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		<title>en&gt;OdedSchramm: capitalization</title>
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		<summary type="html">&lt;p&gt;capitalization&lt;/p&gt;
&lt;p&gt;&lt;b&gt;New page&lt;/b&gt;&lt;/p&gt;&lt;div&gt;{{Infobox enzyme&lt;br /&gt;
| Name = Urease&lt;br /&gt;
| EC_number = 3.5.1.5&lt;br /&gt;
| CAS_number = 9002-13-5&lt;br /&gt;
| IUBMB_EC_number = 3/5/1/5&lt;br /&gt;
| GO_code = &lt;br /&gt;
| image = Urease-1E9Z.jpg&lt;br /&gt;
| width = &lt;br /&gt;
| caption = &amp;#039;&amp;#039;Helicobacter pylori&amp;#039;&amp;#039; Urease drawn from {{PDB|1E9Z}}.&lt;br /&gt;
}}&lt;br /&gt;
&amp;#039;&amp;#039;&amp;#039;Ureases&amp;#039;&amp;#039;&amp;#039; ({{EC number|3.5.1.5}}), functionally, belong to the [[Protein family|superfamily]] of [[amidohydrolases]] and phosphotriestreases.&amp;lt;ref&amp;gt;L. Holm, C. Sander, Proteins 28 (1997) 72–82.&amp;lt;/ref&amp;gt; It is an [[enzyme]] that [[catalysis|catalyzes]] the [[hydrolysis]] of [[urea]] into [[carbon dioxide]] and [[ammonia]]. &lt;br /&gt;
The reaction occurs as follows:                  &lt;br /&gt;
: &amp;lt;big&amp;gt;[[Urea|(NH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;)&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;CO]] + [[Water|H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O]] → [[carbon dioxide|CO&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;]] + 2[[ammonia|NH&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;]]&amp;lt;/big&amp;gt;&lt;br /&gt;
&lt;br /&gt;
More specifically, urease catalyzes the hydrolysis of [[urea]] to produce [[ammonia]] and [[carbamate]], the [[carbamate]] produced is subsequently degraded by spontaneous hydrolysis to produce another [[ammonia]] and [[carbonic acid]].&amp;lt;ref name=&amp;quot;Zimmer&amp;quot;&amp;gt;{{cite journal|last=Zimmer|first=Marc|date=Apr 2000|title=Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease|journal=J Biomol Struct Dyn.|volume=17|issue=5|pages=787–97|doi=10.1080/07391102.2000.10506568|pmid=10798524|url=http://www.tandfonline.com/doi/abs/10.1080/07391102.2000.10506568|accessdate=2013-04-29}}&amp;lt;/ref&amp;gt; Urease activity tends to increase the [[pH]] of the environment in which it is as it produces ammonia, as it is a basic molecule. Ureases are found in numerous [[bacteria]], [[fungi]], [[algae]], plants and some [[invertebrates]], as well as in soils, as a soil enzyme. They are nickel-containing [[metalloenzymes]] of high molecular weight.&amp;lt;ref name=&amp;quot;Krajewska&amp;quot;&amp;gt;{{cite journal|last=Krajewska|first=Barbara|coauthors=Eldik, Rudi; Brindell, Małgorzata|title=Temperature- and pressure-dependent stopped-flow kinetic studies of jack bean urease. Implications for the catalytic mechanism|journal=JBIC Journal of Biological Inorganic Chemistry|date=13 August 2012|volume=17|issue=7|pages=1123–1134|doi=10.1007/s00775-012-0926-8|pmid=22890689|pmc=3442171}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
In 1926, [[James B. Sumner]], an assistant professor at [[Cornell University]], showed that urease is a [[protein]] by examining its crystallized form.&amp;lt;ref name=&amp;quot;karplus&amp;quot;&amp;gt;Karplus, P. A., Pearson, M. A., &amp;amp; Hausinger, R. P. (1997). 70 years of crystalline urease: What have we learned? Accounts of Chemical Research, 30(8), 330-337&amp;lt;/ref&amp;gt; Sumner&amp;#039;s work was the first demonstration that a pure [[protein]] can function as an [[enzyme]], and led eventually to the recognition that most enzymes are in fact proteins, and the award of the [[Nobel prize in chemistry]] to Sumner in 1946.&amp;lt;ref&amp;gt;[http://www.nobelprize.org/nobel_prizes/chemistry/laureates/1946/sumner-bio.html The Nobel Prize in Chemistry 1946]&amp;lt;/ref&amp;gt; The structure of urease was first solved by P. A. Karplus in 1995. Urease was the first ever enzyme crystallized.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Characteristics==&lt;br /&gt;
