biology

Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase

Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase rather than just read about it. In short: Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) is an enzyme that catalyzes the chemical reaction nicotinate mononucleotide + 5,6-dimethylbenzimidazole ⇌ {\displaystyle \rightleftharpoons } nicotinic acid + α-ribazole 5'-phosphate The reaction is part of the biosynthesis of cobalamin (a form of vitamin B12) in bacteria. This enzyme is a glycosyltransferase, specifically a pentosyl…

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Reference excerpt

Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) is an enzyme that catalyzes the chemical reaction

nicotinate mononucleotide + 5,6-dimethylbenzimidazole ⇌ {\displaystyle \rightleftharpoons } nicotinic acid + α-ribazole 5'-phosphate The reaction is part of the biosynthesis of cobalamin (a form of vitamin B12) in bacteria. This enzyme is a glycosyltransferase, specifically a pentosyltransferase. The systematic name of this enzyme class is nicotinate-nucleotide:5,6-dimethylbenzimidazole phospho-D-ribosyltransferase. Other names in common use include CobT, nicotinate mononucleotide-dimethylbenzimidazole phosphoribosyltransferase, nicotinate ribonucleotide:benzimidazole (adenine) phosphoribosyltransferase, nicotinate-nucleotide:dimethylbenzimidazole phospho-D-ribosyltransferase, and nicotinate mononucleotide (NaMN):5,6-dimethylbenzimidazole phosphoribosyltransferase.

Function This enzyme plays a central role in the synthesis of α-ribazole 5'-phosphate, an intermediate for the lower ligand of cobalamin. It is one of the enzymes in the anaerobic pathway of cobalamin biosynthesis, and one of the four proteins (CobU, CobT, CobC, and CobS) involved in the synthesis of the lower ligand and the assembly of the nucleotide loop. The reaction replaces the nicotinic acid group in nicotinate mononucleotide by reaction with 5,6-dimethylbenzimidazole (5,6-DMB), with inversion of stereochemistry.

Biosynthesis of cobalamin

Vitamin B12 (cobalamin) is used as a cofactor in a number of enzyme-catalysed reactions in bacteria, archaea and eukaryotes. The biosynthetic pathway to adenosylcobalamin from its five-carbon precursor, 5-aminolaevulinic acid, can be divided into three sections: (1) the biosynthesis of uroporphyrinogen III from 5-aminolaevulinic acid; (2) the conversion of uroporphyrinogen III into the ring-contracted, deacylated intermediate precorrin 6 or cobalt-precorrin 6; and (3) the transformation of this intermediate to form adenosylcobalamin. Cobalamin is synthesised by bacteria and archaea via two alternative routes that differ primarily in the steps of section 2 that lead to the contraction of the macrocycle and excision of the extruded carbon molecule (and its attached methyl group). One pathway (exemplified by Pseudomonas denitrificans) incorporates molecular oxygen into the macrocycle as a prerequisite to ring contraction, and has consequently been termed the aerobic pathway. The alternative, anaerobic, route (exemplified by Salmonella typhimurium) takes advantage of a chelated cobalt ion, in the absence of oxygen, to set the stage for ring contraction.

Structural studies As of late 2007, 28 structures have been solved for this class of enzymes, with PDB accession codes PDB: 1D0S, PDB: 1D0V, PDB: 1JH8, PDB: 1JHA, PDB: 1JHM, PDB: 1JHP, PDB: 1JHQ, PDB: 1JHR, PDB: 1JHU, PDB: 1JHV, PDB: 1JHX, PDB: 1JHY, PDB: 1L4B, PDB: 1L4E, PDB: 1L4F, PDB: 1L4G, PDB: 1L4H, PDB: 1L4K, PDB: 1L4L, PDB: 1L4M, PDB: 1L4N, PDB: 1L5F, PDB: 1L5K, PDB: 1L5L, PDB: 1L5M, PDB: 1L5N, PDB: 1L5O, and PDB: 1WX1.

References

Illustrations

Worked examples

Example 1 — a first encounter with Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase

Start with the simplest possible case. Write down what Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase

In research: Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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: Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase is common in secondary-school and first-year university syllabi. It links to neighbouring topics EC 2.4.2, Enzymes of known structure, Protein domains, so understanding it makes those chapters shorter.
In everyday life: Look for Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase in simple terms?

Nicotinate-nucleotide-dimethylbenzimidazole phosphoribosyltransferase (EC 2.4.2.21) is an enzyme that catalyzes the chemical reaction nicotinate mononucleotide + 5,6-dimethylbenzimidazole ⇌ {\displaystyle \rightleftharpoons } nicotinic acid + α-ribazole 5'-phosphate The reaction is part of the bios…

Why does Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase 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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase?

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 Nicotinate-nucleotide—dimethylbenzimidazole phosphoribosyltransferase.