DB code: M00030

CATH domain 2.30.40.10 : Urease, subunit C; domain 1
3.20.20.140 : TIM Barrel Catalytic domain
2.10.150.10 : Urease, subunit B
3.30.280.10 : Urease; subunit A
E.C. 3.5.1.5
CSA 1kra
M-CSA 1kra
MACiE M0087

CATH domain Related DB codes (homologues)
2.10.150.10 : Urease, subunit B M00225 M00226
2.30.40.10 : Urease, subunit C; domain 1 D00673 D00675 D00801 D00873 M00225 M00226
3.20.20.140 : TIM Barrel S00231 S00232 M00186 D00673 D00675 D00801 D00873 M00225 M00226
3.30.280.10 : Urease; subunit A M00225 M00226

Uniprot Enzyme Name
UniprotKB Protein name Synonyms MEROPS Pfam RefSeq
P18314 Urease subunit alpha
EC 3.5.1.5
Urea amidohydrolase subunit alpha
M38.982 (Metallo)
PF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
[Graphical View]
P41020 Urease subunit alpha
EC 3.5.1.5
Urea amidohydrolase subunit alpha
M38.982 (Metallo)
PF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
[Graphical View]
P0A660 Urease subunit alpha
EC 3.5.1.5
Urea amidohydrolase subunit alpha
M38.982 (Metallo)
PF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
[Graphical View]
NP_216366.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_336355.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006515250.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
YP_007610509.1 (Protein)
NC_020559.1 (DNA/RNA sequence)
P18315 Urease subunit beta
EC 3.5.1.5
Urea amidohydrolase subunit beta
M38.982 (Metallo)
PF00699 (Urease_beta)
[Graphical View]
P41021 Urease subunit beta
EC 3.5.1.5
Urea amidohydrolase subunit beta
PF00699 (Urease_beta)
[Graphical View]
P0A662 Urease subunit beta
EC 3.5.1.5
Urea amidohydrolase subunit beta
PF00699 (Urease_beta)
[Graphical View]
NP_216365.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_336354.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006515249.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
YP_007610508.1 (Protein)
NC_020559.1 (DNA/RNA sequence)
P18316 Urease subunit gamma
EC 3.5.1.5
Urea amidohydrolase subunit gamma
PF00547 (Urease_gamma)
[Graphical View]
P41022 Urease subunit gamma
EC 3.5.1.5
Urea amidohydrolase subunit gamma
PF00547 (Urease_gamma)
[Graphical View]
P0A676 Urease subunit gamma
EC 3.5.1.5
Urea amidohydrolase subunit gamma
PF00547 (Urease_gamma)
[Graphical View]
NP_216364.1 (Protein)
NC_000962.3 (DNA/RNA sequence)
NP_336353.1 (Protein)
NC_002755.2 (DNA/RNA sequence)
YP_006515248.1 (Protein)
NC_018143.1 (DNA/RNA sequence)
YP_007610507.1 (Protein)
NC_020559.1 (DNA/RNA sequence)

KEGG enzyme name
Urease
Urea amidohydrolase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P18314 URE1_ENTAE Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. The apoenzyme interacts with an accessory complex composed of UreD, UreF and UreG, which is required for the assembly of the nickel containing metallocenter of UreC. The UreE protein may also play a direct role as a metallochaperone in nickel transfer to the urease apoprotein. Cytoplasm (By similarity). Binds 2 nickel ions per subunit.
P41020 URE1_BACPA Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Cytoplasm (By similarity). Binds 2 nickel ions per subunit.
P0A660 URE1_MYCTU Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Cytoplasm (By similarity). Binds 2 nickel ions per subunit.
P18315 URE2_ENTAE Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. The apoenzyme interacts with an accessory complex composed of UreD, UreF and UreG, which is required for the assembly of the nickel containing metallocenter of UreC. The UreE protein may also play a direct role as a metallochaperone in nickel transfer to the urease apoprotein. Cytoplasm (By similarity).