* [[Active site]] requiring [[nickel]] in jack-beans and several bacteria.&amp;lt;ref&amp;gt;[http://www.ncbi.nlm.nih.gov/m/pubmed/6398286/ nickel in biology]&amp;lt;/ref&amp;gt; However, [[in vitro]] activation also has been achieved with [[manganese]] and [[cobalt]]&amp;lt;ref name=&amp;quot;pmid20046957&amp;quot;&amp;gt;{{cite journal|last=Carter|first=Eric L.|coauthors=Flugga, Nicholas; Boer, Jodi L.; Mulrooney, Scott B.; Hausinger, Robert P.|title=Interplay of metal ions and urease|journal=Metallomics|date=1 January 2009|volume=1|issue=3|pages=207–21|doi=10.1039/b903311d|pmid=20046957|pmc=2745169}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
* [[Molecular weight]]: 480 [[Atomic mass unit|kDa]] or 545 [[Atomic mass unit|kDa]] for [[Canavalia ensiformis|jack- bean]] Urease (calculated mass from the amino acid sequence). 840 amino acids per molecule, of which 90 are cysteines.&amp;lt;ref name=&amp;quot;Molecular Catalysis B 2009&amp;quot;&amp;gt;{{cite journal|last=Krajewska|first=Barbara|title=Ureases I. Functional, catalytic and kinetic properties: A review|journal=Journal of Molecular Catalysis B: Enzymatic|date=30 June 2009|volume=59|issue=1–3|pages=9–21|doi=10.1016/j.molcatb.2009.01.003}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
* Optimum [[pH]]: 7.4&lt;br /&gt;
* Optimum Temperature: 60 degrees Celsius&lt;br /&gt;
* Enzymatic specificity: urea and [[hydroxyurea]]&lt;br /&gt;
* [[Enzyme inhibitor|Inhibitor]]s: [[heavy metals]] (Pb&amp;lt;sup&amp;gt;-&amp;lt;/sup&amp;gt; &amp;amp; Pb&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt;)&lt;br /&gt;
&lt;br /&gt;
Bacterial ureases are composed of three distinct subunits, one large (α 60–76kDa) and two small (β 8–21 kDa, γ 6–14 kDa) commonly forming (αβγ)3 trimers [[stoichiometry]] with a 2-fold symmetric structure (note that the image above gives the structure of the asymmetric unit, one-third of the true biological assembly), they are cysteine-rich enzymes, resulting in the enzyme molar masses between 190 and 300kDa.&amp;lt;ref name=&amp;quot;Molecular Catalysis B 2009&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
An exceptional enzyme is the urease of Helicobacter species, which is composed of two subunits, α(61–66 kDa)-β(26–31 kDa), and has been shown to form a supramolecular [[dodecameric]] complex.&amp;lt;ref name=&amp;quot;pmid11373617&amp;quot;&amp;gt;{{cite journal|last=Ha|first=Nam-Chul|coauthors=Oh, Sang-Taek; Sung, Jae Young; Cha, Kyeung Ah; Lee, Mann Hyung; Oh, Byung-Ha|title=Supramolecular assembly and acid resistance of Helicobacter pylori urease|journal=Nature Structural Biology|date=31 May 2001|volume=8|issue=6|pages=505–509|doi=10.1038/88563|pmid=11373617}}&amp;lt;/ref&amp;gt; of repeating α-β subunits, each coupled pair of subunits has an active site, for a total of 12 active sites.&amp;lt;ref name=&amp;quot;pmid11373617&amp;quot; /&amp;gt; (&amp;lt;math&amp;gt;\alpha_{12}\beta_{12}&amp;lt;/math&amp;gt;). It plays an essential function for survival, neutralizing [[gastric acid]] by allowing [[urea]] to enter into [[periplasm]] via a [[proton-gated urea channel]].&amp;lt;ref name=&amp;quot;pmid23222544&amp;quot;&amp;gt;{{cite journal|last=Strugatsky|first=David|coauthors=McNulty, Reginald; Munson, Keith; Chen, Chiung-Kuang; Soltis, S. Michael; Sachs, George; Luecke, Hartmut|title=Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori|journal=Nature|date=8 December 2012|volume=493|issue=7431|pages=255–258|doi=10.1038/nature11684|pmid=23222544}}&amp;lt;/ref&amp;gt; The presence of urease is used in the diagnosis of &amp;#039;&amp;#039;[[Helicobacter]]&amp;#039;&amp;#039; species.&lt;br /&gt;
&lt;br /&gt;
All bacterial ureases are solely cytoplasmic, except for Helicobacter pylori urease, which along with its cytoplasmic activity, has external activity with host cells. In contrast, all plant ureases are cytoplasmic.&amp;lt;ref name=&amp;quot;Molecular Catalysis B 2009&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
