DB code: M00226

CATH domain 3.30.280.10 : Urease; subunit A
2.10.150.10 : Urease, subunit B
2.30.40.10 : Urease, subunit C; domain 1
3.20.20.140 : TIM Barrel Catalytic domain
E.C. 3.5.1.5
CSA
M-CSA
MACiE

CATH domain Related DB codes (homologues)
2.10.150.10 : Urease, subunit B M00030 M00225
2.30.40.10 : Urease, subunit C; domain 1 D00673 D00675 D00801 D00873 M00030 M00225
3.20.20.140 : TIM Barrel S00231 S00232 M00186 D00673 D00675 D00801 D00873 M00030 M00225
3.30.280.10 : Urease; subunit A M00030 M00225

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam
P07374 Urease
EC 3.5.1.5
Urea amidohydrolase
M38.982 (Metallo)
PF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
PF00699 (Urease_beta)
PF00547 (Urease_gamma)
[Graphical View]

KEGG enzyme name
Urease
Urea amidohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07374 UREA_CANEN Urea + H(2)O = CO(2) + 2 NH(3). Homohexamer. Binds 2 nickel ions per subunit (By similarity).

KEGG Pathways
Map code Pathways E.C.
MAP00220 Urea cycle and metabolism of amino groups
MAP00230 Purine metabolism
MAP00791 Atrazine degradation

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00291 C00086 C00001 C00011 C00014 I00127 C01563
E.C.
Compound Nickel Urea H2O CO2 NH3 Diaminohydroxymethanolate Carbamate
Type heavy metal amide group,amine group H2O others amine group,organic ion
ChEBI 28112
16199
48376
15377
16526
16134
PubChem 935
1176
22247451
962
280
222
3la4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3la4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3la4A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound
3la4A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_NI Unbound Unbound Unbound Transition-state-analogue:PO4_843 Unbound

Reference for Active-site residues
resource references E.C.
Swiss-prot;P18314, P41020, P69996 & literature [17], [22], [31]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
3la4A01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CME 59
3la4A02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain CME 207
3la4A03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain
3la4A04 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain HIS 492;ASP 494;HIS 593;ARG 609 KCX 490(Nickel-1 & -2);HIS 519;HIS 545(Nickel-1);HIS 407;HIS 409;ASP 633(Nickel-2) KCX 490(Carbamylated LYS);CME 592

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[7]
figure, p.996
[12]
Figure 2, Figure 6, p.333-337
[17]
Figure 8, p.211-213
[19]
Figure 7, p.5394-5395
[20]
FIGURE 1, FIGURE 8, p.8583-8584
[22]
Figure 2, Figure 3, Figure 4, p.796
[23]
[24]
Fig.6, p.787
[31]
Figure 3, Figure 7, Figure 8, Figure 10, p.15335-15337
[34]
Figure 13, p.6943
[35]
Figure 4, Figure 11, p.11842
[36]
Figure 4, Figure 5, Figure 6, Figure 13, Figure 16, Figure 18
[37]
Figure 1, Figure 2, Figure 3
[40]
Scheme 2, p.521

