engineering

Glycerate dehydrogenase

Glycerate dehydrogenase is a engineering topic covered in the lgStudy science library. This page brings together a partial reference excerpt, illustrations, worked examples, real-world applications and a short study plan, so you can understand Glycerate dehydrogenase rather than just read about it. In short: In enzymology, a glycerate dehydrogenase (EC 1.1.1.29) is an enzyme that catalyzes the chemical reaction The two substrates of this enzyme are (R)-glyceric acid and oxidised nicotinamide adenine dinucleotide (NAD+). Its products are hydroxypyruvic acid, reduced NADH, and a proton.

Key takeaways

Glycerate dehydrogenase belongs to engineering; place it in that map before memorising details.
Learn the definition first, then one example that makes the definition concrete.
Connect Glycerate dehydrogenase to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Glycerate dehydrogenase from memory before moving on to harder problems.

Reference excerpt

In enzymology, a glycerate dehydrogenase (EC 1.1.1.29) is an enzyme that catalyzes the chemical reaction

The two substrates of this enzyme are (R)-glyceric acid and oxidised nicotinamide adenine dinucleotide (NAD+). Its products are hydroxypyruvic acid, reduced NADH, and a proton. These enzymes can catalyze the reverse reaction as well. That is, hydroxypyruvate, NADH, and H+ can act as the substrates while (R)-glycerate and NAD+ are formed as products. Additionally, NADPH can take the place of NADH in this reaction. This enzyme belongs to the family of oxidoreductases, specifically those acting on the CH-OH group of donor with NAD+ or NADP+ as acceptor. The systematic name of this enzyme class is (R)-glycerate:NAD+ oxidoreductase. Other names in common use include D-glycerate dehydrogenase, and hydroxypyruvate reductase (due to the reversibility of the reaction). This enzyme participates in glycine, serine and threonine metabolism and glyoxylate and dicarboxylate metabolism.

Enzyme structure This class of enzyme is part of a larger superfamily of enzymes known as D-2-hydroxy-acid dehydrogenases. Many organisms from Hyphomicrobium methylovorum to humans have some form of the glycerate dehydrogenase protein. There are currently several structures that have been solved for this class of enzyme including those for the two mentioned above with PDB access code PDB: 1GDH, D-glycerate dehydrogenase, and the human homolog Glyoxylate reductase/Hydroxypyruvate reductase (GRHPR), PDB: 2WWR. These studies have yielded a better understanding of the structure and function of these enzymes. It has been shown that these proteins are homodimeric enzymes. This means that 2 identical proteins are linked forming one larger complex. The active site is found in each subunit between the two distinct α/β/α globular domains, the substrate binding domain and the coenzyme binding domain. This coenzyme binding domain is slightly larger than the substrate binding domain and contains a NAD(P) Rossmann fold along with the "dimerisation loop" which holds the two subunits of the homodimer together. In addition to linking the two proteins together, the "dimerisation loop" of each subunit protrudes into the active site of the other subunit increasing the specificity of the enzyme, by preventing the binding of pyruvate as a substrate. Hydroxypyruvate is still able to bind to the active site due to extra stabilization from hydrogen bonds with neighboring amino-acid residues.

Glyoxylate reductase/Hydroxypyruvate reductase

Biological relevance Glyoxylate reductase/Hydroxypyruvate reductase (GRHPR) is the glycerate dehydrogenase found, predominantly in the liver, of humans encoded by the gene GRHPR. Under physiological conditions, the production of D-glycerate is favored over its consumption as a substrate. It can then be converted to 2-phosphoglycerate, which can then enter into glycolysis, gluconeogenesis, or the serine pathway. As the name suggests, in addition to the glycerate dehydrogenase and hydroxypyruvate reductase activity, the protein also exhibits glyoxylate reductase activity. The ability of GRHPR to reduce glyoxylate to glycolate is found in other glycerate dehydrogenase homologs as well. This is important for the intracellular regulation of glyoxylate levels, which has important medical ramifications. As mentioned earlier, these enzymes have the ability to use either NADH or NADPH as the coenzyme. This gives them an advantage over other enzymes that can only use a single form of the coenzyme. Lactate dehydrogenase(LDH) is one such enzyme that directly competes with GRHPR for substrates and converts glyoxylate to oxalate. However, due to the relatively large concentration of NADPH compared to NADH under normal cellular concentration, the GRHPR activity is greater than that of LDH so the production of glycolate is dominant.