Fungal and plant ureases are made up of identical subunits (~90 kDa each), most commonly assembled as trimers and hexamers. For example, [[Jack Bean]] urease has two structural and one catalytic subunit. The α subunit contains the active site, it is composed of 840 amino acids per molecule (90 cysteines), its molecular mass without Ni(II) ions amounting to 90.77 kDa. The mass of the [[hexamer]] with the 12 nickel ions is 545.34 kDa. It is structurally related to the (αβγ)3 trimer of bacterial ureases. Other examples of homohexameric structures of plant ureases are those of soybean, pigeon pea and cotton seeds enzymes.&amp;lt;ref name=&amp;quot;Molecular Catalysis B 2009&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is important to note, that although composed of different types of subunits, ureases from different sources extending from bacteria to plants and fungi exhibit high homology of amino acid sequences.&amp;lt;ref name=&amp;quot;Molecular Catalysis B 2009&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Active site==&lt;br /&gt;
&lt;br /&gt;
The [[active site]] of all ureases known are located in the α (alpha) [[Protein subunit|subunits]]. It is a bis-μ-hydroxo [[Protein dimer|dimeric]] [[nickel]] center, with an interatomic distance of ~3.5 Å,&amp;lt;ref name=&amp;quot;karplus&amp;quot; /&amp;gt; [[magnetic susceptibility]] experiments have indicated that, in jack bean urease, [[high spin]] octahedrally coordinated Ni(II) ions are weakly [[Antiferromagnetism|antiferromagnetically]] coupled.&amp;lt;ref&amp;gt;Coordination Chemistry Reviews 190–192 (1999) 331–355&amp;lt;/ref&amp;gt; The nickel ions bridged by a carbamylated lysine through its O-atoms and by a [[hydroxide]] ion. Ni(1) is [[coordinated]] by N-atoms of histidines residues and one water molecule, is it said to be pseudo square pyramidal. Ni(2) is coordinated by two histidines also through N-atoms and additionally by aspartic acid through its O- atom and two water molecules.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot; /&amp;gt;&lt;br /&gt;
[[X-ray absorption spectroscopy]] (XAS) studies of &amp;#039;&amp;#039;[[Canavalia ensiformis]]&amp;#039;&amp;#039;  (jack bean), &amp;#039;&amp;#039;Klebsiella aerogenes&amp;#039;&amp;#039;  and &amp;#039;&amp;#039;[[Sporosarcina pasteurii]]&amp;#039;&amp;#039; (formerly known as &amp;#039;&amp;#039;Bacillus pasteurii&amp;#039;&amp;#039;)&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt; confirm 5–6 coordinate nickel ions with exclusively O/N ligands (two [[imidazoles]] per nickel).&amp;lt;ref name=&amp;quot;pmid20046957&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
The water molecules are located towards the opening of the active site and form a tetrahedral cluster that fills the cavity site through [[hydrogen bonds]], and it&amp;#039;s here where [[urea]] binds to the active site for the reaction, displacing the water molecules. The amino acid residues participate in the substrate binding, mainly through hydrogen bonding, stabilize the catalytic [[transition state]] and accelerate the reaction. Additionally, the amino acid residues involved in the architecture of the [[active site]] compose part of the mobile flap of the site, which is said to act as a gate for the substrate.&amp;lt;ref name=&amp;quot;Krajewska&amp;quot; /&amp;gt; Cysteine residues are common in the flap region of the enzymes, which have been determined not to be essential in catalysis, although involved in positioning other key residues in the active site appropriately.&amp;lt;ref name=&amp;quot;Martin&amp;quot;&amp;gt;{{cite journal|last=Martin|first=PR|coauthors=Hausinger, RP|title=Site-directed mutagenesis of the active site cysteine in &amp;#039;&amp;#039;Klebsiella aerogenes&amp;#039;&amp;#039; urease|journal=The Journal of biological chemistry|date=Oct 5, 1992|volume=267|issue=28|pages=20024–7|pmid=1400317}}&amp;lt;/ref&amp;gt; In the structure of &amp;#039;&amp;#039;[[Sporosarcina pasteurii]]&amp;#039;&amp;#039; urease the flap was found in the open conformation, while its closed conformation is apparently needed for the reaction.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;&amp;gt;{{cite journal|last=Benini|first=Stefano|coauthors=Rypniewski, Wojciech R; Wilson, Keith S; Miletti, Silvia; Ciurli, Stefano; Mangani, Stefano|title=A new proposal for urease mechanism based on the crystal structures of the native and inhibited enzyme from Bacillus pasteurii: why urea hydrolysis costs two nickels|journal=Structure|date=31 January 1999|volume=7|issue=2|pages=205–216|doi=10.1016/S0969-2126(99)80026-4|pmid=10368287}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
