A 13C-N.M.R. study of intermediates in the l-type pentose phosphate cycle

Franke, Fritz P.; Kapuscinski, Mirek; MacLeod, John K.; Williams, John F.

doi:10.1016/0008-6215(84)85155-1

Cited by 24 publications

(6 citation statements)

References 15 publications

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“…One significant difference was found with d -arabinose and its derivatives. Previously, FBP aldolase was shown to utilize d -arabinose-5-P to give d - glycero - d - ido -octulo-1,8-bisphosphate . This finding was reproduced during this study, and the product was confirmed by comparison with the published NMR chemical shifts (data not shown).…”

Section: Discussionsupporting

confidence: 82%

“…Previously, FBP aldolase was shown to utilize Darabinose-5-P to give D-glycero-D-ido-octulo-1,8-bisphosphate. 53 This finding was reproduced during this study, and the product was confirmed by comparison with the published NMR chemical shifts (data not shown). However, YdjI shows no measurable activity with D-arabinose-5-P, D-arabinose, or Darabinuronic acid.…”

Section: ■ Discussionsupporting

confidence: 80%

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Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12

et al. 2019

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The ydj gene cluster is found in 80% of sequenced Escherichia coli genomes and other closely related species in the human microbiome. On the basis of the annotations of the enzymes located in this cluster, it is expected that together they catalyze the catabolism of an unknown carbohydrate. The focus of this investigation is on YdjI, which is in the ydj gene cluster of E. coli K-12. It is predicted to be a class II aldolase of unknown function. Here we describe a structural and functional characterization of this enzyme. YdjI catalyzes the hydrogen/deuterium exchange of the pro-S hydrogen at C3 of dihydroxyacetone phosphate (DHAP). In the presence of DHAP, YdjI catalyzes an aldol condensation with a variety of aldo sugars. YdjI shows a strong preference for higher-order (seven-, eight-, and nine-carbon) monosaccharides with specific hydroxyl stereochemistries and a negatively charged terminus (carboxylate or phosphate). The best substrate is L-arabinuronic acid with an apparent k cat of 3.0 s −1 . The product, L-glycero-L-galacto-octuluronate-1-phosphate, has a k cat /K m value of 2.1 × 10 3 M −1 s −1 in the retro-aldol reaction with YdjI. This is the first recorded synthesis of L-glycero-L-galacto-octuluronate-1-phosphate and six similar carbohydrates. The crystal structure of YdjI, determined to a nominal resolution of 1.75 Å (Protein Data Bank entry 6OFU), reveals unusual positions for two arginine residues located near the active site. Computational docking was utilized to distinguish preferable binding orientations for L-glycero-L-galacto-octuluronate-1-phosphate. These results indicate a possible alternative binding orientation for L-glycero-L-galacto-octuluronate-1-phosphate compared to that observed in other class II aldolases, which utilize shorter carbohydrate molecules.

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Section: Discussionsupporting

confidence: 82%

Section: ■ Discussionsupporting

confidence: 80%

Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12

et al. 2019

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“…D-Sedoheptulose-7-phosphate (29.9 g) was isolated as its Ba salt. Its organic purity was high, neither β-hydroxypyruvate nor D-ribose-5-phosphate being detected by 1 H, 13 C or 31 P NMR experiments. 31 P and 13 C NMR data fitted with those published earlier [12] and [13].…”

Section: Synthesis Of Sedoheptulose-7-phosphate Barium Saltmentioning

confidence: 94%

Preparative scale enzymatic synthesis of d-sedoheptulose-7-phosphate from β-hydroxypyruvate and d-ribose-5-phosphate

Charmantray

Hélaine

Légeret

et al. 2009

Journal of Molecular Catalysis B: Enzymatic

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“…However, this molecule was previously synthesized using FBP aldolase. 16 Briefly, D-arabinose-5-P (0.052 mmol) was mixed with DHAP (0.042 mmol) in 50 mM HEPES/K + buffer (pH 8.5). To this solution was added ∼50 units (4.0 mg) of FBP aldolase (Sigma-Aldrich), and the reaction was monitored for 96 h. The aldolase was removed, and D-glycero-D-idooctulose-1,8-bis-P was purified by anion exchange as described above.…”

Section: ■ Materials and Methodsmentioning

confidence: 99%

“…d -glycero- d -ido -Octulose-1,8-bis-phosphate ( 17 ) cannot be synthesized using YdjI, DHAP, and d -arabinose-5-P. However, this molecule was previously synthesized using FBP aldolase . Briefly, d -arabinose-5-P (0.052 mmol) was mixed with DHAP (0.042 mmol) in 50 mM HEPES/K + buffer (pH 8.5).…”

Section: Methodsmentioning

confidence: 99%

Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12

Huddleston

Raushel

2019

Biochemistry

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The ydj gene cluster is annotated to catalyze the catabolism of an unknown carbohydrate. Previously, YdjI, a class II aldolase, was shown to catalyze the retro-aldol cleavage of l-glycero-l-galacto-octuluronate-1-phosphate into DHAP and l-arabinuronate. In this report, the functional characterization of YdjH is presented. YdjH catalyzes the phosphorylation of 2-keto-monosaccharides at the C1 hydroxyl group with a substrate profile significantly more stringent than that of YdjI. Similar to YdjI, YdjH shows a strong preference for higher-order monosaccharides (seven to nine carbons) with a carboxylate terminus. The best substrate was determined to be l-glycero-l-galacto-octuluronate, yielding l-glycero-l-galacto-octuluronate-1-phosphate with a k cat of 16 s–1 and a k cat/K m of 2.1 × 104 M–1 s–1. This is apparently the first reported example of kinase activity with eight-carbon monosaccharides. Two crystal structures of YdjH were previously determined to 2.15 and 1.8 Å resolution (Protein Data Bank entries 3H49 and 3IN1). We present an analysis of the active site layout and use computational docking to identify potential key residues in the binding of l-glycero-l-galacto-octuluronate.

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A 13C-N.M.R. study of intermediates in the l-type pentose phosphate cycle

Cited by 24 publications

References 15 publications

Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12

Structural and Functional Characterization of YdjI, an Aldolase of Unknown Specificity in Escherichia coli K12

Preparative scale enzymatic synthesis of d-sedoheptulose-7-phosphate from β-hydroxypyruvate and d-ribose-5-phosphate

Functional Characterization of YdjH, a Sugar Kinase of Unknown Specificity in Escherichia coli K12

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