DB code: M00225
| 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 | ||
| M-CSA | ||
| MACiE | ||
| CATH domain | Related DB codes (homologues) |
|---|---|
| 2.30.40.10 : Urease, subunit C; domain 1 | D00673 D00675 D00801 D00873 M00030 M00226 |
| 3.20.20.140 : TIM Barrel | S00231 S00232 M00186 D00673 D00675 D00801 D00873 M00030 M00226 |
| 3.30.280.10 : Urease; subunit A | M00030 M00226 |
| 2.10.150.10 : Urease, subunit B | M00030 M00226 |
| Uniprot Enzyme Name | UniprotKB | Protein name | Synonyms | RefSeq | MEROPS | Pfam |
|---|---|---|---|---|---|
| P69996 |
Urease subunit beta
|
EC
3.5.1.5
Urea amidohydrolase subunit beta |
NP_206872.1
(Protein)
NC_000915.1 (DNA/RNA sequence) YP_006933994.1 (Protein) NC_018939.1 (DNA/RNA sequence) |
M38.982
(Metallo)
|
PF01979
(Amidohydro_1)
PF00449 (Urease_alpha) [Graphical View] |
| D3UJ80 |
|
None |
YP_003517278.1
(Protein)
NC_013949.1 (DNA/RNA sequence) |
M38.982
(Metallo)
|
PF01979
(Amidohydro_1)
PF00449 (Urease_alpha) [Graphical View] |
| P14916 |
Urease subunit alpha
|
EC
3.5.1.5
Urea amidohydrolase subunit alpha |
NP_206873.1
(Protein)
NC_000915.1 (DNA/RNA sequence) YP_006933995.1 (Protein) NC_018939.1 (DNA/RNA sequence) |
PF00699
(Urease_beta)
PF00547 (Urease_gamma) [Graphical View] |
|
| D3UJ81 |
|
None |
YP_003517279.1
(Protein)
NC_013949.1 (DNA/RNA sequence) |
PF00699
(Urease_beta)
PF00547 (Urease_gamma) [Graphical View] |
| KEGG enzyme name |
|---|
|
Urease
Urea amidohydrolase |
| UniprotKB: Accession Number | Entry name | Activity | Subunit | Subcellular location | Cofactor |
|---|---|---|---|---|---|
| P69996 | URE2_HELPY | Urea + H(2)O = CO(2) + 2 NH(3). | Heterohexamer of 3 UreA (alpha) and 3 UreB (beta) subunits. Four heterohexamers assemble to form a 16 nm dodecameric complex. | Cytoplasm. Note=Also associates with the outer membrane upon autolysis of neighboring bacteria. | Binds 2 nickel ions per subunit. |
| D3UJ80 | D3UJ80_HELM1 | Urea + H(2)O = CO(2) + 2 NH(3). | Heterohexamer of 3 UreA (alpha) and 3 UreB (beta) subunits (By similarity). | Cytoplasm (By similarity). | Binds 2 nickel ions per subunit (By similarity). |
| P14916 | URE23_HELPY | Urea + H(2)O = CO(2) + 2 NH(3). | Heterohexamer of 3 UreA (alpha) and 3 UreB (beta) subunits. Four heterohexamers assemble to form a 16 nm dodecameric complex. | Cytoplasm. Note=Also associates with the outer membrane upon autolysis of neighboring bacteria. | |
| D3UJ81 | D3UJ81_HELM1 | Urea + H(2)O = CO(2) + 2 NH(3). |
| 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 |
|||||||
| 1e9yB01 |
|
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|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1e9zB01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaC01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaF01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaI01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaL01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaO01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaR01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkC01 |
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkF01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkI01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkL01 |
|
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkO01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkR01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1e9yB02 |
|
|
|
|
|
Bound:2x_NI | Unbound | Unbound | Unbound | Unbound | Intermediate-analogue:HAE | |
| 1e9zB02 |
|
|
|
|
|
Bound:2x_NI | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaC02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaF02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaI02 |
|
|
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|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaL02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaO02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaR02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkC02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkF02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkI02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkL02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkO02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkR02 |
|
|
|
|
|
Analogue:2x_FE | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1e9yA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1e9zA01 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaD02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaG02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaJ02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaM02 |
|
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaP02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkA02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkD02 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkG02 |
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkJ02 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkM02 |
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkP02 |
|
|
|
|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1e9yA02 |
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 1e9zA02 |
|
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|
|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaA01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaD01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaG01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaJ01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaM01 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgaP01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkA01 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkD01 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkG01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkJ01 |
