biology

Protein-arginine deiminase

Protein-arginine deiminase is a biology 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 Protein-arginine deiminase rather than just read about it. In short: In enzymology, a protein-arginine deiminase (PAD) (EC 3.5.3.15) is an enzyme that catalyzes a form of post translational modification called arginine de-imination or citrullination: protein L-arginine + H2O ⇌ {\displaystyle \rightleftharpoons } protein L-citrulline + NH3 Thus, the two substrates of this enzyme are protein L-arginine (arginine residue inside a protein) and H2O, whereas its two products are protein L…

Key takeaways

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Reference excerpt

In enzymology, a protein-arginine deiminase (PAD) (EC 3.5.3.15) is an enzyme that catalyzes a form of post translational modification called arginine de-imination or citrullination:

protein L-arginine + H2O ⇌ {\displaystyle \rightleftharpoons } protein L-citrulline + NH3 Thus, the two substrates of this enzyme are protein L-arginine (arginine residue inside a protein) and H2O, whereas its two products are protein L-citrulline and NH3:

This enzyme belongs to the family of hydrolases, those acting on carbon-nitrogen bonds other than peptide bonds, specifically in linear amidines. The systematic name of this enzyme class is protein-L-arginine iminohydrolase. This enzyme is also called peptidylarginine deiminase.

Structural studies As of late 2007, seven structures have been solved for this class of enzymes, with PDB accession codes PDB: 1WD8, PDB: 1WD9, PDB: 1WDA, PDB: 2DEW, PDB: 2DEX, PDB: 2DEY, and PDB: 2DW5.

Mammalian proteins Mammals have 5 protein-arginine deiminases, with symbols

PADI1, PADI2, PADI3, PADI4, PADI6 except for rodents, there the letter case is different:

Padi1, Padi2, Padi3, Padi4, Padi6 The different case is just a historical artifact. It doesn't indicate that the rodent proteins are special.

Inhibitors Irreversible inhibitors

Cl-amidine, BB-Cl-Amidine, YW3-56 Reversible inhibitors

GSK484, GSK199

References

Fujisaki M, Sugawara K (January 1981). "Properties of peptidylarginine deiminase from the epidermis of newborn rats". J. Biochem. 89 (1). Tokyo: 257–63. doi:10.1093/oxfordjournals.jbchem.a133189. PMID 7217033. protein-arginine+deiminase at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

Illustrations

Worked examples

Example 1 — a first encounter with Protein-arginine deiminase

Start with the simplest possible case. Write down what Protein-arginine deiminase claims or describes in one sentence, then invent the smallest concrete situation in which that sentence is true. In biology, 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 Protein-arginine deiminase 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 Protein-arginine deiminase 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 Protein-arginine deiminase

In research: Protein-arginine deiminase appears in biology 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 Protein-arginine deiminase 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: Protein-arginine deiminase is common in secondary-school and first-year university syllabi. It links to neighbouring topics EC 3.5.3, EC 3.5 stubs, Enzymes of known structure, so understanding it makes those chapters shorter.
In everyday life: Look for Protein-arginine deiminase 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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Frequently asked questions

What is Protein-arginine deiminase in simple terms?

In enzymology, a protein-arginine deiminase (PAD) (EC 3.5.3.15) is an enzyme that catalyzes a form of post translational modification called arginine de-imination or citrullination: protein L-arginine + H2O ⇌ {\displaystyle \rightleftharpoons } protein L-citrulline + NH3 Thus, the two substrates of…

Why does Protein-arginine deiminase matter?

Because it connects several biology 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 Protein-arginine deiminase?

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?

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