How Does Urease Work? Mechanism and Key Applications
Urease is an enzyme that catalyzes urea hydrolysis, forming carbon dioxide and ammonia. It is found in large quantities in soybeans, jack beans, and other plant seeds and also occurs in intestinal microorganisms and some animal tissues. In the history of enzymology, urease enzyme is significant as the first enzyme to be purified and crystallized (in 1926, by James B. Sumner). This achievement has laid the groundwork for the subsequent demonstration, in which urease and other enzymes are proteins.
Structure
Focusing on urease enzyme, a study by jack bean in 1984 found that the active site contains a pair of nickel centers. Also, in vitro activation, it has been achieved with cobalt and manganese in place of nickel. The salts of lead are inhibiting.
The molecular weight is given as either 480 or 545 kDa for jack-bean urease (it is the calculated mass from the amino acid sequence)—840 amino acids per one molecule, where 90 are cysteine residues.
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The optimum pH is given as 7.4, and the optimum temperature is given as 60 °C. Substrates include hydroxyurea and urea.
Bacterial ureases can be composed of three distinct subunits, one large (α 60–76kDa) and the two small (β 8–21 kDa, γ 6–14 kDa), which are commonly forming (αβγ)3 trimers stoichiometry with a 2-fold symmetric structure (note that the above-given image is the structure of an asymmetric unit, one-third of true biological assembly), they are the cysteine-rich enzymes by resulting in the enzyme molar masses between 190 kDa and 300 kDa.
An exceptional urease enzyme can be obtained from the Helicobacter sp. These may be composed of two subunits, which are α(26–31 kDa) and β(61–66 kDa). These particular subunits form a supramolecular dodecameric complex. By repeating the α-β subunits, every coupled pair of subunits holds an active site, for a total of 12 active sites 12 12.
It plays an important function for survival, neutralizing gastric acid by allowing urea to enter into periplasm through a proton-gated urea channel. The urease presence can be used in the Helicobacter species diagnosis.
Active State
The ureases’ active site is located in the α (alpha) subunits and is a bis-μ-hydroxo dimeric nickel center, with an interatomic distance of ~3.5 Å.[5] > The pair of Ni (II) are coupled weakly antiferromagnetically. The X-ray absorption spectroscopy (i.e., XAS) studies of Canavalia ensiformis (by jack bean), Sporosarcina pasteurii (formerly known as Bacillus pasteurii), and Klebsiella aerogene confirm the 5–6 coordinate nickel ions with exclusively O/N ligation, with two imidazole ligands per nickel. Urea substrate may be proposed to displace the aquo ligands.
Water molecules that are located towards the active site opening form a tetrahedral cluster, which fills the cavity site via hydrogen bonds. A few amino acid residues are proposed to produce the site’s mobile flap, which gates for the substrate. In the flap region of the enzymes, cysteine residues are common, which have been determined not to be important in catalysis, although it is involved in positioning the other key residues in the active site nearly.
Proposed Mechanisms
Let us look at some of the proposed mechanisms.
Hausinger/Karplus
This mechanism was proposed by Karplus and Hausinger, attempting to revise a few issues apparent in the Zerner and Blakely pathway and focuses on the side chain’s positions making up the urea-binding pocket. aerogenes urease enzyme, from the crystal structures from K, it was argued that the general base that is used in the Blakely mechanism (His320) was too far away, which is from the Ni2-bound water to deprotonate to form the attacking hydroxide moiety. Additionally, the general acidic ligand needed to protonate the urea nitrogen was not identified.
Ciurli or Mangani
This mechanism is proposed by Mangani and Ciurli, which is one of the more recent and currently accepted views of the mechanism of urease. It is primarily based on the various roles of the two nickel ions in the active site. One of which binds and activates the area, whereas the other nickel ion binds and activates nucleophilic water molecule. With greater regards to this proposal, urea enters into the active site cavity when the mobile ‘flap’ (that allows for the urea entrance into the active site) is open. The stability of urea binding to the active site can be achieved through a hydrogen-bonding network by orienting the substrate into the catalytic cavity.