P41021 URE2_BACPA Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Cytoplasm (By similarity).
P0A662 URE2_MYCTU Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Cytoplasm (By similarity).
P18316 URE3_ENTAE Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. The apoenzyme interacts with an accessory complex composed of UreD, UreF and UreG, which is required for the assembly of the nickel containing metallocenter of UreC. The UreE protein may also play a direct role as a metallochaperone in nickel transfer to the urease apoprotein. Cytoplasm (By similarity).
P41022 URE3_BACPA Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Cytoplasm (By similarity).
P0A676 URE3_MYCTU Urea + H(2)O = CO(2) + 2 NH(3). Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme. Cytoplasm (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
28112
16199
48376
16199
48376
15377
15377
16526
16526
16134
16134
PubChem 935
935
1176
1176
22247451
962
22247451
962
280
280
222
222
1a5kC01 Unbound Unbound Unbound Unbound Unbound Unbound
1a5lC01 Unbound Unbound Unbound Unbound Unbound Unbound
1a5mC01 Unbound Unbound Unbound Unbound Unbound Unbound
1a5nC01 Unbound Unbound Unbound Unbound Unbound Unbound
1a5oC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ef2A01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejrC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejsC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejtC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejuC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejvC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejwC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ejxC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwaC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwbC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwcC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwdC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fweC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwfC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwgC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwhC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwiC01 Unbound Unbound Unbound Unbound Unbound Unbound
1fwjC01 Unbound Unbound Unbound Unbound Unbound Unbound
1kauC01 Unbound Unbound Unbound Unbound Unbound Unbound
1kraC01 Unbound Unbound Unbound Unbound Unbound Unbound
1krbC01 Unbound Unbound Unbound Unbound Unbound Unbound
1krcC01 Unbound Unbound Unbound Unbound Unbound Unbound
2kauC01 Unbound Unbound Unbound Unbound Unbound Unbound
3kauC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ie7C01 Unbound Unbound Unbound Unbound Unbound Unbound
1s3tC01 Unbound Unbound Unbound Unbound Unbound Unbound
1ubpC01 Unbound Unbound Unbound Unbound Unbound Unbound
2ubpC01 Unbound Unbound Unbound Unbound Unbound Unbound
3ubpC01 Unbound Unbound Unbound Unbound Unbound Unbound
4ubpC01 Unbound Unbound Unbound Unbound Unbound Unbound
1a5kC02 Unbound Unbound Unbound Unbound Unbound Unbound
1a5lC02 Unbound Unbound Unbound Unbound Unbound Unbound
1a5mC02 Unbound Unbound Unbound Unbound Unbound Unbound
1a5nC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1a5oC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ef2A02 Analogue:2x_MN Unbound Unbound Unbound Unbound Unbound
1ejrC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ejsC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ejtC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ejuC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ejvC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ejwC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1ejxC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fwaC02 Bound:2x_NI Unbound Unbound Unbound Unbound Intermediate-analogue:CO3
