Prediction of Structurally Conserved Regions of D-Specific Hydroxy Acid Dehydrogenases by Multiple Alignment with Formate Dehydrogenase

Vinals, C; Depiereux, Eric; Feytmans, Ernest

doi:10.1006/bbrc.1993.1398

Cited by 67 publications

(47 citation statements)

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“…E. coli SerA enzyme is a member of a D-isomer-specific family of 2-hydroxyacid dehydrogenases which includes E. coli PdxB 4-phosphoerythronate dehydrogenase; D-lactate dehydrogenases from Lactobacillus plantarum and Lactobacillus casei; Pseudomonas formate dehydrogenase; and NADH-dependent hydroxypyruvate reductase, glycerate dehydrogenase, and 2-hydroxyisocarproate dehydrogenase from cucumber (15,33,40,41). In this family, only the SerA and PdxB enzymes use phosphorylated substrates.…”

Section: Discussionmentioning

confidence: 99%

“…The SerA structure has several unique features that may play roles in catalysis and allosteric inhibition by Ser and Gly (34a). SerA 3PG dehydrogenase is a member of a family of evolutionarily related 2-hydroxyacid dehydrogenases that includes the pdxB-encoded 4-phosphoerythronate (4PE) dehydrogenase (15,33,40,41). 4PE dehydrogenase catalyzes the second committed step in one branch of pyridoxine 5Ј-phosphate and pyridoxal 5Ј-phosphate coenzyme biosynthesis in E. coli (20,25,33,46).…”

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confidence: 99%

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A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria

1996

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Escherichia coli serA-encoded 3-phosphoglycerate (3PG) dehydrogenase catalyzes the first step of the major phosphorylated pathway of L-serine (Ser) biosynthesis. The SerA enzyme is evolutionarily related to the pdxB gene product, 4-phosphoerythronate dehydrogenase, which catalyzes the second step in one branch of pyridoxal 5-phosphate coenzyme biosynthesis. Both the Ser and pyridoxal 5-phosphate biosynthetic pathways use the serC(pdxF)-encoded transaminase in their next steps. In an analysis of these parallel pathways, we attempted to couple the transaminase and dehydrogenase reactions in the reverse direction. Unexpectedly, we found that the SerA enzyme catalyzes a previously undetected reduction of ␣-ketoglutarate (␣KG) to 2-hydroxyglutaric acid (HGA). Numerous criteria ruled out the possibility that this SerA ␣KG reductase activity was caused by contamination in the substrate or purified enzyme preparations. HGA was confirmed as the product of the

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Section: Discussionmentioning

confidence: 99%

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confidence: 99%

A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria

1996

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“…101 is a member of the family of D-specific 2-hydroxyacid dehydrogenases acting on o-stereoisomers of the respective substrates. There is strong sequence similarity between FDH and these dehydrogenases [1]. Crystal structures of FDH [2] and two D-specific dehydrogenases, D-phosphoglycerate dehydrogenase [3] and o-glycerate dehydrogenase [4], revealed significant similarities in the three-dimensional fold of these proteins.…”

Section: Introductionmentioning

confidence: 98%

“…An invariant pair of residues, histidine and a carboxylic acid, occupying conserved positions is found in the active centres of a number of D-and L-specific dehydrogenases [9]. They function as a composite acid-base catalyst facilitating proton transfer to and from the 2-hydroxylic group of the substrate [1,3,4,[6][7][8][9].…”

Section: Introductionmentioning

confidence: 99%

Site‐directed mutagenesis of the formate dehydrogenase active centre: role of the His³³²‐Gln³¹³ pair in enzyme catalysis

et al. 1996

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“…Recent reports have demonstrated that D-LDH belongs to a family of NADH-dependent 2-hydroxyacid dehydrogenases evolutionarily distinct from L-LDH (6,28,29,50). Sequence comparisons reported so far indicate that Dhydroxyisocaproate dehydrogenase (D-HDH), which prefers 2-hydroxyacid substrates with a straight or branched aliphatic chain, is a member of this new family (7, 32), which also includes D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95), erythronate 4-phosphate dehydrogenase, D-glycerate dehydrogenase (EC 1.1.1.81), and formate dehydrogenase (22,23,30,55).We report here the cloning, sequencing, and transcriptional analysis of the gene encoding D-LDH in Pediococcus acidilactici. This species was chosen because of its main contribution to lactate production in silage (17), inasmuch as the availability of a cloned ldhD gene from P. acidilactici would allow metabolic engineering with the goal of exclusive L-lactate fermentation (16).…”