Occurrence
Naturally, urea is found in the environment and also introduced artificially, comprising more than half of all the synthetic nitrogen fertilizers that are used globally. Heavy urea use is thought to promote eutrophication, despite any observation that urea is transformed rapidly by microbial ureases, and therefore generally does not persist. Often, the environmental urease activity can be measured as an indicator of the microbial health communities.
Applications
Agricultural Applications
Generally, in the absence of plants, urease activity in soil is attributed to the heterotrophic microorganisms, although it has been described that a few chemoautotrophic ammonium oxidizing bacteria are capable of urea growth as a sole source of nitrogen, carbon, and energy.
FAQs on Urease: Definition, Structure & Importance
1. What is the urease enzyme and what is its primary function?
Urease is a metalloenzyme containing nickel that catalyses the hydrolysis of urea into ammonia and carbon dioxide. Its primary function is to break down urea, a nitrogen-containing compound. This reaction is crucial for many organisms, including bacteria, fungi, and plants, as it provides a usable source of nitrogen. The overall chemical reaction is: (NH₂)₂CO + H₂O → 2NH₃ + CO₂.
2. What is the basic structure of the urease enzyme?
The structure of urease is complex as it is a protein, typically consisting of multiple identical subunits. The most critical part of its structure is the active site, which contains two nickel (Ni²⁺) ions. These nickel ions are essential for the enzyme's catalytic activity, as they bind to the urea molecule and help activate it for the chemical reaction.
3. What is the chemical reaction catalysed by urease?
The urease enzyme catalyses the hydrolysis of urea, converting it into ammonia and carbon dioxide. This reaction significantly increases the pH of the surrounding environment due to the production of ammonia, a weak base. The balanced chemical equation for this process is:
(NH₂)₂CO + H₂O → CO₂ + 2NH₃.
4. How can urease activity be harmful to humans?
While the enzyme itself is not toxic, its activity can be harmful in certain medical conditions. For example, in urinary tract infections (UTIs) caused by urease-producing bacteria like Proteus mirabilis, the enzyme breaks down urea in urine into ammonia. This raises the urinary pH, causing minerals to precipitate and form infection stones (struvite stones), which can lead to kidney damage and blockages.
5. What is the role of urease in Helicobacter pylori infections?
Helicobacter pylori (H. pylori) uses the urease enzyme as a key survival tool to colonise the highly acidic environment of the stomach. The enzyme generates ammonia from urea, which neutralises the surrounding stomach acid. This creates a more hospitable microenvironment, allowing the bacterium to survive and cause conditions like gastritis and peptic ulcers. A urease breath test is a common method for diagnosing an H. pylori infection.
6. Why doesn't the urease enzyme have a simple chemical formula like water (H₂O)?
Urease does not have a simple chemical formula because it is a protein—a complex macromolecule made of hundreds of amino acids folded into a specific 3D shape. Its identity and function are determined by this complex structure, not a simple ratio of atoms. While we know its elemental composition, it is scientifically described by its amino acid sequence and structural models, not a chemical formula like simple compounds.
7. What is urease inhibition and why is it important in agriculture?
Urease inhibition is the process of using chemicals to block the enzyme's activity. This is very important in agriculture where urea is a common nitrogen fertiliser. When applied to soil, urease from soil microbes can rapidly convert urea to ammonia gas, which is then lost to the atmosphere (a process called ammonia volatilisation). Urease inhibitors are added to fertilisers to slow this process, ensuring more nitrogen stays in the soil for plants to absorb, thus increasing fertiliser efficiency and reducing environmental impact.
8. How do the nickel ions in the urease active site help break down urea?
The two nickel ions in the urease active site work together in a mechanism to catalyse the hydrolysis of urea. A simplified explanation is as follows:
- One nickel ion acts as a Lewis acid, binding to the carbonyl oxygen of the urea molecule, making it more susceptible to attack.
- The other nickel ion activates a water molecule, effectively making it a stronger nucleophile (a hydroxide ion).
- This activated hydroxide ion then attacks the carbonyl carbon of the urea.
This coordinated action by the two nickel ions efficiently breaks the C-N bonds in urea, releasing ammonia and carbamate, which then decomposes into more ammonia and carbon dioxide.
