Urease

Urease

Helicobacter pylori Urease drawn from PDB: 1E9Z​.
Identifiers
EC number 3.5.1.5
CAS number 9002-13-5
Databases
IntEnz IntEnz view
BRENDA BRENDA entry
ExPASy NiceZyme view
KEGG KEGG entry
MetaCyc metabolic pathway
PRIAM profile
PDB structures RCSB PDB PDBe PDBsum

Ureases (EC 3.5.1.5), functionally, belong to the superfamily of amidohydrolases and phosphotriesterases.[1] It is an enzyme that catalyzes the hydrolysis of urea into carbon dioxide and ammonia. The reaction occurs as follows:

(NH2)2CO + H2O → CO2 + 2NH3

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.[2] Urease activity tends to increase the pH of its environment as it produces ammonia, 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.[3]

In 1926, James B. Sumner, an assistant professor at Cornell University, showed that urease is a protein by examining its crystallized form.[4] Sumner'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.[5] The structure of urease was first solved by P. A. Karplus in 1995. Urease was the first ever enzyme crystallized.[4]

Characteristics

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.[8]

An exceptional enzyme is the urease of Helicobacter species, which is composed of two subunits, α(26–31 kDa)-β(61–66 kDa), and has been shown to form a supramolecular dodecameric complex.[9] of repeating α-β subunits, each coupled pair of subunits has an active site, for a total of 12 active sites.[9] (). It plays an essential function for survival, neutralizing gastric acid by allowing urea to enter into periplasm via a proton-gated urea channel.[10] The presence of urease is used in the diagnosis of Helicobacter species.

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.[8]

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.[8]

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.[8]

Active site

The active site of all ureases known are located in the α (alpha) subunits. It is a bis-μ-hydroxo dimeric nickel center, with an interatomic distance of ~3.5 Å,[4] magnetic susceptibility experiments have indicated that, in jack bean urease, high spin octahedrally coordinated Ni(II) ions are weakly antiferromagnetically coupled.[11] X-ray absorption spectroscopy (XAS) studies of Canavalia ensiformis (jack bean), Klebsiella aerogenes and Sporosarcina pasteurii (formerly known as Bacillus pasteurii)[12] confirm 5–6 coordinate nickel ions with exclusively O/N ligands (two imidazoles per nickel).[7]

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'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.[3] 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.[13] In the structure of Sporosarcina pasteurii urease the flap was found in the open conformation, while its closed conformation is apparently needed for the reaction.[12]

When compared, the α subunits of Helicobacter pylori urease and other bacterial ureases align with the jack bean ureases, suggesting that all ureases are evolutionary variants of one ancestral enzyme.[13]

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.[8]

Activity

The kcat/Km of urease in the processing of urea is 1014 times greater than the rate of the uncatalyzed elimination reaction of urea.[4] 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.[4] 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.[4]

Proposed mechanisms

Blakeley/Zerner

One mechanism for the catalysis of this reaction by urease was proposed by Blakely and Zerner.[14] 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 NH2+ of the coordinated substrate interacts with a nearby negatively charged group. Blakeley and Zerner proposed this nearby group to be a Carboxylate ion

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.

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.

The carbamate produced then spontaneously degrades to produce another ammonia and carbonic acid.[2]

Hausinger/Karplus

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.[4] From the crystal structures from K. aerogenes urease, it was argued that the general base used in the Blakely mechanism, His320, 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.[15] Hausinger and Karplus suggests a reverse protonation scheme, where a protonated form of the His320 ligand plays the role of the general acid and the Ni2-bound water is already in the deprotonated state.[4] The mechanism follows the same path, with the general base omitted (as there is no more need for it) and His320 donating its proton to form the ammonia molecule, which is then released from the enzyme. While the majority of the His320 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.[4] 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.[4] Placing the His320 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.[4]

Ciurli/Mangani

The mechanism proposed by Ciurli and Mangani[16] 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.[12] One of which binds and activates urea, the other nickel ion binds and activates the nucleophilic water molecule.[12] 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.[12] 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.[12] The binding of the urea carbonyl oxygen atom to Ni1 is stabilized through the protonation state of Hisα222 Nԑ. Additionally, the conformational change from the open to closed state of the mobile flap generates a rearrangement of Alaα222 carbonyl group in such a way that its oxygen atom points to Ni2.[12] The Alaα170 and Alaα366 are now oriented in a way that their carbonyl groups act as hydrogen-bond acceptors towards NH2 group of urea, thus aiding its binding to Ni2.[12] Urea is a very poor chelating ligand due to low Lewis base character of its NH2 groups. However the carbonyl oxygens of Alaα170 and Alaα366 enhance the basicity of the NH2 groups and allow for binding to Ni2.[12] 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.[12] The main structural difference between the Ciurli/Mangani mechanism and the other two is that it incorporates a nitrogen, oxygen bridging urea that is attacked by a bridging hydroxide.[2]