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confidence: 99%

Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis

et al. 1995

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The gene encoding D-lactate dehydrogenase was isolated on a 2.9-kb insert from a library of Pediococcus acidilactici DNA by complementation for growth under anaerobiosis of an Escherichia coli lactate dehydrogenase and pyruvate-formate lyase double mutant. The nucleotide sequence of ldhD encodes a protein of 331 amino acids (predicted molecular mass of 37,210 Da) which shows similarity to the family of D-2-hydroxyacid dehydrogenases. The enzyme encoded by the cloned fragment is equally active on pyruvate and hydroxypyruvate, indicating that the enzyme has both D-lactate and D-glycerate dehydrogenase activities. Three other open reading frames were found in the 2.9-kb insert, one of which (rpsB) is highly similar to bacterial genes coding for ribosomal protein S2. Northern (RNA) blotting analyses indicated the presence of a 2-kb dicistronic transcript of ldhD (a metabolic gene) and rpsB (a putative ribosomal protein gene) together with a 1-kb monocistronic rpsB mRNA. These transcripts are abundant in the early phase of exponential growth but steadily fade away to disappear in the stationary phase. Primer extension analysis identified two distinct promoters driving either cotranscription of ldhD and rpsB or transcription of rpsB alone.The NADH-dependent lactate dehydrogenase (LDH) is a key enzyme in the fermentative metabolism of lactic acid bacteria, which include members of the genera Pediococcus, Lactobacillus, Lactococcus, Streptococcus, Leuconostoc, Propionibacterium, and Bifidobacterium. LDH catalyzes reoxidation of NADH into NAD ϩ , which is required for glycolysis, through the concomitant reduction of pyruvate to lactate, which is the major end product of metabolism during growth of lactic acid bacteria. The reduction of pyruvate to L-(ϩ)-or D-(Ϫ)-lactate is catalyzed by two different NAD-dependent enzymes, the L-(ϩ)-LDH (L-LDH; EC 1.1.1.27) and the D-(Ϫ)-LDH (D-LDH; EC 1.1.1.28).The regulation of LDH activity at a molecular level is poorly understood, particularly with respect to transcriptional regulation. Reports have demonstrated that some lactic acid bacteria produce both D-and L-lactate, and that the ratio of the two isomers changes throughout the growth cycle. In Leuconostoc mesenteroides, malic acid has been shown to have a stimulatory effect on the synthesis of both LDHs (for a review, see reference 19). In the genus Lactococcus, allosteric regulation by fructose 1,6-bisphosphate has been shown to control the flux of metabolites by modulating the activity of L-LDH (14,52,53,58).The amino acid sequences of many bacterial L-LDHs have been determined, and L-LDH has been the subject of intensive investigations relating to structure and catalysis (for reviews, see references 15 and 57). In contrast, little is known about bacterial D-LDH. Recent reports have demonstrated that D-LDH belongs to a family of NADH-dependent 2-hydroxyacid dehydrogenases evolutionarily distinct from L-LDH (6,28,29,50). Sequence comparisons reported so far indicate that Dhydroxyisocaproate dehydrogenase (D-HDH), which prefers 2...

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Prediction of Structurally Conserved Regions of D-Specific Hydroxy Acid Dehydrogenases by Multiple Alignment with Formate Dehydrogenase

Cited by 67 publications

References 0 publications

A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria

A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria

Site‐directed mutagenesis of the formate dehydrogenase active centre: role of the His³³²‐Gln³¹³ pair in enzyme catalysis

Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis

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Prediction of Structurally Conserved Regions of D-Specific Hydroxy Acid Dehydrogenases by Multiple Alignment with Formate Dehydrogenase

Cited by 67 publications

References 0 publications

A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria

A novel alpha-ketoglutarate reductase activity of the serA-encoded 3-phosphoglycerate dehydrogenase of Escherichia coli K-12 and its possible implications for human 2-hydroxyglutaric aciduria

Site‐directed mutagenesis of the formate dehydrogenase active centre: role of the His332‐Gln313 pair in enzyme catalysis

Pediococcus acidilactici ldhD gene: cloning, nucleotide sequence, and transcriptional analysis

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Site‐directed mutagenesis of the formate dehydrogenase active centre: role of the His³³²‐Gln³¹³ pair in enzyme catalysis