When compared, the α subunits of &amp;#039;&amp;#039;[[Helicobacter pylori]]&amp;#039;&amp;#039; urease and other bacterial ureases align with the jack bean ureases, suggesting that all ureases are evolutionary variants of one [[ancestral]] enzyme.&amp;lt;ref name=&amp;quot;Martin&amp;quot; /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
It is important to note that the coordination of urea to the active site of urease has never been observed in a resting state of the enzyme.&amp;lt;ref name=&amp;quot;Molecular Catalysis B 2009&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Urease Activity==&lt;br /&gt;
&lt;br /&gt;
The &amp;#039;&amp;#039;k&amp;#039;&amp;#039;&amp;lt;sub&amp;gt;cat&amp;lt;/sub&amp;gt;/&amp;#039;&amp;#039;K&amp;#039;&amp;#039;&amp;lt;sub&amp;gt;m&amp;lt;/sub&amp;gt; of urease in the processing of [[urea]] is 10&amp;lt;sup&amp;gt;14&amp;lt;/sup&amp;gt; times greater than the rate of the uncatalyzed elimination reaction of [[urea]].&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt; There are many reasons for this observation in nature. The proximity of [[urea]] to active groups in the active site along with the correct orientation of urea allow [[hydrolysis]] to occur rapidly. [[Urea]] alone is very stable due to the resonance forms it can adopt. The stability of urea is understood to be due to its [[resonance]] energy, which has been estimated at 30-40 kcal/mol.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt; This is because the [[zwitterionic]] resonance forms all donate electrons to the [[carbonyl]] carbon making it less of an [[electrophile]] making it less reactive to nucleophilic attack.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Proposed  Mechanisms of Urease==&lt;br /&gt;
&lt;br /&gt;
&amp;#039;&amp;#039;&amp;#039;&amp;lt;big&amp;gt;The Blakeley/Zerner Proposed Mechanism&amp;lt;/big&amp;gt;&amp;#039;&amp;#039;&amp;#039;&lt;br /&gt;
&lt;br /&gt;
One mechanism for the catalysis of this reaction by urease was proposed by Blakely and Zerner.&amp;lt;ref name=&amp;quot;pmid6788353&amp;quot;&amp;gt;{{cite journal|last=Dixon|first=NE|coauthors=Riddles PW, Blakeley RL, Zerner B|title=Jack Jack Bean Urease (EC3.5.1.5). V. On the Mechanism of action of urease on urea, formamide, acetamide,N-methylurea, and related compounds|journal=Canadian Journal of Biochemistry|year=1979|volume=58|issue=12|pages=1335–1344|pmid=6788353|doi=10.1139/o80-181}}&amp;lt;/ref&amp;gt; It begins with a nucleophilic attack by the [[carbonyl]] oxygen of the [[urea]] molecule onto the 5-coordinate Ni (Ni-1). A weakly coordinated water ligand is displaced in its place. A lone pair of electrons from one of the nitrogen atoms on the [[Urea]] molecule creates a double bond with the central carbon, and the resulting NH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;&amp;lt;sup&amp;gt;+&amp;lt;/sup&amp;gt; of the coordinated substrate interacts with a nearby negatively charged group. Blakeley and Zerner proposed this nearby group to be a [[Carboxylate|Carboxylate ion]]&lt;br /&gt;
&lt;br /&gt;
A hydroxide ligand on the six coordinate Ni is deprotonated by a base. The carbonyl carbon is subsequently attacked by the electronegative oxygen. A pair of electrons from the nitrogen-carbon double bond returns to the nitrogen and neutralizes the charge on it, while the now 4-coordinate carbon assumes an intermediate tetrahedral orientation.&lt;br /&gt;
&lt;br /&gt;
The breakdown of this intermediate is then helped by a sulfhydryl group of a [[cysteine]] located near the active site. A hydrogen bonds to one of the nitrogen atoms, breaking its bond with carbon, and releasing an NH3 molecule.  Simultaneously, the bond between the oxygen and the 6-coordinate nickel is broken. This leaves a carbamate ion coordinated to the 5-coordinate Ni, which is then displaced by a water molecule, regenerating the enzyme.&lt;br /&gt;