Action in pathogenesis

Bacterial ureases are often the mode of pathogenesis for many medical conditions. They are associated with hepatic encephalopathy / Hepatic coma, infection stones, and peptic ulceration.[17]

Infection stones

Infection induced urinary stones are a mixture of struvite (MgNH4PO4•6H2O) and carbonate apatite [Ca10(PO4)6•CO3].[17] 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.[17] The resultant alkalinization results in stone crystallization.[17] In humans the microbial urease, Proteus mirabilis, is the most common in infection induced urinary stones.[18]

Urease in hepatic encephalopathy / hepatic coma

Studies have shown that Helicobacter pylori along with cirrhosis of the liver cause hepatic encephalopathy and hepatic coma.[19] Heliobacter pylori 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.[19] This results in elevated ammonia levels in the blood and is coined as hyperammonemia, eradication of Heliobacter pylori show marked decreases in ammonia levels.[19]

Urease in peptic ulcers

Helicobacter pylori is also the cause of peptic ulcers with its manifestation in 55–68% reported cases.[20] This was confirmed by decreased ulcer bleeding and ulcer reoccurrence after eradication of the pathogen.[20] In the stomach there is an increase in pH of the mucosal lining as a result of urea hydrolysis, which prevents movement of hydrogen ions between gastric glands and gastric lumen.[17] 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.[17]

Environmental Significance

Urea is found naturally in the environment and is also artificially introduced, comprising more than half of all synthetic nitrogen fertilizers used globally.[21] Heavy use of urea is thought to promote eutrophication, despite the observation that urea is rapidly transformed by microbial ureases, and thus usually does not persist.[22] Environmental urease activity is often measured as an indicator of the health of microbial communities. In the absence of plants, urease activity in soil is generally attributed to heterotrophic microorganisms, although it has been demonstrated that some chemoautotrophic ammonium oxidizing bacteria are capable of growth on urea as a sole source of carbon, nitrogen, and energy.[23]

As diagnostic test

Main article: Rapid urease test

Many gastrointestinal or urinary tract pathogens produce urease, enabling the detection of urease to be used as a diagnostic to detect presence of pathogens.

Urease-positive pathogens include:

Extraction

First isolated as a crystal in 1926 by Sumner, using acetone solvation and centrifuging.[24] Modern biochemistry has increased its demand for urease. Jack bean meal,[25] watermelon seeds,[26] and pea seeds[27] have all proven useful sources of urease.

