engineering

Shikimate dehydrogenase

Shikimate 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 Shikimate dehydrogenase rather than just read about it. In short: In enzymology, a shikimate dehydrogenase (EC 1.1.1.25) is an enzyme that catalyzes the chemical reaction The two substrates of this enzyme are shikimate and oxidised nicotinamide adenine dinucleotide phosphate (NADP+). Its products are 3-dehydroshikimate, reduced NADPH, and a proton.

Key takeaways

Shikimate 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 Shikimate dehydrogenase to a quantity you can measure, compute or draw — that is where exam questions come from.
Reproduce the core statement of Shikimate dehydrogenase from memory before moving on to harder problems.

Reference excerpt

In enzymology, a shikimate dehydrogenase (EC 1.1.1.25) is an enzyme that catalyzes the chemical reaction

The two substrates of this enzyme are shikimate and oxidised nicotinamide adenine dinucleotide phosphate (NADP+). Its products are 3-dehydroshikimate, reduced NADPH, and a proton. This enzyme participates in phenylalanine, tyrosine and tryptophan biosynthesis.

Function Shikimate dehydrogenase is an enzyme that catalyzes one step of the shikimate pathway. This pathway is found in bacteria, plants, fungi, algae, and parasites and is responsible for the biosynthesis of aromatic amino acids (phenylalanine, tyrosine, and tryptophan) from the metabolism of carbohydrates. In contrast, animals and humans lack this pathway hence products of this biosynthetic route are essential amino acids that must be obtained through an animal's diet. There are seven enzymes that play a role in this pathway. Shikimate dehydrogenase (also known as 3-dehydroshikimate dehydrogenase) is the fourth step of the seven step process. This step converts 3-dehydroshikimate to shikimate as well as reduces NADP+ to NADPH.

Nomenclature 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 shikimate:NADP+ 3-oxidoreductase. Other names in common use include:

Reaction

Shikimate Dehydrogenase catalyzes the reversible NADPH-dependent reaction of 3-dehydroshikimate to shikimate. The enzyme reduces the carbon-oxygen double bond of a carbonyl functional group to a hydroxyl (OH) group, producing the shikimate anion. The reaction is NADPH dependent with NADPH being oxidised to NADP+.

Structure

N terminal domain

The Shikimate dehydrogenase substrate binding domain found at the N-terminus binds to the substrate, 3-dehydroshikimate. It is considered to be the catalytic domain. It has a structure of six beta strands forming a twisted beta sheet with four alpha helices.

C terminal domain

The C-terminal domain binds to NADPH. It has a special structure, a Rossmann fold, whereby six-stranded twisted and parallel beta sheet with loops and alpha helices surrounding the core beta sheet. The Structure of Shikimate dehydrogenase is characterized by two domains, two alpha helices and two beta sheets with a large cleft separating the domains of the monomer. The enzyme is symmetrical. Shikimate dehydrogenase also has an NADPH binding site that contains a Rossmann fold. This binding site normally contains a glycine P-loop. The domains of the monomer show a fair amount of flexibility suggesting that the enzyme can open in close to bind with the substrate 3-Dehydroshikimate. Hydrophobic interactions occur between the domains and the NADPH binding site. This hydrophobic core and its interactions lock the shape of the enzyme even though the enzyme is a dynamic structure. There is also evidence to support that the structure of the enzyme is conserved, meaning the structure takes sharp turns in order to take up less space.

Paralogs Escherichia coli (E. coli) expresses two different forms of shikimate dehydrogenase, AroE and YdiB. These two forms are paralogs of each other. The two forms of shikimate dehydrogenase have different primary sequences in different organisms but catalyze the same reactions. There is about 25% similarity between the sequences of AroE and YdiB, but their two structures have similar structures with similar folds. YdiB can utilize NAD or NADP as a cofactor and also reacts with quinic acid. They both have high affinity of their ligands as shown by their similar enzyme (Km) values. Both forms of the enzyme are independently regulated.

Applications The shikimate pathway is a target for herbicides and other non-toxic drugs because the shikimate pathway is not present in humans. Glyphosate, a commonly used herbicide, is an inhibitor of 5-enolpyruvylshikimate 3-phosphate synthase or EPSP synthase, an enzyme in the shikimate pathway. The problem is that this herbicide has been utilized for about 20 years and now some plants have now emerged that are glyphosate-resistant. This has relevance to research on shikimate dehydrogenase because it is important to maintain diversity in the enzyme blocking process in the shikimate pathway and with more research shikimate dehydrogenase could be the next enzyme to be inhibited in the shikimate pathway. In order to design new inhibitors the structures for all the enzymes in the pathway have needed to be elucidated. The presence of two forms of the enzyme complicate the design of potential drugs because one could compensate for the inhibition of the other. Also there the TIGR data base shows that there are 14 species of bacteria with the two forms of shikimate dehydrogenase. This is a problem for drug makers because there are two enzymes that a potential drug would need to inhibit at the same time.

References

Illustrations

Worked examples

Example 1 — a first encounter with Shikimate dehydrogenase

Start with the simplest possible case. Write down what Shikimate 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 Shikimate 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 Shikimate 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 Shikimate dehydrogenase

In research: Shikimate 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 Shikimate 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: Shikimate dehydrogenase is common in secondary-school and first-year university syllabi. It links to neighbouring topics EC 1.1.1, Enzymes of known structure, NADPH-dependent enzymes, so understanding it makes those chapters shorter.
In everyday life: Look for Shikimate 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.

Ask Teacher Smith questions about this articleOpens your AI tutor with a question about “Shikimate dehydrogenase” →

Affiliate

Preply — study more efficiently by working with a personal tutor. 50% off.

How to study Shikimate dehydrogenase in 20 minutes

Read the reference excerpt below once, without taking notes.
Close the page and write down what Shikimate 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.
Explain Shikimate dehydrogenase out loud to somebody else — or to Teacher Smith in the lgStudy chat.

Frequently asked questions

What is Shikimate dehydrogenase in simple terms?

In enzymology, a shikimate dehydrogenase (EC 1.1.1.25) is an enzyme that catalyzes the chemical reaction The two substrates of this enzyme are shikimate and oxidised nicotinamide adenine dinucleotide phosphate (NADP+). Its products are 3-dehydroshikimate, reduced NADPH, and a proton.

Why does Shikimate 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 Shikimate 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 Shikimate dehydrogenase.