2-Hydroxyglutarate production is necessary for the reaction catalyzed by 3-phosphoglycerate dehydrogenase in Escherichia coli

Gusyatiner, M. M.; Ziyatdinov, M. Kh.

doi:10.1134/s2079978015010021

Cited by 5 publications

(4 citation statements)

References 53 publications

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“…The coenzyme released over time corresponded virtually exclusively to NAD + (NADH represented <1% of the released coenzyme measured). These results confirm not only that Ser3, Ser33, and h PHGDH tightly bind NAD + in addition to NADH but also, as shown or suggested for homologues of other species, that NADH binds the yeast and human proteins with affinities higher than those of NAD + . ,,, …”

Section: Resultssupporting

confidence: 83%

“…These results confirm not only that Ser3, Ser33, and hPHGDH tightly bind NAD + in addition to NADH but also, as shown or suggested for homologues of other species, that NADH binds the yeast and human proteins with affinities higher than those of NAD + . 19,25,26,37 Ser3 and Ser33 but Not Human PHGDH Are Inhibited by NADHX and L-Serine. NADHX is a noncanonical redoxinactive derivative of NADH that can be formed spontaneously or by enzymatic side reactions through hydration of the nicotinamide ring and has been found to inhibit several dehydrogenases in vitro.…”

Section: Biochemistrymentioning

confidence: 96%

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3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis

et al. 2019

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The enzymatic mechanism of 3-phosphoglycerate to 3-phosphohydroxypyruvate oxidation, which forms the first step of the main conserved de novo serine synthesis pathway, has been revisited recently in certain microorganisms. While this step is classically considered to be catalyzed by an NAD-dependent dehydrogenase (e.g., PHGDH in mammals), evidence has shown that in Pseudomonas, Escherichia coli, and Saccharomyces cerevisiae, the PHGDH homologues act as transhydrogenases. As such, they use α-ketoglutarate, rather than NAD+, as the final electron acceptor, thereby producing D-2-hydroxyglutarate in addition to 3-phosphohydroxypyruvate during 3-phosphoglycerate oxidation. Here, we provide a detailed biochemical and sequence–structure relationship characterization of the yeast PHGDH homologues, encoded by the paralogous SER3 and SER33 genes, in comparison to the human and other PHGDH enzymes. Using in vitro assays with purified recombinant enzymes as well as in vivo growth phenotyping and metabolome analyses of yeast strains engineered to depend on either Ser3, Ser33, or human PHGDH for serine synthesis, we confirmed that both yeast enzymes act as transhydrogenases, while the human enzyme is a dehydrogenase. In addition, we show that the yeast paralogs differ from the human enzyme in their sensitivity to inhibition by serine as well as hydrated NADH derivatives. Importantly, our in vivo data support the idea that a 3PGA transhydrogenase instead of dehydrogenase activity confers a growth advantage under conditions where the NAD+:NADH ratio is low. The results will help to elucidate why different species evolved different reaction mechanisms to carry out a widely conserved metabolic step in central carbon metabolism.

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Section: Resultssupporting

confidence: 83%

Section: Biochemistrymentioning

confidence: 96%

3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis

et al. 2019

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“…Therefore, because E. coli efficiently produces l -serine in vivo , some compensating mechanism must be operational. In a recent review, Gusyatiner and Ziyatdinov hypothesized that the production of αHG from αKG by ec PGDH is necessary to convert the bound NADH to NAD + for the forward reaction to proceed toward l -serine biosynthesis. However, this review presented the hypothesis only, and no experimental results confirming it were included.…”

mentioning

confidence: 99%

Elucidation of a Self-Sustaining Cycle in Escherichia coli l-Serine Biosynthesis That Results in the Conservation of the Coenzyme, NAD⁺