See also

References

  1. ↑ Holm L, Sander C (1997). "An evolutionary treasure: unification of a broad set of amidohydrolases related to urease". Proteins. 28 (1): 72–82. doi:10.1002/(SICI)1097-0134(199705)28:1<72::AID-PROT7>3.0.CO;2-L. PMID 9144792.
  2. 1 2 3 Zimmer M (Apr 2000). "Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease". J Biomol Struct Dyn. 17 (5): 787–97. doi:10.1080/07391102.2000.10506568. PMID 10798524.
  3. 1 2 Krajewska B, van Eldik R, Brindell M (13 August 2012). "Temperature- and pressure-dependent stopped-flow kinetic studies of jack bean urease. Implications for the catalytic mechanism". JBIC Journal of Biological Inorganic Chemistry. 17 (7): 1123–1134. doi:10.1007/s00775-012-0926-8. PMC 3442171Freely accessible. PMID 22890689.
  4. 1 2 3 4 5 6 7 8 9 10 11 Karplus PA, Pearson MA, Hausinger RP (1997). "70 years of crystalline urease: What have we learned?". Accounts of Chemical Research. 30 (8): 330–337. doi:10.1021/ar960022j.
  5. ↑ The Nobel Prize in Chemistry 1946
  6. ↑ Anke M, Groppel B, Kronemann H, Grün M (1984). "Nickel--an essential element". IARC Sci. Publ.: 339–65. PMID 6398286.
  7. 1 2 Carter EL, Flugga N, Boer JL, Mulrooney SB, Hausinger RP (1 January 2009). "Interplay of metal ions and urease". Metallomics. 1 (3): 207–21. doi:10.1039/b903311d. PMC 2745169Freely accessible. PMID 20046957.
  8. 1 2 3 4 5 6 Krajewska, Barbara (30 June 2009). "Ureases I. Functional, catalytic and kinetic properties: A review". Journal of Molecular Catalysis B: Enzymatic. 59 (1–3): 9–21. doi:10.1016/j.molcatb.2009.01.003.
  9. 1 2 Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH (31 May 2001). "Supramolecular assembly and acid resistance of Helicobacter pylori urease". Nature Structural Biology. 8 (6): 505–509. doi:10.1038/88563. PMID 11373617.
  10. ↑ Strugatsky D, McNulty R, Munson K, Chen CK, Soltis SM, Sachs G, Luecke H (8 December 2012). "Structure of the proton-gated urea channel from the gastric pathogen Helicobacter pylori". Nature. 493 (7431): 255–258. doi:10.1038/nature11684. PMID 23222544.
  11. ↑ Ciurli S, Benini S, Rypniewski WR, Wilson KS, Miletti S, Mangani S (1999). "Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms". Coordination Chemistry Reviews. 190-192: 331–355. doi:10.1016/S0010-8545(99)00093-4.
  12. 1 2 3 4 5 6 7 8 9 10 Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S (31 January 1999). "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". Structure. 7 (2): 205–216. doi:10.1016/S0969-2126(99)80026-4. PMID 10368287.
  13. 1 2 Martin PR, Hausinger RP (Oct 5, 1992). "Site-directed mutagenesis of the active site cysteine in Klebsiella aerogenes urease". The Journal of Biological Chemistry. 267 (28): 20024–7. PMID 1400317.
  14. ↑ Dixon NE, Riddles PW, Gazzola C, Blakeley RL, Zerner B (1979). "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". Canadian Journal of Biochemistry. 58 (12): 1335–1344. doi:10.1139/o80-181. PMID 6788353.
  15. ↑ Jabri E, Carr MB, Hausinger RP, Karplus PA (May 19, 1995). "The crystal structure of urease from Klebsiella aerogenes". Science. 268 (5213): 998–1004. doi:10.1126/science.7754395. PMID 7754395.
  16. ↑ Zambelli B, Musiani F, Benini S, Ciurli S (19 July 2011). "Chemistry of Ni2+ in Urease: Sensing, Trafficking, and Catalysis". Accounts of Chemical Research. 44 (7): 520–530. doi:10.1021/ar200041k. PMID 21542631.
  17. 1 2 3 4 5 6 Mobley HL, Hausinger RP (March 1989). "Microbial ureases: significance, regulation, and molecular characterization". Microbiological reviews. 53 (1): 85–108. PMC 372718Freely accessible. PMID 2651866.
  18. ↑ Rosenstein IJ (1 January 1986). "Urinary Calculi: Microbiological and Crystallographic Studies". Critical Reviews in Clinical Laboratory Sciences. 23 (3): 245–277. doi:10.3109/10408368609165802. PMID 3524996.
  19. 1 2 3 Agrawal A, Gupta A, Chandra M, Koowar S (17 March 2011). "Role of Helicobacter pylori infection in the pathogenesis of minimal hepatic encephalopathy and effect of its eradication". Indian Journal of Gastroenterology. 30 (1): 29–32. doi:10.1007/s12664-011-0087-7. PMID 21416318.
  20. 1 2 Tang JH, Liu NJ, Cheng HT, Lee CS, Chu YY, Sung KF, Lin CH, Tsou YK, Lien JM, Cheng CL (February 2009). "Endoscopic diagnosis of Helicobacter pylori infection by rapid urease test in bleeding peptic ulcers: a prospective case-control study". Journal of Clinical Gastroenterology. 43 (2): 133–9. doi:10.1097/MCG.0b013e31816466ec. PMID 19230239.
  21. ↑ Glibert P, Harrison J, Heil C, Seitzinger S (2006). "Escalating worldwide use of urea – a global change contributing to coastal eutrophication". Biogeochemistry. 77: 441–463. doi:10.1007/s10533-005-3070-5.
  22. ↑ Daigh AL, Savin MC, Brye K, Norman R, Miller D (2014). "Urea persistence in floodwater and soil used for flooded rice production". Soil Use and Management. 30 (4): 463–470. doi:10.1111/sum.12142.
  23. ↑ Marsh, K. L., G. K. Sims, and R. L. Mulvaney. 2005. Availability of urea to autotrophic ammonia-oxidizing bacteria as related to the fate of 14C- and 15N-labeled urea added to soil. Biol. Fert. Soil. 42:137-145.
  24. ↑ Gorin, G; Butler, M. F.; Katyal, J. M.; Buckley, J. E. (1959). "Isolation of Crystalline Urease" (PDF). proceedings of the Oklahoma Academy of Sciences. Retrieved Dec 7, 2014.
  25. ↑ Sung HY, Lee WM, Chiou MJ, Chang CT (Oct 13, 1989). "procedure for purifying jack bean urease for clinical use". Proc Natl Sci Counc Repub China B. 13 (4): 250–7. PMID 2517764.
  26. ↑ Prakash, O; Brushan, G (Jan 1, 1997). "Isolation, purification and partial characterisation of urease from seeds of water melon (Citrullus vulgaris)". Journal of Plant Biochemistry and Biotechnology. 6: 45–47. doi:10.1007/BF03263009.
  27. ↑ El-Hefnawy ME, Sakran M, Ismail AI, Aboelfetoh EF (2014). "Extraction, purification, kinetic and thermodynamic properties of urease from germinating Pisum Sativum L. seeds". BMC Biochemistry. 15 (1): 15. doi:10.1186/1471-2091-15-15. PMID 25065975.
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