References
[1]
Resource
Comments
Medline ID
PubMed ID 1400317
Journal J Biol Chem
Year 1992
Volume 267
Pages 20024-7
Authors Martin PR, Hausinger RP
Title Site-directed mutagenesis of the active site cysteine in Klebsiella aerogenes urease.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 1404395
Journal J Mol Biol
Year 1992
Volume 227
Pages 934-7
Authors Jabri E, Lee MH, Hausinger RP, Karplus PA
Title Preliminary crystallographic studies of urease from jack bean and from Klebsiella aerogenes.
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 8318888
Journal Protein Sci
Year 1993
Volume 2
Pages 1034-41
Authors Park IS, Hausinger RP
Title Site-directed mutagenesis of Klebsiella aerogenes urease: identification of histidine residues that appear to function in nickel ligation, substrate binding, and catalysis.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 7565414
Journal Microbiol Rev
Year 1995
Volume 59
Pages 451-80
Authors Mobley HL, Island MD, Hausinger RP
Title Molecular biology of microbial ureases.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 8535259
Journal Protein Sci
Year 1995
Volume 4
Pages 2234-6
Authors Moncrief MB, Hom LG, Jabri E, Karplus PA, Hausinger RP
Title Urease activity in the crystalline state.
Related PDB
Related UniProtKB
[6]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 95273988
PubMed ID 7754395
Journal Science
Year 1995
Volume 268
Pages 998-1004
Authors Jabri E, Carr MB, Hausinger RP, Karplus PA
Title The crystal structure of urease from Klebsiella aerogenes.
Related PDB 1kau 2kau 3kau
Related UniProtKB P18314 P18315 P18316
[7]
Resource
Comments
Medline ID
PubMed ID 7754394
Journal Science
Year 1995
Volume 268
Pages 996-7
Authors Lippard SJ
Title At last--the crystal structure of urease.
Related PDB
Related UniProtKB
[8]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 96346054
PubMed ID 8718850
Journal Biochemistry
Year 1996
Volume 35
Pages 10616-26
Authors Jabri E, Karplus PA
Title Structures of the Klebsiella aerogenes urease apoenzyme and two active-site mutants.
Related PDB 1kra 1krb 1krc
Related UniProtKB P18314 P18315 P18316
[9]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 8702515
Journal J Biol Chem
Year 1996
Volume 271
Pages 18632-7
Authors Park IS, Michel LO, Pearson MA, Jabri E, Karplus PA, Wang S, Dong J, Scott RA, Koehler BP, Johnson MK, Hausinger RP
Title Characterization of the mononickel metallocenter in H134A mutant urease.
Related PDB 1fwi
Related UniProtKB
[10]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 9201965
Journal Biochemistry
Year 1997
Volume 36
Pages 8164-72
Authors Pearson MA, Michel LO, Hausinger RP, Karplus PA
Title Structures of Cys319 variants and acetohydroxamate-inhibited Klebsiella aerogenes urease.
Related PDB 1fwa 1fwb 1fwc 1fwd 1fwe 1fwf 1fwg 1fwh 1fwj
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 9144792
Journal Proteins
Year 1997
Volume 28
Pages 72-82
Authors Holm L, Sander C
Title An evolutionary treasure: unification of a broad set of amidohydrolases related to urease.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID
Journal Acc Chem Res
Year 1997
Volume 30
Pages 330?7
Authors Karplus PA, Pearson MA, Hausinger RP
Title 70 Years of Crystalline Urease:? What Have We Learned?
Related PDB
Related UniProtKB
[13]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID
PubMed ID 9761912
Journal Acta Crystallogr D Biol Crystallogr
Year 1998
Volume 54
Pages 409-12
Authors Benini S, Ciurli S, Rypniewski WR, Wilson KS, Mangani S
Title Crystallization and preliminary high-resolution X-ray diffraction analysis of native and beta-mercaptoethanol-inhibited urease from Bacillus pasteurii.
Related PDB
Related UniProtKB P41020 P41021 P41022
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 98226663
PubMed ID 9558361
Journal Biochemistry
Year 1998
Volume 37
Pages 6214-20
Authors Pearson MA, Schaller RA, Michel LO, Karplus PA, Hausinger RP
Title Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand.
Related PDB 1a5k 1a5l 1a5m 1a5n 1a5o
Related UniProtKB P18314 P18315 P18316
[15]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID
Journal J Biol Inorg Chem
Year 1998
Volume 3
Pages 268-73
Authors Benini S, Rypniewski WR, Wilson KS, Ciurli S, Mangani S
Title The complex of Bacillus pasteurii urease with beta-mercaptoethanol from X-ray data at 1.65-angstrom resolution.
Related PDB 1ubp
Related UniProtKB
[16]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID
PubMed ID 10555581
Journal J Biol Inorg Chem
Year 1999
Volume 4
Pages 468-77
Authors Yamaguchi K, Cosper NJ, Stalhandske C, Scott RA, Pearson MA, Karplus PA, Hausinger RP
Title Characterization of metal-substituted Klebsiella aerogenes urease.
Related PDB 1ef2
Related UniProtKB P18314 P18315 P18316
[17]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
Medline ID 99148127
PubMed ID 10368287
Journal Structure Fold Des
Year 1999
Volume 7
Pages 205-16
Authors 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.
Related PDB 2ubp 3ubp
Related UniProtKB P41020 P41021 P41022
[18]
Resource
Comments
Medline ID
PubMed ID 11996109
Journal Acta Biochim Pol
Year 2000
Volume 47
Pages 1189-95
Authors Sirko A, Brodzik R
Title Plant ureases: roles and regulation.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 10820010
Journal Biochemistry
Year 2000
Volume 39
Pages 5389-96
Authors Todd MJ, Hausinger RP
Title Fluoride inhibition of Klebsiella aerogenes urease: mechanistic implications of a pseudo-uncompetitive, slow-binding inhibitor.
Related PDB
Related UniProtKB
[20]
Resource
Comments X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), AND MUTAGENESIS OF HIS-219; ASP-221; HIS-320 AND ARG-336.
Medline ID
PubMed ID 10913264
Journal Biochemistry
Year 2000
Volume 39
Pages 8575-84
Authors Pearson MA, Park IS, Schaller RA, Michel LO, Karplus PA, Hausinger RP