&lt;br /&gt;
The [[carbamate]] produced then sponaneously degrades to produce another ammonia and [[carbonic acid]].&amp;lt;ref name=&amp;quot;Zimmer&amp;quot;&amp;gt;Zimmer, M. (2000). Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease. Journal of Biomolecular Structure and Dynamics, 17(5), 787-797&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;#039;&amp;#039;&amp;#039;&amp;lt;big&amp;gt;The Hausinger/Karplus Proposed Mechanism&amp;lt;/big&amp;gt;&amp;#039;&amp;#039;&amp;#039;&lt;br /&gt;
&lt;br /&gt;
The mechanism proposed by Hausinger and Karplus attempts to revise some of the issues apparent in the Blakely and Zerner pathway, and focuses on the positions of the side chains making up the urea-binding pocket.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;  From the crystal structures from K. aerogenes urease, it was argued that the general base used in the Blakely mechanism, His&amp;lt;sup&amp;gt;320&amp;lt;/sup&amp;gt;, was too far away from the Ni2-bound water to deprotonate in order to form the attacking hydroxide moiety.  In addition, the general acidic ligand required to protonate the urea nitrogen was not identified.&amp;lt;ref name=&amp;quot;Jabri&amp;quot;&amp;gt;{{cite journal|last=Jabri|first=E|coauthors=Carr, MB; Hausinger, RP; Karplus, PA|title=The crystal structure of urease from Klebsiella aerogenes|journal=Science|date=May 19, 1995|volume=268|issue=5213|pages=998–1004|pmid=7754395|doi=10.1126/science.7754395}}&amp;lt;/ref&amp;gt; Hausinger and Karplus suggests a reverse protonation scheme, where a protonated form of the His&amp;lt;sup&amp;gt;320&amp;lt;/sup&amp;gt; ligand plays the role of the general acid and the Ni2-bound water is already in the deprotonated state.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;  The mechanism follows the same path, with the general base omitted (as there is no more need for it) and His&amp;lt;sup&amp;gt;320&amp;lt;/sup&amp;gt; donating its proton to form the ammonia molecule, which is then released from the enzyme.  While the majority of the His&amp;lt;sup&amp;gt;320&amp;lt;/sup&amp;gt; ligands and bound water will not be in their active forms (protonated and deprotonated, respectively,) it was calculated that approximately 0.3% of total urease enzyme would be active at any one time.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;  While logically, this would imply that the enzyme is not very efficient, contrary to established knowledge, usage of the reverse protonation scheme provides an advantage in increased reactivity for the active form, balancing out the disadvantage.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;  Placing the His&amp;lt;sup&amp;gt;320&amp;lt;/sup&amp;gt; ligand as an essential component in the mechanism also takes into account the mobile flap region of the enzyme.  As this histidine ligand is part of the mobile flap, binding of the urea substrate for catalysis closes this flap over the active site and with the addition of the hydrogen bonding pattern to urea from other ligands in the pocket, speaks to the selectivity of the urease enzyme for urea.&amp;lt;ref name=&amp;quot;karplus&amp;quot;/&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;#039;&amp;#039;&amp;#039;&amp;lt;big&amp;gt;The Ciurli/Mangani Proposed Mechanism&amp;lt;/big&amp;gt;&amp;#039;&amp;#039;&amp;#039;&lt;br /&gt;
&lt;br /&gt;
