Authors: Matthew D Kundrat, Jochen AutschbachAbstract:Time Dependent Density Functional Theory (TDDFT) along with the COnductor-like Screening MOdel (COSMO) has been applied to model the specific rotation at 589.3 nm and the optical rotatory dispersion (ORD) of the Aromatic Amino Acids phenylalanine, tyrosine, histidine, and tryptophan. Solution structures at low, neutral, and high pH were determined. Both the anomalous dispersion absorbing (resonance) region and the lower energy (transparent) region of the ORD of the compounds were modeled. Linear response calculation of the specific rotation and ORD as well as Kramers-Kronig transformations of calculated circular dichroism spectra to model resonant ORD were compared with experimental data from the literature. proline, and serine, where the carboxylate chromophore was primarily responsible for the chiroptical response. 4 Here our calculations are extended to the larger, Aromatic Amino Acids, in which two distinct chromophores contribute to the optical rotation. To faithfully model chiroptical response properties one must first correctly determine the structures of the molecules being studied, and so this paper begins with a discussion of the optimized geometries of the Amino Acids. Some attention will be paid to the basis set effects on the relative energies of these geometries, and the relationship between basis set and the difficulty in correctly modeling the extent of intramolecular hydrogen bonding will be noted briefly. The computed mole fractions (Boltzmann populations) of the various conformers of some of these Amino Acids will be compared with experi- mentally derived Boltzmann populations from the literature. Next the specific rotations of select ionic states of these Amino Acids will be computed, and the results compared with experi- mental rotations. Particular attention will be paid to how the two different chromophores affect specific rotation, and how this varies depending on the conformation of the molecule. For some cases where the sign of the computed and measured specific rotation do not agree at 589 nm, it will be demonstrated how comparison of computed and measured optical rotatory dispersion curves would be a better method for assigning absolute configuration than comparison at 589 nm alone. Finally the anomalous optical rotatory dispersion of tyrosine in the near UV will be modeled in various protonation states via the Kramers-Kronig transformation of computed CD spectra and the results compared with experimental ORD.
William B. Whitman - One of the best experts on this subject based on the ideXlab platform.
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biochemical and genetic characterization of an early step in a novel pathway for the biosynthesis of Aromatic Amino Acids and p Aminobenzoic acid in the archaeon methanococcus maripaludis
Molecular Microbiology, 2006Co-Authors: Iris Porat, Magdalena Sieprawskalupa, Fredrick J Bohanon, Quincy Teng, William B. WhitmanAbstract:Summary Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon and facultative autotroph capable of biosynthesizing all the Amino Acids and vitamins required for growth. In this work, the novel 6-deoxy-5-ketofructose-1-phosphate (DKFP) pathway for the biosynthesis of Aromatic Amino Acids (AroAAs) and p-Aminobenzoic acid (PABA) was demonstrated in M. maripaludis. Moreover, PABA was shown to be derived from an early intermediate in AroAA biosynthesis and not from chorismate. Follow- ing metabolic labelling with (U- 13 C)-acetate, the expected enrichments for phenylalanine and ary- lamine derived from PABA were observed. DKFP pathway activity was reduced following growth with aryl Acids, an alternative source of the AroAAs. Lastly, a deletion mutant of aroA, which encodes the first step in the DKFP pathway, required AroAAs and PABA for growth. Complementation of the mutants by an aroA expression vector restored the wild-type phenotype. In contrast, a deletion of aroB, which encodes the second step in the DKFP pathway, did not require AroAAs or PABA for growth. Presumably, methanococci contain an alternative activity for this step. These results identify the initial reactions of a new pathway for the biosynthesis of PABA in methanococci.
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two biosynthetic pathways for Aromatic Amino Acids in the archaeon methanococcus maripaludis
Journal of Bacteriology, 2004Co-Authors: Iris Porat, Brian W Waters, Quincy Teng, William B. WhitmanAbstract:Methanococcus maripaludis is a strictly anaerobic, methane-producing archaeon. Aromatic Amino Acids (AroAAs) are biosynthesized in this autotroph either by the de novo pathway, with chorismate as an intermediate, or by the incorporation of exogenous aryl Acids via indolepyruvate oxidoreductase (IOR). In order to evaluate the roles of these pathways, the gene that encodes the third step in the de novo pathway, 3-dehydroquinate dehydratase (DHQ), was deleted. This mutant required all three AroAAs for growth, and no DHQ activity was detectible in cell extracts, compared to 6.0 ± 0.2 mU mg−1 in the wild-type extract. The growth requirement for the AroAAs could be fulfilled by the corresponding aryl Acids phenylacetate, indoleacetate, and p-hydroxyphenylacetate. The specific incorporation of phenylacetate into phenylalanine by the IOR pathway was demonstrated in vivo by labeling with [1-13C]phenylacetate. M. maripaludis has two IOR homologs. A deletion mutant for one of these homologs contained 76, 74, and 42% lower activity for phenylpyruvate, p-hydoxyphenylpyruvate, and indolepyruvate oxidation, respectively, than the wild type. Growth of this mutant in minimal medium was inhibited by the aryl Acids, but the AroAAs partially restored growth. Genetic complementation of the IOR mutant also restored much of the wild-type phenotype. Thus, aryl Acids appear to regulate the expression or activity of the de novo pathway. The aryl Acids did not significantly inhibit the activity of the biosynthetic enzymes chorismate mutase, prephenate dehydratase, and prephenate dehydrogenase in cell extracts, so the inhibition of growth was probably not due to an effect on these enzymes.
Cynthia K Holland - One of the best experts on this subject based on the ideXlab platform.
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brassicaceae specific gretchen hagen 3 acyl acid amido synthetases conjugate Amino Acids to chorismate a precursor of Aromatic Amino Acids and salicylic acid
Journal of Biological Chemistry, 2019Co-Authors: Cynthia K Holland, Corey S Westfall, Jason E Schaffer, Alejandro De Santiago, Chloe Zubieta, Sophie Alvarez, Joseph M JezAbstract:To modulate responses to developmental or environmental cues, plants use Gretchen Hagen 3 (GH3) acyl acid amido synthetases to conjugate an Amino acid to a plant hormone, a reaction that regulates free hormone concentration and downstream responses. The model plant Arabidopsis thaliana has 19 GH3 proteins, of which 8 have confirmed biochemical functions. One Brassicaceae-specific clade of GH3 proteins was predicted to use benzoate as a substrate and includes AtGH3.7 and AtGH3.12/PBS3. Previously identified as a 4-hydroxybenzoic acid-glutamate synthetase, AtGH3.12/PBS3 influences pathogen defense responses through salicylic acid. Recent work has shown that AtGH3.12/PBS3 uses isochorismate as a substrate, forming an isochorismate-glutamate conjugate that converts into salicylic acid. Here, we show that AtGH3.7 and AtGH3.12/PBS3 can also conjugate chorismate to cysteine and glutamate, which act as precursors to Aromatic Amino Acids and salicylic acid, respectively. The X-ray crystal structure of AtGH3.12/PBS3 in complex with AMP and chorismate at 1.94 A resolution, along with site-directed mutagenesis, revealed how the active site potentially accommodates this substrate. Examination of Arabidopsis knockout lines indicated that the gh3.7 mutants do not alter growth and showed no increased susceptibility to the pathogen Pseudomonas syringae, unlike gh3.12 mutants, which were more susceptible than WT plants, as was the gh3.7/gh3.12 double mutant. The findings of our study suggest that GH3 proteins can use metabolic precursors of Aromatic Amino Acids as substrates.