1fwbC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fwcC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fwdC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fweC02 Bound:2x_NI Unbound Unbound Unbound Unbound Intermediate-analogue:HAE
1fwfC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fwgC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fwhC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1fwiC02 Bound:_NI Unbound Unbound Unbound Unbound Unbound
1fwjC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1kauC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1kraC02 Unbound Unbound Unbound Unbound Unbound Unbound
1krbC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
1krcC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
2kauC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
3kauC02 Unbound Unbound Unbound Unbound Unbound Unbound
1ie7C02 Bound:2x_NI Unbound Unbound Unbound Transition-state-analogue:PO4 Unbound
1s3tC02 Bound:2x_NI Analogue:BO3 Bound:HOH_604 Unbound Unbound Unbound Unbound
1ubpC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
2ubpC02 Bound:2x_NI Unbound Unbound Unbound Unbound Unbound
3ubpC02 Bound:2x_NI Unbound Unbound Unbound Transition-state-analogue:2PA Unbound
4ubpC02 Bound:2x_NI Unbound Unbound Unbound Unbound Intermediate-analogue:HAE
1a5kB Unbound Unbound Unbound Unbound Unbound Unbound
1a5lB Unbound Unbound Unbound Unbound Unbound Unbound
1a5mB Unbound Unbound Unbound Unbound Unbound Unbound
1a5nB Unbound Unbound Unbound Unbound Unbound Unbound
1a5oB Unbound Unbound Unbound Unbound Unbound Unbound
1ef2B Unbound Unbound Unbound Unbound Unbound Unbound
1ejrB Unbound Unbound Unbound Unbound Unbound Unbound
1ejsB Unbound Unbound Unbound Unbound Unbound Unbound
1ejtB Unbound Unbound Unbound Unbound Unbound Unbound
1ejuB Unbound Unbound Unbound Unbound Unbound Unbound
1ejvB Unbound Unbound Unbound Unbound Unbound Unbound
1ejwB Unbound Unbound Unbound Unbound Unbound Unbound
1ejxB Unbound Unbound Unbound Unbound Unbound Unbound
1fwaB Unbound Unbound Unbound Unbound Unbound Unbound
1fwbB Unbound Unbound Unbound Unbound Unbound Unbound
1fwcB Unbound Unbound Unbound Unbound Unbound Unbound
1fwdB Unbound Unbound Unbound Unbound Unbound Unbound
1fweB Unbound Unbound Unbound Unbound Unbound Unbound
1fwfB Unbound Unbound Unbound Unbound Unbound Unbound
1fwgB Unbound Unbound Unbound Unbound Unbound Unbound
1fwhB Unbound Unbound Unbound Unbound Unbound Unbound
1fwiB Unbound Unbound Unbound Unbound Unbound Unbound
1fwjB Unbound Unbound Unbound Unbound Unbound Unbound
1kauB Unbound Unbound Unbound Unbound Unbound Unbound
1kraB Unbound Unbound Unbound Unbound Unbound Unbound
1krbB Unbound Unbound Unbound Unbound Unbound Unbound
1krcB Unbound Unbound Unbound Unbound Unbound Unbound
2kauB Unbound Unbound Unbound Unbound Unbound Unbound
3kauB Unbound Unbound Unbound Unbound Unbound Unbound
1ie7B Unbound Unbound Unbound Unbound Unbound Unbound
1s3tB Unbound Unbound Unbound Unbound Unbound Unbound
1ubpB Unbound Unbound Unbound Unbound Unbound Unbound
2ubpB Unbound Unbound Unbound Unbound Unbound Unbound
3ubpB Unbound Unbound Unbound Unbound Unbound Unbound
4ubpB Unbound Unbound Unbound Unbound Unbound Unbound
1a5kA Unbound Unbound Unbound Unbound Unbound Unbound
1a5lA Unbound Unbound Unbound Unbound Unbound Unbound
1a5mA Unbound Unbound Unbound Unbound Unbound Unbound
1a5nA Unbound Unbound Unbound Unbound Unbound Unbound
1a5oA Unbound Unbound Unbound Unbound Unbound Unbound
1ef2C Unbound Unbound Unbound Unbound Unbound Unbound
1ejrA Unbound Unbound Unbound Unbound Unbound Unbound
1ejsA Unbound Unbound Unbound Unbound Unbound Unbound