The mechanism proposed by Ciurli and Mangani&amp;lt;ref name=&amp;quot;pmid21542631&amp;quot;&amp;gt;{{cite journal|last=Zambelli|first=Barbara|coauthors=Musiani, Francesco; Benini, Stefano; Ciurli, Stefano|title=Chemistry of Ni2+ in Urease: Sensing, Trafficking, and Catalysis|journal=Accounts of Chemical Research|date=19 July 2011|volume=44|issue=7|pages=520–530|doi=10.1021/ar200041k|pmid=21542631}}&amp;lt;/ref&amp;gt; is one of the more recent and currently accepted views of the mechanism of urease and is based primarily on the different roles of the two [[nickel]] ions in the active site.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot; /&amp;gt; One of which binds and activates urea, the other nickel ion binds and activates the nucleophilic water molecule.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt;  With regards to this proposal, urea enters the active site cavity when the mobile ‘flap’ (which allows for the entrance of urea into the active site) is open. Stability of the binding of urea to the active site is achieved via a [[hydrogen-bonding]] network, orienting the substrate into the catalytic cavity.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt;  Urea binds to the five-coordinated nickel (Ni1) with the carbonyl [[oxygen]] atom. It approaches the six-coordinated nickel (Ni2) with one of its amino groups and subsequently bridges the two nickel centers.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt;  The binding of the urea carbonyl oxygen atom to Ni1 is stabilized through the protonation state of His&amp;lt;sup&amp;gt;α222&amp;lt;/sup&amp;gt; Nԑ. Additionally, the conformational change from the open to closed state of the mobile flap generates a rearrangement of Ala&amp;lt;sup&amp;gt;α222&amp;lt;/sup&amp;gt; carbonyl group in such a way that its oxygen atom points to Ni2.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt;  The Ala&amp;lt;sup&amp;gt;α170&amp;lt;/sup&amp;gt; and Ala&amp;lt;sup&amp;gt;α366&amp;lt;/sup&amp;gt; are now oriented in a way that their carbonyl groups act as hydrogen-bond acceptors towards NH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; group of urea, thus aiding its binding to Ni2.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt;  Urea is a very poor [[chelating ligand]] due to low [[Lewis base]] character of its NH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups. However the carbonyl oxygens of Ala&amp;lt;sup&amp;gt;α170&amp;lt;/sup&amp;gt; and Ala&amp;lt;sup&amp;gt;α366&amp;lt;/sup&amp;gt; enhance the basicity of the NH&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt; groups and allow for binding to Ni2.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt; Therefore in this proposed mechanism, the positioning of urea in the active site is induced by the structural features of the active site residues which are positioned to act as hydrogen-bond donors in the vicinity of Ni1 and as acceptors in the vicinity of Ni2.&amp;lt;ref name=&amp;quot;Benini, S. 1999&amp;quot;/&amp;gt;  The main structural difference between the Ciurli/Mangani mechanism and the other two are that it incorporates a [[nitrogen]], oxygen bridging urea that is attacked by a bridging [[hydroxide]].&amp;lt;ref name=Zimmer /&amp;gt;&lt;br /&gt;
&lt;br /&gt;
==Action of Urease in Pathogenesis==&lt;br /&gt;
&lt;br /&gt;
Bacterial ureases are most often the mode of [[pathogenesis]] for many medical conditions. They are associated with [[hepatic encephalopathy]] / [[Hepatic coma]], infection stones, and peptic ulceration.&amp;lt;ref name=&amp;quot;mobley&amp;quot;&amp;gt;{{cite journal|last=Mobley|first=HL|coauthors=Hausinger, RP|title=Microbial ureases: significance, regulation, and molecular characterization|journal=Microbiological reviews|date=March 1989|volume=53|issue=1|pages=85–108|pmid=2651866|pmc=372718}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
&lt;br /&gt;
&amp;#039;&amp;#039;&amp;#039;&amp;lt;big&amp;gt;Infection Stones&amp;lt;/big&amp;gt;&amp;#039;&amp;#039;&amp;#039;&lt;br /&gt;