Grant

2018

Biochemistry

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The equilibrium of the reaction catalyzed by d-3-phosphoglycerate dehydrogenase (PGDH), the first enzyme in the l-serine biosynthetic pathway, is far in the direction away from serine synthesis. As such, the enzyme is usually assayed in this direction. To easily assay it in the direction of l-serine synthesis, it can be coupled to the next enzyme in the pathway, phosphoserine aminotransferase (PSAT), with the activity monitored by the conversion of NAD to NADH by PGDH. However, when PGDHs from several different species were coupled to PSAT, it was found that one of them, ecPGDH, conserves the coenzyme in the production of l-serine by utilizing an intrinsic cycle of NAD/NADH interconversion coupled with the conversion of α-ketoglutarate (αKG) to α-hydroxyglutarate. Furthermore, the cycle can be maintained by production of αKG by the second enzyme in the pathway, PSAT, and does not require any additional enzymes. This is not the case for PGDH from another bacterial source, Mycobacterium tuberculosis, and a mammalian source, human liver, where net consumption of NAD occurs. Both NAD and NADH appear to remain tightly bound to ecPGDH during the cycle, effectively removing a requirement for the presence of an exogenous coenzyme pool to maintain the pathway and significantly reducing the energy requirement needed to maintain this major metabolic pathway.

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“…(Table 1) (13)(14)(15)(16)(17) The "promiscuous" activity of 2-KG reduction to D-2-HG is required for SerA to overcome the thermodynamic barrier and regenerate the NAD ϩ for D-3-PG dehydrogenation (4,18,19). PdxB is a homolog of SerA, which catalyzes the oxidization of 4-phospho-D-erythronate to 2-oxo-3-hydroxy-4-phosphobutanoate (20).…”

mentioning

confidence: 99%

d-2-Hydroxyglutarate dehydrogenase plays a dual role in l-serine biosynthesis and d-malate utilization in the bacterium Pseudomonas stutzeri

Guo

Zhang

Cao

et al. 2018

Journal of Biological Chemistry

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is a very large bacterial genus in which several species can use d-malate for growth. However, the enzymes that can metabolize d-malate, such as d-malate dehydrogenase, appear to be absent in most species. d-3-Phosphoglycerate dehydrogenase (SerA) can catalyze the production of d-2-hydroxyglutarate (d-2-HG) from 2-ketoglutarate to support d-3-phosphoglycerate dehydrogenation, which is the initial reaction in bacterial l-serine biosynthesis. In this study, we show that SerA of the strain A1501 reduces oxaloacetate to d-malate and that d-2-HG dehydrogenase (D2HGDH) from displays d-malate-oxidizing activity. Of note, D2HGDH participates in converting a trace amount of d-malate to oxaloacetate during bacterial l-serine biosynthesis. Moreover, D2HGDH is crucial for the utilization of d-malate as the sole carbon source for growth of A1501. We also found that the D2HGDH expression is induced by the exogenously added d-2-HG or d-malate and that a flavoprotein functions as a soluble electron carrier between D2HGDH and electron transport chains to support d-malate utilization by These results support the idea that D2HGDH evolves as an enzyme for both d-malate and d-2-HG dehydrogenation in In summary, D2HGDH from A1501 participates in both a core metabolic pathway for l-serine biosynthesis and utilization of extracellular d-malate.

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2-Hydroxyglutarate production is necessary for the reaction catalyzed by 3-phosphoglycerate dehydrogenase in Escherichia coli

Cited by 5 publications

References 53 publications

3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis

3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis

Elucidation of a Self-Sustaining Cycle in Escherichia coli l-Serine Biosynthesis That Results in the Conservation of the Coenzyme, NAD⁺

d-2-Hydroxyglutarate dehydrogenase plays a dual role in l-serine biosynthesis and d-malate utilization in the bacterium Pseudomonas stutzeri

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2-Hydroxyglutarate production is necessary for the reaction catalyzed by 3-phosphoglycerate dehydrogenase in Escherichia coli

Cited by 5 publications

References 53 publications

3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis

3-Phosphoglycerate Transhydrogenation Instead of Dehydrogenation Alleviates the Redox State Dependency of Yeast de Novo l-Serine Synthesis

Elucidation of a Self-Sustaining Cycle in Escherichia coli l-Serine Biosynthesis That Results in the Conservation of the Coenzyme, NAD+

d-2-Hydroxyglutarate dehydrogenase plays a dual role in l-serine biosynthesis and d-malate utilization in the bacterium Pseudomonas stutzeri

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Elucidation of a Self-Sustaining Cycle in Escherichia coli l-Serine Biosynthesis That Results in the Conservation of the Coenzyme, NAD⁺