biology

Methane monooxygenase

Methane monooxygenase 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 Methane monooxygenase rather than just read about it. In short: Methane monooxygenase (MMO) is an enzyme capable of oxidizing the C-H bond in methane as well as other alkanes. Methane monooxygenase belongs to the class of oxidoreductase enzymes (EC 1.14.13.25).The chemical formula is:C11359H17084O3246N3084S64 There are two forms of MMO: the well-studied soluble form (sMMO) and the particulate form (pMMO).

Key takeaways

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

Reference excerpt

Methane monooxygenase (MMO) is an enzyme capable of oxidizing the C-H bond in methane as well as other alkanes. Methane monooxygenase belongs to the class of oxidoreductase enzymes (EC 1.14.13.25).The chemical formula is:C11359H17084O3246N3084S64 There are two forms of MMO: the well-studied soluble form (sMMO) and the particulate form (pMMO). The active site in sMMO contains a di-iron center bridged by an oxygen atom (Fe-O-Fe), whereas the active site in pMMO utilizes copper. Structures of both proteins have been determined by X-ray crystallography; however, the location and mechanism of the active site in pMMO is still poorly understood and is an area of active research. The particulate methane monooxygenase and related ammonia monooxygenase are integral membrane proteins, occurring in methanotrophs and ammonia oxidisers, respectively, which are thought to be related. These enzymes have a relatively wide substrate specificity and can catalyse the oxidation of a range of substrates including ammonia, methane, halogenated hydrocarbons, and aromatic molecules. These enzymes are homotrimers composed of 3 subunits - A (InterPro: IPR003393), B (InterPro: IPR006833) and C (InterPro: IPR006980) and most contain two monocopper centers. The A subunit from Methylococcus capsulatus (Bath) resides primarily within the membrane and consists of 7 transmembrane helices and a beta-hairpin, which interacts with the soluble region of the B subunit. A conserved glutamate residue is thought to contribute to a metal center. Methane monooxygenases are found in methanotrophic bacteria, a class of bacteria that exist at the interface of aerobic (oxygen-containing) and anaerobic (oxygen-devoid) environments. One of the more widely studied bacteria of this type is Methylococcus capsulatus (Bath). This bacterium was discovered in the hot springs of Bath, England. Notably, strictly anaerobic methanotrophs may also harbour methane monooxygenases, although there are critical mismatches in the gene which prevent common methanotroph-seeking primers from matching.

Soluble methane monooxygenase systems Methanotrophic bacteria play an essential role of cycling carbon through anaerobic sediments. The chemistry behind the cycling takes a chemically inert hydrocarbon, methane, and converts it to a more active species, methanol. Other hydrocarbons are oxidized by MMOs, so a new hydroxylation catalyst based on the understanding of MMO systems could possibly make a more efficient use of the world supply of natural gas. This is a classic monooxygenase reaction in which two reducing equivalents from NAD(P)H are utilized to split the O-O bond of O2. One atom is reduced to water by a 2 e- reduction and the second is incorporated into the substrate to yield methanol:

CH4 + O2 + NAD(P)H + H+ → CH3OH + NAD(P)+ + H2O Two forms of MMO have been found: soluble and particulate. The best characterized forms of soluble MMO contains three protein components: hydroxylase, the β unit, and the reductase. Each of which is necessary for effective substrate hydroxylation and NADH oxidation.

Structure

X-ray crystallography of the MMO shows that it is a dimer formed of three subunits, α2β2γ2. With 2.2 A resolution, the crystallography shows that MMO is a relatively flat molecule with the dimensions of 60 x 100 x 120 A. In addition, there is a wide canyon running along the dimer interface with an opening in the center of the molecule. Most of the protomers involves helices from the α and β subunits with no participation from the γ subunit. Also, the interactions with the protomers resembles ribonucleotide reductase R2 protein dimer interaction, resembling a heart. Each iron has a six coordinate octahedral environment. The dinuclear iron centers are positioned in the α subunit. Each iron atom is also coordinated to a histidine δN atom, Fe 1 to a His 147 and Fe 2 to His 246, Fe 1 is a ligated to a monodentate carboxylate, Glu 114, a semi bridging carboxylate, Glu 144, and a water molecule. The substrate must bind near the active site in order for the reaction to take place. Near to the iron centers, there are hydrophobic pockets. It is thought that here the methane binds and is held until needed. From the X-ray crystallography, there is no direct path to these packets. However, a slight conformation change in the Phe 188 or The 213 side-chains could allow access. This conformational change could be triggered by the binding of a coupling protein and the activase. Upon reduction, one of the carboxylate ligands undergoes a “1,2 carboxylate” shift from behind a terminal monodentate ligand to a bridging ligand for the two irons, with the second oxygen coordinated to Fe 2. In the reduced form of MMOHred, the ligand environment for the Fe effectively becomes five coordinated, a form that permits the cluster to activate dioxygen. The two irons are at this point oxidized to FeIV and have changed from low-spin ferromagnetic to high-spin antiferromagnetic.

Proposed catalytic cycle and mechanism

… excerpt ends here. Continue reading the full article.

Illustrations

Methane monooxygenase: The proposed catalytic Cycle for MMO. — The proposed catalytic Cycle for MMO.

Worked examples

Example 1 — a first encounter with Methane monooxygenase

Start with the simplest possible case. Write down what Methane monooxygenase 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 Methane monooxygenase 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 Methane monooxygenase 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 Methane monooxygenase

In research: Methane monooxygenase 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 Methane monooxygenase 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: Methane monooxygenase is common in secondary-school and first-year university syllabi. It links to neighbouring topics Copper enzymes, EC 1.14.13, Enzymes, so understanding it makes those chapters shorter.
In everyday life: Look for Methane monooxygenase 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 Methane monooxygenase in 20 minutes

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

Frequently asked questions

What is Methane monooxygenase in simple terms?

Why does Methane monooxygenase 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 Methane monooxygenase?

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 Methane monooxygenase.