1ejtA Unbound Unbound Unbound Unbound Unbound Unbound
1ejuA Unbound Unbound Unbound Unbound Unbound Unbound
1ejvA Unbound Unbound Unbound Unbound Unbound Unbound
1ejwA Unbound Unbound Unbound Unbound Unbound Unbound
1ejxA Unbound Unbound Unbound Unbound Unbound Unbound
1fwaA Unbound Unbound Unbound Unbound Unbound Unbound
1fwbA Unbound Unbound Unbound Unbound Unbound Unbound
1fwcA Unbound Unbound Unbound Unbound Unbound Unbound
1fwdA Unbound Unbound Unbound Unbound Unbound Unbound
1fweA Unbound Unbound Unbound Unbound Unbound Unbound
1fwfA Unbound Unbound Unbound Unbound Unbound Unbound
1fwgA Unbound Unbound Unbound Unbound Unbound Unbound
1fwhA Unbound Unbound Unbound Unbound Unbound Unbound
1fwiA Unbound Unbound Unbound Unbound Unbound Unbound
1fwjA Unbound Unbound Unbound Unbound Unbound Unbound
1kauA Unbound Unbound Unbound Unbound Unbound Unbound
1kraA Unbound Unbound Unbound Unbound Unbound Unbound
1krbA Unbound Unbound Unbound Unbound Unbound Unbound
1krcA Unbound Unbound Unbound Unbound Unbound Unbound
2kauA Unbound Unbound Unbound Unbound Unbound Unbound
3kauA Unbound Unbound Unbound Unbound Unbound Unbound
1ie7A Unbound Unbound Unbound Unbound Unbound Unbound
1s3tA Unbound Unbound Unbound Unbound Unbound Unbound
1ubpA Unbound Unbound Unbound Unbound Unbound Unbound
2ubpA Unbound Unbound Unbound Unbound Unbound Unbound
3ubpA Unbound Unbound Unbound Unbound Unbound Unbound
4ubpA Unbound Unbound Unbound Unbound Unbound Unbound
2fvhA Unbound Unbound Unbound Unbound Unbound Unbound
2fvhB Unbound Unbound Unbound Unbound Unbound Unbound
2fvhC Unbound Unbound Unbound Unbound Unbound 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
1a5kC01
1a5lC01
1a5mC01
1a5nC01
1a5oC01
1ef2A01
1ejrC01
1ejsC01
1ejtC01
1ejuC01
1ejvC01
1ejwC01
1ejxC01
1fwaC01
1fwbC01
1fwcC01
1fwdC01
1fweC01
1fwfC01
1fwgC01
1fwhC01
1fwiC01
1fwjC01
1kauC01
1kraC01
1krbC01
1krcC01
2kauC01
3kauC01
1ie7C01
1s3tC01
1ubpC01
2ubpC01
3ubpC01
4ubpC01
1a5kC02 HIS 219;ASP 221;HIS 320;ARG 336 ;HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) mutant K217E
1a5lC02 HIS 219;ASP 221; ; ;HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) mutant K217C, C319A, invisible 309-338
1a5mC02 HIS 219;ASP 221;HIS 320;ARG 336 ;HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) mutant K217A
1a5nC02 HIS 219;ASP 221;;ARG 336 ;HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) mutant K217A, invisible 316-330
1a5oC02 HIS 219;ASP 221;HIS 320;ARG 336 ;HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) mutant K217C, C319A
1ef2A02 HIS 1219;ASP 1221;HIS 1320;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS)
1ejrC02 HIS 1219; ; ;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS) mutant D1221A, invisible 1318-1330
1ejsC02 ;ASP 1221;HIS 1320;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS) mutant H1219N
1ejtC02 ;ASP 1221;HIS 1320;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS) mutant H1219Q
1ejuC02 HIS 1219;ASP 1221; ;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS) mutant H1320N, invisible 1318-1330
1ejvC02 HIS 1219;ASP 1221; ;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS) mutant H1320Q, invisible 1318-1330
1ejwC02 HIS 1219;ASP 1221;HIS 1320;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS)
1ejxC02 HIS 1219;ASP 1221; ;ARG 1336 KCX 1217(Nickel-1 & -2);HIS 1246;HIS 1272(Nickel-1);HIS 1134;HIS 1136;ASP 1360(Nickel-2) KCX 1217(Carbamylated LYS) invisible 1320-1329
1fwaC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319A
1fwbC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319A
1fwcC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319A
1fwdC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319A