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Infection induced urinary stones are a mixture of [[struvite]] (MgNH&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;PO&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;•6H&amp;lt;sub&amp;gt;2&amp;lt;/sub&amp;gt;O) and [[carbonate]] [[apatite]] [Ca&amp;lt;sub&amp;gt;10&amp;lt;/sub&amp;gt;(PO&amp;lt;sub&amp;gt;4&amp;lt;/sub&amp;gt;)6•CO&amp;lt;sub&amp;gt;3&amp;lt;/sub&amp;gt;].&amp;lt;ref name=&amp;quot;mobley&amp;quot;/&amp;gt; These polyvalent ions are soluble but become insoluble when [[ammonia]] is produced from microbial urease during [[urea]] [[hydrolysis]], as this increases the surrounding environments [[pH]] from roughly 6.5 to 9.&amp;lt;ref name=&amp;quot;mobley&amp;quot;/&amp;gt; The resultant alkalinization results in stone [[crystallization]].&amp;lt;ref name=&amp;quot;mobley&amp;quot;/&amp;gt; In humans the microbial urease, &amp;#039;&amp;#039;Proteus mirabilis&amp;#039;&amp;#039;, is the most common in infection induced urinary stones.&amp;lt;ref name=&amp;quot;pmid3524996&amp;quot;&amp;gt;{{cite journal|last=Rosenstein|first=Isobel J. M.|coauthors=Griffith, Donald P.|title=Urinary Calculi: Microbiological and Crystallographic Studies|journal=Critical Reviews in Clinical Laboratory Sciences|date=1 January 1986|volume=23|issue=3|pages=245–277|doi=10.3109/10408368609165802|pmid=3524996}}&amp;lt;/ref&amp;gt;&lt;br /&gt;
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&amp;#039;&amp;#039;&amp;#039;&amp;lt;big&amp;gt;Urease in Hepatic Encephalopathy/ Hepatic coma&amp;lt;/big&amp;gt;&amp;#039;&amp;#039;&amp;#039;&lt;br /&gt;
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Studies have shown that &amp;#039;&amp;#039;[[Helicobacter pylori]]&amp;#039;&amp;#039; along with [[cirrhosis]] of the liver cause [[hepatic encephalopathy]] and [[hepatic coma]].&amp;lt;ref name=&amp;quot;agrawal&amp;quot;&amp;gt;{{cite journal|last=Agrawal|first=Avinash|coauthors=Gupta, Alok; Chandra, Mam; Koowar, Sciddhartha|title=Role of Helicobacter pylori infection in the pathogenesis of minimal hepatic encephalopathy and effect of its eradication|journal=Indian Journal of Gastroenterology|date=17 March 2011|volume=30|issue=1|pages=29–32|doi=10.1007/s12664-011-0087-7|pmid=21416318}}&amp;lt;/ref&amp;gt; &amp;#039;&amp;#039;Heliobacter pylori&amp;#039;&amp;#039;  are microbial ureases found in the stomach. As ureases they hydrolyze [[urea]] to produce [[ammonia]] and [[carbonic acid]]. As the bacteria are localized to the stomach [[ammonia]] produced is readily taken up by the [[circulatory system]] from the gastric [[lumen (anatomy)|lumen]].&amp;lt;ref name=&amp;quot;agrawal&amp;quot;/&amp;gt; This results in elevated [[ammonia]] levels in the blood and is coined as  [[hyperammonemia]], eradication of &amp;#039;&amp;#039;Heliobacter pylori&amp;#039;&amp;#039; show marked decreases in [[ammonia]] levels.&amp;lt;ref name=&amp;quot;agrawal&amp;quot;/&amp;gt;&lt;br /&gt;
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&amp;#039;&amp;#039;&amp;#039;&amp;lt;big&amp;gt;Urease in Peptic Ulcers&amp;lt;/big&amp;gt;&amp;#039;&amp;#039;&amp;#039;&lt;br /&gt;
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&amp;#039;&amp;#039;Helicobacter pylori&amp;#039;&amp;#039; is also  the cause of peptic ulcers with its manifestation in 55%-68% reported cases. .&amp;lt;ref name=&amp;quot;tang&amp;quot;&amp;gt;{{cite journal|last=Tang|first=JH|coauthors=Liu, NJ; Cheng, HT; Lee, CS; Chu, YY; Sung, KF; Lin, CH; Tsou, YK; Lien, JM; Cheng, CL|title=Endoscopic diagnosis of Helicobacter pylori infection by rapid urease test in bleeding peptic ulcers: a prospective case-control study|journal=Journal of clinical gastroenterology|date=February 2009|volume=43|issue=2|pages=133–9|pmid=19230239|doi=10.1097/MCG.0b013e31816466ec}}&amp;lt;/ref&amp;gt;  This was confirmed by decreased [[ulcer]] bleeding and [[ulcer]] reoccurrence after eradication of the [[pathogen]].&amp;lt;ref name=&amp;quot;tang&amp;quot;/&amp;gt; In the stomach there is an increase in [[pH]] of the mucosal lining as a result of [[urea]] [[hydrolysis]] this prevents movement of [[hydrogen ions]] between gastric glands and gastric [[lumen (anatomy)|lumen]].&amp;lt;ref name=&amp;quot;mobley&amp;quot;/&amp;gt;  In addition, the high [[ammonia]] concentrations have an effect on  intercellular [[tight junctions]] increasing permeability and also disrupting the gastric [[mucous membrane]] of the stomach.&amp;lt;ref name=&amp;quot;mobley&amp;quot;/&amp;gt;&lt;br /&gt;
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== As diagnostic test ==&lt;br /&gt;