|
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Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkM01 |
|
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|
Unbound | Unbound | Unbound | Unbound | Unbound | Unbound | |
| 3qgkP01 |
|
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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 | |||||
| 1e9yB01 |
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| 1e9zB01 |
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| 3qgaC01 |
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| 3qgaF01 |
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| 3qgaI01 |
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| 3qgaL01 |
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| 3qgaO01 |
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| 3qgaR01 |
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| 3qgkC01 |
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| 3qgkF01 |
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| 3qgkI01 |
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| 3qgkL01 |
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| 3qgkO01 |
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| 3qgkR01 |
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| 1e9yB02 |
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|
HIS 221;ASP 223;HIS 322;ARG 338 | KCX 219(Nickel-1 & -2);HIS 248;HIS 274(Nickel-1);HIS 136;HIS 138;ASP 362(Nickel-2) | KCX 219(Carbamylated LYS) | ||
| 1e9zB02 |
|
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|
HIS 221;ASP 223;HIS 322;ARG 338 | KCX 219(Nickel-1 & -2);HIS 248;HIS 274(Nickel-1);HIS 136;HIS 138;ASP 362(Nickel-2) | KCX 219(Carbamylated LYS) | ||
| 3qgaC02 |
|
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|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgaF02 |
|
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|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgaI02 |
|
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|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgaL02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgaO02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgaR02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgkC02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgkF02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgkI02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgkL02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgkO02 |
|
|
|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 3qgkR02 |
|
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|
|
|
HIS 220;ASP 222;HIS 321;ARG 337 | KCX 218(Nickel-1 & -2);HIS 247;HIS 273(Nickel-1);HIS 135;HIS 137;ASP 361(Nickel-2) | KCX 218(Carbamylated LYS) | invisible 329-332 | |
| 1e9yA01 |
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| 1e9zA01 |
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| 3qgaA02 |
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| 3qgaD02 |
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| 3qgaG02 |
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| 3qgaJ02 |
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| 3qgaM02 |
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| 3qgaP02 |
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| 3qgkA02 |
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| 3qgkD02 |
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| 3qgkG02 |
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| 3qgkJ02 |
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| 3qgkM02 |
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| 3qgkP02 |
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| 1e9yA02 |
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| 1e9zA02 |
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| 3qgaA01 |
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| 3qgaD01 |
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| 3qgaG01 |
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| 3qgaJ01 |
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| 3qgaM01 |
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| 3qgaP01 |
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| 3qgkA01 |
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| 3qgkD01 |
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| 3qgkG01 |
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| 3qgkJ01 |
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| 3qgkM01 |
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| 3qgkP01 |
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| 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, |
| 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, |
| Related PDB | |
| Related UniProtKB | |
| [20] | |
| Resource | |
| Comments |
X-RAY CRYSTALLOGRAPHY (1.6 ANGSTROMS), |
| 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), |
| 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. |
| 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, |
| Related PDB | |
| Related UniProtKB | |
| Comments |
|---|
|
There are several types of urease enzymes based on the composition of subunits. According to the literature, (i) Hydrolysis by a reverse protonation mechanism: Carbonyl oxygen of urea is bound to Nickel-1, (ii) Hydrolysis by nucleophilic attack of a bridging hydroxide: Carbonyl oxygen of urea is bound to Nickel-1, (iii) Elimination through cyanic acid (see [23], Alghough these reported mechanisms lead to a debate, |
| Created | Updated |
|---|---|
| 2005-10-18 | 2012-03-23 |