1fweC02 HIS 219;ASP 221;;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319A, invisible 318-331
1fwfC02 HIS 219;ASP 221;;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319D, invisible 317-331
1fwgC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319S
1fwhC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant C319Y
1fwiC02 HIS 219;ASP 221;;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1); ;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant H134A, invisible 317-331
1fwjC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS)
1kauC02 HIS 219;ASP 221;HIS 320;ARG 336 LYS 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) CBX 217(Carbamylated LYS)
1kraC02 HIS 219;ASP 221;HIS 320;ARG 336 LYS 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2)
1krbC02 ;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS) mutant H219A
1krcC02 HIS 219;ASP 221;;ARG 336 LYS 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) CO2 576(Carbamylated LYS) mutant H320A
2kauC02 HIS 219;ASP 221;HIS 320;ARG 336 KCX 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2) KCX 217(Carbamylated LYS)
3kauC02 HIS 219;ASP 221;HIS 320;ARG 336 LYS 217(Nickel-1 & -2);HIS 246;HIS 272(Nickel-1);HIS 134;HIS 136;ASP 360(Nickel-2)
1ie7C02 HIS 222;ASP 224;HIS 323;ARG 339 KCX 220(Nickel-1 & -2);HIS 249;HIS 275(Nickel-1);HIS 137;HIS 139;ASP 363(Nickel-2) KCX 220(Carbamylated LYS)
1s3tC02 HIS 222;ASP 224;HIS 323;ARG 339 KCX 220(Nickel-1 & -2);HIS 249;HIS 275(Nickel-1);HIS 137;HIS 139;ASP 363(Nickel-2) KCX 220(Carbamylated LYS)
1ubpC02 HIS 222;ASP 224;HIS 323;ARG 339 KCX 220(Nickel-1 & -2);HIS 249;HIS 275(Nickel-1);HIS 137;HIS 139;ASP 363(Nickel-2) KCX 220(Carbamylated LYS)
2ubpC02 HIS 222;ASP 224;HIS 323;ARG 339 KCX 220(Nickel-1 & -2);HIS 249;HIS 275(Nickel-1);HIS 137;HIS 139;ASP 363(Nickel-2) KCX 220(Carbamylated LYS)
3ubpC02 HIS 222;ASP 224;HIS 323;ARG 339 KCX 220(Nickel-1 & -2);HIS 249;HIS 275(Nickel-1);HIS 137;HIS 139;ASP 363(Nickel-2) KCX 220(Carbamylated LYS)
4ubpC02 HIS 222;ASP 224;HIS 323;ARG 339 KCX 220(Nickel-1 & -2);HIS 249;HIS 275(Nickel-1);HIS 137;HIS 139;ASP 363(Nickel-2) KCX 220(Carbamylated LYS)
1a5kB
1a5lB
1a5mB
1a5nB
1a5oB
1ef2B
1ejrB
1ejsB
1ejtB
1ejuB
1ejvB
1ejwB
1ejxB
1fwaB
1fwbB
1fwcB
1fwdB
1fweB
1fwfB
1fwgB
1fwhB
1fwiB
1fwjB
1kauB
1kraB
1krbB
1krcB
2kauB
3kauB
1ie7B
1s3tB
1ubpB
2ubpB
3ubpB
4ubpB
1a5kA
1a5lA
1a5mA
1a5nA
1a5oA
1ef2C
1ejrA
1ejsA
1ejtA
1ejuA
1ejvA
1ejwA
1ejxA
1fwaA
1fwbA
1fwcA
1fwdA
1fweA
1fwfA
1fwgA
1fwhA
1fwiA
1fwjA
1kauA
1kraA
1krbA
1krcA
2kauA
3kauA
1ie7A
1s3tA
1ubpA
2ubpA
3ubpA
4ubpA
2fvhA
2fvhB
2fvhC

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

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Related UniProtKB
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Medline ID
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Related UniProtKB
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Medline ID
PubMed ID 8318888
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Related UniProtKB
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Medline ID
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Medline ID
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Related UniProtKB
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Medline ID
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Related UniProtKB
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Related UniProtKB
[11]
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Medline ID
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Related PDB
Related UniProtKB
[12]
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Comments
Medline ID
PubMed ID
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Title 70 Years of Crystalline Urease:? What Have We Learned?
