Editing Urease (section)

===Active site===

The [[active site]] of ureases is located in the α (alpha) [[Protein subunit|subunits]]. It is a bis-μ-hydroxo dimeric [[nickel]] center, with an interatomic distance of ~3.5 Å.<ref name="karplus" /> > The Ni(II) pair are weakly [[Antiferromagnetism|antiferromagnetically]] coupled.<ref>{{cite journal | vauthors = Ciurli S, Benini S, Rypniewski WR, Wilson KS, Miletti S, Mangani S | title = Structural properties of the nickel ions in urease: novel insights into the catalytic and inhibition mechanisms | journal = Coordination Chemistry Reviews | year = 1999 | volume = 190–192 | pages = 331–355 | doi = 10.1016/S0010-8545(99)00093-4 }}</ref> [[X-ray absorption spectroscopy]] (XAS) studies of ''[[Canavalia ensiformis]]''  (jack bean), ''Klebsiella aerogenes''  and ''[[Sporosarcina pasteurii]]'' (formerly known as ''Bacillus pasteurii'')<ref name="Benini, S. 1999"/> confirm 5–6 coordinate nickel ions with exclusively O/N ligation, including two [[imidazole]] ligands per nickel.<ref name="pmid20046957" /> Urea substrate is proposed to displace [[aquo ligand]]s.

Water molecules located towards the opening of the active site form a tetrahedral cluster that fills the cavity site through [[hydrogen bonds]].  Some amino acid residues are proposed to form mobile flap of the site, which gate for the substrate.<ref name="Krajewska" /> 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.<ref name="Martin">{{cite journal | vauthors = Martin PR, Hausinger RP | title = Site-directed mutagenesis of the active site cysteine in ''Klebsiella aerogenes'' urease | journal = The Journal of Biological Chemistry | volume = 267 | issue = 28 | pages = 20024–7 | date = Oct 5, 1992 | doi = 10.1016/S0021-9258(19)88659-3 | pmid = 1400317 | doi-access = free }}</ref> In ''[[Sporosarcina pasteurii]]'' urease, the flap was found in the open conformation, while its closed conformation is apparently needed for the reaction.<ref name="Benini, S. 1999">{{cite journal | vauthors = Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S | 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 | volume = 7 | issue = 2 | pages = 205–216 | date = 31 January 1999 | pmid = 10368287 | doi = 10.1016/S0969-2126(99)80026-4 | doi-access = free }}</ref>

When compared, the α subunits of ''[[Helicobacter pylori]]'' urease and other bacterial ureases align with the jack bean ureases.<ref name="Martin" />

The binding of urea to the active site of urease has not been observed.<ref name="Molecular Catalysis B 2009"/>