{{Main|Rapid urease test}}&lt;br /&gt;
Many gastrointestinal or urinary tract pathogens produce urease, enabling the detection of urease to be used as a diagnostic to detect presence of pathogens.&lt;br /&gt;
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Urease-positive pathogens include:&lt;br /&gt;
*&amp;#039;&amp;#039;[[Proteus mirabilis]]&amp;#039;&amp;#039; and &amp;#039;&amp;#039;[[Proteus vulgaris]]&amp;#039;&amp;#039;&lt;br /&gt;
*&amp;#039;&amp;#039;[[Ureaplasma urealyticum]]&amp;#039;&amp;#039;, a relative of &amp;#039;&amp;#039;[[Mycoplasma]]&amp;#039;&amp;#039; spp.&lt;br /&gt;
*&amp;#039;&amp;#039;[[Nocardia]]&lt;br /&gt;
*&amp;#039;&amp;#039;[[Campylobacter ureolyticus]]&amp;#039;&amp;#039;&lt;br /&gt;
*&amp;#039;&amp;#039;[[Cryptococcus (fungus)|Cryptococcus]]&amp;#039;&amp;#039; spp., an [[opportunistic infection|opportunistic]] fungus&lt;br /&gt;
*&amp;#039;&amp;#039;[[Helicobacter pylori]]&amp;#039;&amp;#039;&lt;br /&gt;
*Certain [[Enteric bacteria]] including &amp;#039;&amp;#039;[[Proteus (bacterium)|Proteus]]&amp;#039;&amp;#039; spp., &amp;#039;&amp;#039;[[Klebsiella]]&amp;#039;&amp;#039; spp., &amp;#039;&amp;#039;[[Morganella (bacterium)|Morganella]]&amp;#039;&amp;#039;, &amp;#039;&amp;#039;[[Providencia (bacterium)|Providencia]]&amp;#039;&amp;#039;, and possibly &amp;#039;&amp;#039;[[Serratia]]&amp;#039;&amp;#039; spp.&lt;br /&gt;
*&amp;#039;&amp;#039;[[Brucella]]&lt;br /&gt;
* Staphylococcus saprophyticus&lt;br /&gt;
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== Other uses ==&lt;br /&gt;
Urease conductometric biosensors for detection of heavy-metal ions {{Expand section|date=May 2008}}&lt;br /&gt;
Urease conductometric biosensors for detection of heavy-metal ions consisting of interdigitated gold electrodes and enzyme membranes formed on their sensitive parts have been used for a quantitative estimation of general water pollution with heavy-metal ions. The measurements of the urease residual activity have been carried out in Tris-HNO&amp;lt;sub&amp;gt;3&amp;gt;&amp;lt;/sub&amp;gt; buffer after preincubation in model metal-salt solution. The detection limits, depending on preincubation time and dynamic ranges, have been determined in model solutions of heavy-metal ions. The sequence of metals ions relative to their toxicity toward urease is: Hg&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; &amp;gt; Cu&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; &amp;gt; Cd&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; &amp;gt; Co&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; &amp;gt; Pb&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; &amp;gt; Sr&amp;lt;sup&amp;gt;2+&amp;lt;/sup&amp;gt; &amp;gt; . The conditions for practical applications of the biosensors have been investigated and critically evaluated for optimization. Urease reactivation by EDTA after inhibition by heavy-metal ions has been demonstrated. The performance characteristics of the conductometric biosensor are discussed by G. A. Zhylyaka, S. V. Dzyadevichb, Y. I. Korpana, A. P. Soldatkina and A. V. El&amp;#039;skayaa in their paper.&lt;br /&gt;
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==See also==&lt;br /&gt;
*[[Urea carboxylase]]&lt;br /&gt;
*[[Allophanate hydrolase]]&lt;br /&gt;
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==References==&lt;br /&gt;
{{reflist|2}}&lt;br /&gt;
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==External links==&lt;br /&gt;
* {{cite book|last=Mobley|first=Harry L. T.|title=Helicobacter pylori: Physiology and Genetics|year=2001|publisher=ASM Press|location=Washington (DC)|url=http://www.ncbi.nlm.nih.gov/books/NBK2417/|editor=Mobley HLT, Mendz GL, Hazell SL,|chapter=Chapter 16:Urease|isbn=1-55581-213-9|pmid=21290719}}&lt;br /&gt;
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[[Category:Nickel enzymes]]&lt;br /&gt;
[[Category:Hydrolases acting on nonpeptide C-N bonds]]&lt;/div&gt;</summary>
		<author><name>en&gt;OdedSchramm</name></author>
	</entry>
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