Medical relevance Primary hyperoxaluria is a condition that results in the overproduction of oxalate which combines with calcium to generate calcium oxalate, the main component of kidney stones. Primary Hyperoxaluria type 2 is caused by any one of several mutations to the GRHPR gene and results in the accumulation of calcium oxalate in the kidneys, bones, and many other organs. The mutations to GRHPR prevent it from converting glyoxylate to glycolate, leading to a build-up of glyoxylate. This excess glyoxylate is then oxidized by lactate dehydrogenase to produce the oxalate that is characteristic of hyperoxaluria.

References

Holzer H, Holldorf A (1957). "[Isolation of D-glycerate dehydrogenase, some properties of the enzyme and its application to the enzymic-optic determination of hydroxypyruvate in presence of pyruvate]". Biochem. Z. (in German). 329 (4): 292–312. PMID 13522707. Stafford HA, Magaldi A, Vennesland B (1954). "The enzymatic reduction of hydroxypyruvic acid to D-glyceric acid in higher plants". J. Biol. Chem. 207 (2): 621–9. doi:10.1016/S0021-9258(18)65678-9. PMID 13163046. Rumsby, G; Pagon, RA; Bird, TD; Dolan, CR; Stephens, K; Adam, MP (1993). "Primary Hyperoxaluria Type 2". PMID 20301742. {{cite journal}}: Cite journal requires |journal= (help) Cramer, SD; Ferree, PM; Lin, K; Milliner, DS; Holmes, RP (October 1999). "The gene encoding hydroxypyruvate reductase (GRHPR) is mutated in patients with primary hyperoxaluria type II". Human Molecular Genetics. 8 (11): 2063–9. doi:10.1093/hmg/8.11.2063. PMID 10484776.

Illustrations

Worked examples

Example 1 — a first encounter with Glycerate dehydrogenase

Start with the simplest possible case. Write down what Glycerate dehydrogenase claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In engineering, the smallest case is usually a single object, a single equation or a single measurement. Check that every symbol or term in your sentence has a meaning in that case.

Example 2 — changing one variable

Take the situation from Example 1 and change exactly one quantity: double it, halve it, or set it to zero. Predict what should happen to Glycerate dehydrogenase before you calculate. Comparing your prediction with the result is the fastest way to find out whether you understand the idea or only the words.

Example 3 — an exam-style question

Typical questions about Glycerate dehydrogenase ask you to (a) state it precisely, (b) apply it to given data, and (c) explain a limitation. Practise writing all three answers in under five minutes; the third part is what separates a full-mark answer from an average one.

Applications of Glycerate dehydrogenase

In research: Glycerate dehydrogenase appears in engineering research whenever the underlying quantities have to be modelled precisely. Papers usually cite it as a starting assumption and then explore where it breaks down.
In technology and industry: Engineering practice reuses Glycerate dehydrogenase in design rules, simulations and safety margins. Knowing the idea lets you read a specification sheet and understand why the numbers look the way they do.
In the classroom: Glycerate dehydrogenase is common in secondary-school and first-year university syllabi. It links to neighbouring topics EC 1.1.1, Enzymes of known structure, NADH-dependent enzymes, so understanding it makes those chapters shorter.
In everyday life: Look for Glycerate dehydrogenase outside the textbook — in sport, cooking, traffic, electronics or the sky above you. An example you found yourself is remembered far longer than one you were given.

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How to study Glycerate dehydrogenase in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Glycerate dehydrogenase means in your own words.
Compare your version with the excerpt and mark what you missed.
Work through the three examples above with pen and paper.
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Frequently asked questions

What is Glycerate dehydrogenase in simple terms?

In enzymology, a glycerate dehydrogenase (EC 1.1.1.29) is an enzyme that catalyzes the chemical reaction The two substrates of this enzyme are (R)-glyceric acid and oxidised nicotinamide adenine dinucleotide (NAD+). Its products are hydroxypyruvic acid, reduced NADH, and a proton.

Why does Glycerate dehydrogenase matter?

Because it connects several engineering ideas at once: it gives you a definition you can apply, a quantity you can calculate, and a way to check whether a result is plausible.

How should I study Glycerate dehydrogenase?

Read the excerpt, restate it from memory, then work through the examples and applications listed on this page. The five-step study plan above takes about twenty minutes.

What does this page cover?

It gives you a compact reference excerpt plus original lgStudy explanations, examples, applications and study material on Glycerate dehydrogenase.