Title Kinetic and structural characterization of urease active site variants.
Related PDB 1ejr 1ejs 1ejt 1eju 1ejv
Related UniProtKB P18314 P18315 P18316
[21]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10766443
Journal J Biol Inorg Chem
Year 2000
Volume 5
Pages 110-8
Authors Benini S, Rypniewski WR, Wilson KS, Miletti S, Ciurli S, Mangani S
Title The complex of Bacillus pasteurii urease with acetohydroxamate anion from X-ray data at 1.55 A resolution.
Related PDB 4ubp
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 10798524
Journal J Biomol Struct Dyn
Year 2000
Volume 17
Pages 787-97
Authors Zimmer M
Title Molecular mechanics evaluation of the proposed mechanisms for the degradation of urea by urease.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID
Journal J Am Chem Soc
Year 2000
Volume 122
Pages 9172-77
Authors Barrios AM, Lippard SJ
Title Interaction of Urea with a Hydroxide-Bridged Dinuclear Nickel Center:? An Alternative Model for the Mechanism of Urease.
Related PDB
Related UniProtKB
[24]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11713685
Journal J Biol Inorg Chem
Year 2001
Volume 6
Pages 778-90
Authors Benini S, Rypniewski WR, Wilson KS, Ciurli S, Mangani S
Title Structure-based rationalization of urease inhibition by phosphate: novel insights into the enzyme mechanism.
Related PDB 1ie7
Related UniProtKB
[25]
Resource
Comments
Medline ID
PubMed ID 11315566
Journal J Biol Inorg Chem
Year 2001
Volume 6
Pages 300-14
Authors Musiani F, Arnofi E, Casadio R, Ciurli S
Title Structure-based computational study of the catalytic and inhibition mechanisms of urease.
Related PDB
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11373609
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 480-2
Authors Dunn BE, Grutter MG
Title Helicobacter pylori springs another surprise.
Related PDB
Related UniProtKB
[27]
Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), AND SUBUNIT STRUCTURE.
Medline ID
PubMed ID 11373617
Journal Nat Struct Biol
Year 2001
Volume 8
Pages 505-9
Authors Ha NC, Oh ST, Sung JY, Cha KA, Lee MH, Oh BH
Title Supramolecular assembly and acid resistance of Helicobacter pylori urease.
Related PDB 1e9y 1e9z
Related UniProtKB P14916 P69996
[28]
Resource
Comments
Medline ID
PubMed ID 11300826
Journal Inorg Chem
Year 2001
Volume 40
Pages 1250-5
Authors Barrios AM, Lippard SJ
Title Decomposition of alkyl-substituted urea molecules at a hydroxide-bridged dinickel center.
Related PDB
Related UniProtKB
[29]
Resource
Comments
Medline ID
PubMed ID 11807281
Journal Acta Crystallogr D Biol Crystallogr
Year 2002
Volume 58
Pages 374-6
Authors Sheridan L, Wilmot CM, Cromie KD, van der Logt P, Phillips SE
Title Crystallization and preliminary X-ray structure determination of jack bean urease with a bound antibody fragment.
Related PDB
Related UniProtKB
[30]
Resource
Comments
Medline ID
PubMed ID 12121941
Journal Antimicrob Agents Chemother
Year 2002
Volume 46
Pages 2613-8
Authors Mishra H, Parrill AL, Williamson JS
Title Three-dimensional quantitative structure-activity relationship and comparative molecular field analysis of dipeptide hydroxamic acid Helicobacter pylori urease inhibitors.
Related PDB
Related UniProtKB
[31]
Resource
Comments
Medline ID
PubMed ID 14664576
Journal J Am Chem Soc
Year 2003
Volume 125
Pages 15324-37
Authors Suarez D, Diaz N, Merz KM Jr
Title Ureases: quantum chemical calculations on cluster models.
Related PDB
Related UniProtKB
[32]
Resource
Comments
Medline ID
PubMed ID 12913138
Journal Plant Physiol
Year 2003
Volume 132
Pages 1801-10
Authors Goldraij A, Beamer LJ, Polacco JC
Title Interallelic complementation at the ubiquitous urease coding locus of soybean.
Related PDB
Related UniProtKB
[33]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 15038715
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 3714-5
Authors Benini S, Rypniewski WR, Wilson KS, Mangani S, Ciurli S
Title Molecular details of urease inhibition by boric acid: insights into the catalytic mechanism.
Related PDB 1s3t
Related UniProtKB
[34]
Resource
Comments
Medline ID
PubMed ID 15174863
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 6932-44
Authors Estiu G, Merz KM Jr
Title The hydrolysis of urea and the proficiency of urease.
Related PDB
Related UniProtKB
[35]
Resource
Comments
Medline ID
PubMed ID 15382918
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 11832-42
Authors Estiu G, Merz KM Jr
Title Enzymatic catalysis of urea decomposition: elimination or hydrolysis?
Related PDB
Related UniProtKB
[36]
Resource
Comments
Medline ID
PubMed ID 16584179
Journal Biochemistry
Year 2006
Volume 45
Pages 4429-43
Authors Estiu G, Merz KM Jr
Title Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease.
Related PDB
Related UniProtKB
[37]
Resource
Comments
Medline ID
PubMed ID 17676790
Journal J Phys Chem B
Year 2007
Volume 111
Pages 10263-74
Authors Estiu G, Merz KM Jr
Title Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea.
Related PDB
Related UniProtKB
[38]
Resource
Comments
Medline ID
PubMed ID 20471401
Journal J Mol Biol
Year 2010
Volume 400
Pages 274-83
Authors Balasubramanian A, Ponnuraj K
Title Crystal structure of the first plant urease from jack bean: 83 years of journey from its first crystal to molecular structure.
Related PDB 3la4
Related UniProtKB
[39]
Resource
Comments
Medline ID
PubMed ID 21788478
Journal Proc Natl Acad Sci U S A
Year 2011
Volume 108
Pages 13095-9
Authors Carter EL, Tronrud DE, Taber SR, Karplus PA, Hausinger RP
Title Iron-containing urease in a pathogenic bacterium.
Related PDB 3qga 3qgk
Related UniProtKB
[40]
Resource
Comments
Medline ID
PubMed ID 21542631
Journal Acc Chem Res
Year 2011
Volume 44
Pages 520-30
Authors Zambelli B, Musiani F, Benini S, Ciurli S
Title Chemistry of Ni2+ in urease: sensing, trafficking, and catalysis.
Related PDB
Related UniProtKB