Related PDB
Related UniProtKB
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Comments X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS).
Medline ID
PubMed ID 9761912
Journal Acta Crystallogr D Biol Crystallogr
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Related PDB
Related UniProtKB P41020 P41021 P41022
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Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
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Title Chemical rescue of Klebsiella aerogenes urease variants lacking the carbamylated-lysine nickel ligand.
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Related UniProtKB P18314 P18315 P18316
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Resource
Comments X-ray crystallography
Medline ID
PubMed ID
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Related PDB 1ubp
Related UniProtKB
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Resource
Comments X-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
Medline ID
PubMed ID 10555581
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Related UniProtKB P18314 P18315 P18316
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PubMed ID 10368287
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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
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Year 2000
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Related PDB
Related UniProtKB
[19]
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Comments
Medline ID
PubMed ID 10820010
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Year 2000
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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
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Related UniProtKB P18314 P18315 P18316
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Resource
Comments X-ray crystallography
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PubMed ID 10766443
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Related UniProtKB
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Medline ID
PubMed ID 10798524
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Related UniProtKB
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Medline ID
PubMed ID
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Related PDB
Related UniProtKB
[24]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 11713685
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Pages 778-90
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Related PDB 1ie7
Related UniProtKB
[25]
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Medline ID
PubMed ID 11315566
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Year 2001
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Pages 300-14
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Related PDB
Related UniProtKB
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Medline ID
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Year 2001
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Related UniProtKB
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Resource
Comments X-RAY CRYSTALLOGRAPHY (3.0 ANGSTROMS), AND SUBUNIT STRUCTURE.
Medline ID
PubMed ID 11373617
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Related PDB 1e9y 1e9z
Related UniProtKB P14916 P69996
[28]
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Medline ID
PubMed ID 11300826
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Pages 1250-5
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Related UniProtKB
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Medline ID
PubMed ID 11807281
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Related UniProtKB
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Medline ID
PubMed ID 12121941
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Related UniProtKB
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Medline ID
PubMed ID 14664576
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Related UniProtKB
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Medline ID
PubMed ID 12913138
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Related UniProtKB
[33]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 15038715
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Volume 126
Pages 3714-5
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Related PDB 1s3t
Related UniProtKB
[34]
Resource
Comments
Medline ID
PubMed ID 15174863
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Year 2004
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Pages 6932-44
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Related PDB
Related UniProtKB
[35]
Resource
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Medline ID
PubMed ID 15382918
Journal J Am Chem Soc
Year 2004
Volume 126
Pages 11832-42
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Title Enzymatic catalysis of urea decomposition: elimination or hydrolysis?
Related PDB
Related UniProtKB
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Medline ID
PubMed ID 16584179
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Year 2006
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Title Catalyzed decomposition of urea. Molecular dynamics simulations of the binding of urea to urease.
Related PDB
Related UniProtKB
[37]
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Medline ID
PubMed ID 17676790
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Authors Estiu G, Merz KM Jr
Title Competitive hydrolytic and elimination mechanisms in the urease catalyzed decomposition of urea.
Related PDB
Related UniProtKB
[38]
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Medline ID
PubMed ID 20471401
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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
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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
(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. His320 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.
There are several types of urease enzymes based on the composition of subunits. This enzyme is composed of three subunits, one of which has 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). His320 (PDB;1a5k) 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])

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