[Chemistry Class Notes] on Urease Pdf for Exam

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.

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.