Comments
There are several types of urease enzymes based on the composition of subunits. This enzyme is composed of a single subunit, which contains a catalytic domain.
According to the literature, at least three catalytic mechanisms have been reported. Two mechanisms for hydrolysis, which proceeds through a tetrahedral intermediate (diaminohydroxymethanolate) that gives finally carbamate and ammonia (see [12], [17] and [20]). One mechanism for elimination, which proceeds through an intermediate, cyanic acid (see [23] and [28]).
(i) Hydrolysis by a reverse protonation mechanism: Carbonyl oxygen of urea is bound to Nickel-1, whereas a hydrolytic water is bound to Nickel-2. The hydrolytic water makes a nucleophilic attack on the carbonyl carbon of urea, forming a tetrahedral intermediate (diaminohydroxymethanolate). His593 acts as a general acid to protonate a leaving amino group, although the residue has a low pKa. Thus, carbamate and an ammonia can be produced. (see [12], [14], [19] and [20])
(ii) Hydrolysis by nucleophilic attack of a bridging hydroxide: Carbonyl oxygen of urea is bound to Nickel-1, whereas an amine group is bound to Nickel-2. The bridging hydroxide between the two nickel ions acts as a nucleophile, which attacks on the carbonyl carbon, forming a tetrahedral intermediate. The Asp residue, which is bound to Nickel-2, transfers proton from the hydroxyl group of the intermediate to the leaving amine group. His593 may stabilize the intermediate, rather than acting as a general acid. (see [17], [24], [33] and [40])
(iii) Elimination through cyanic acid (see [23], [28], [35], [36] and [37])
Alghough these reported mechanisms lead to a debate, the hydrolysis mechanism by bridging hydroxide seems to be the most reasonable, from structural viewpoints.

Created Updated
2005-10-18 2012-03-23