EzCatDB: M00030
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DB codeM00030
CATH domainDomain 12.30.40.10 : Urease, subunit C; domain 1
Domain 23.20.20.140 : TIM BarrelCatalytic domain
Domain 32.10.150.10 : Urease, subunit B
Domain 43.30.280.10 : Urease; subunit A
E.C.3.5.1.5
CSA1kra
MACiEM0087

CATH domainRelated DB codes (homologues)
2.10.150.10 : Urease, subunit BM00225,M00226
2.30.40.10 : Urease, subunit C; domain 1D00673,D00675,D00801,D00873,M00225,M00226
3.20.20.140 : TIM BarrelS00231,S00232,M00186,D00673,D00675,D00801,D00873,M00225,M00226
3.30.280.10 : Urease; subunit AM00225,M00226

Enzyme Name
UniProtKBKEGG

P18314P41020P0A660P18315P41021P0A662P18316P41022P0A676
Protein nameUrease subunit alphaUrease subunit alphaUrease subunit alphaUrease subunit betaUrease subunit betaUrease subunit betaUrease subunit gammaUrease subunit gammaUrease subunit gammaUrease
Urea amidohydrolase
SynonymsEC 3.5.1.5
Urea amidohydrolase subunit alpha
EC 3.5.1.5
Urea amidohydrolase subunit alpha
EC 3.5.1.5
Urea amidohydrolase subunit alpha
EC 3.5.1.5
Urea amidohydrolase subunit beta
EC 3.5.1.5
Urea amidohydrolase subunit beta
EC 3.5.1.5
Urea amidohydrolase subunit beta
EC 3.5.1.5
Urea amidohydrolase subunit gamma
EC 3.5.1.5
Urea amidohydrolase subunit gamma
EC 3.5.1.5
Urea amidohydrolase subunit gamma
RefSeq

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)


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)


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)
MEROPSM38.982 (Metallo)
M38.982 (Metallo)
M38.982 (Metallo)
M38.982 (Metallo)





PfamPF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
[Graphical view]
PF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
[Graphical view]
PF01979 (Amidohydro_1)
PF00449 (Urease_alpha)
[Graphical view]
PF00699 (Urease_beta)
[Graphical view]
PF00699 (Urease_beta)
[Graphical view]
PF00699 (Urease_beta)
[Graphical view]
PF00547 (Urease_gamma)
[Graphical view]
PF00547 (Urease_gamma)
[Graphical view]
PF00547 (Urease_gamma)
[Graphical view]

KEGG pathways
MAP codePathways
MAP00220Urea cycle and metabolism of amino groups
MAP00230Purine metabolism
MAP00791Atrazine degradation

UniProtKB:Accession NumberP18314P41020P0A660P18315P41021P0A662P18316P41022P0A676
Entry nameURE1_ENTAEURE1_BACPAURE1_MYCTUURE2_ENTAEURE2_BACPAURE2_MYCTUURE3_ENTAEURE3_BACPAURE3_MYCTU
ActivityUrea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).Urea + H(2)O = CO(2) + 2 NH(3).
SubunitHeterotrimer 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.Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme.Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme.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.Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme.Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme.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.Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme.Heterotrimer of UreA (gamma), UreB (beta) and UreC (alpha) subunits. Three heterotrimers associate to form the active enzyme.
Subcellular locationCytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).Cytoplasm (By similarity).
CofactorBinds 2 nickel ions per subunit.Binds 2 nickel ions per subunit.Binds 2 nickel ions per subunit.






Compound table: links to PDB-related databases & PoSSuM

CofactorsSubstratesProductsintermediates
KEGG-idC00291C00086C00001C00011C00014I00127C01563
CompoundNickelUreaH2OCO2NH3DiaminohydroxymethanolateCarbamate
Typeheavy metalamide group,amine groupH2Oothersamine group,organic ion

ChEBI28112
16199
48376
15377
16526
16134


PubChem935
1176
962
22247451
280
222


               
1a5kC01UnboundUnbound UnboundUnboundUnboundUnbound
1a5lC01UnboundUnbound UnboundUnboundUnboundUnbound
1a5mC01UnboundUnbound UnboundUnboundUnboundUnbound
1a5nC01UnboundUnbound UnboundUnboundUnboundUnbound
1a5oC01UnboundUnbound UnboundUnboundUnboundUnbound
1ef2A01UnboundUnbound UnboundUnboundUnboundUnbound
1ejrC01UnboundUnbound UnboundUnboundUnboundUnbound
1ejsC01UnboundUnbound UnboundUnboundUnboundUnbound
1ejtC01UnboundUnbound UnboundUnboundUnboundUnbound
1ejuC01UnboundUnbound UnboundUnboundUnboundUnbound
1ejvC01UnboundUnbound UnboundUnboundUnboundUnbound
1ejwC01UnboundUnbound UnboundUnboundUnboundUnbound
1ejxC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwaC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwbC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwcC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwdC01UnboundUnbound UnboundUnboundUnboundUnbound
1fweC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwfC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwgC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwhC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwiC01UnboundUnbound UnboundUnboundUnboundUnbound
1fwjC01UnboundUnbound UnboundUnboundUnboundUnbound
1kauC01UnboundUnbound UnboundUnboundUnboundUnbound
1kraC01UnboundUnbound UnboundUnboundUnboundUnbound
1krbC01UnboundUnbound UnboundUnboundUnboundUnbound
1krcC01UnboundUnbound UnboundUnboundUnboundUnbound
2kauC01UnboundUnbound UnboundUnboundUnboundUnbound
3kauC01UnboundUnbound UnboundUnboundUnboundUnbound
1ie7C01UnboundUnbound UnboundUnboundUnboundUnbound
1s3tC01UnboundUnbound UnboundUnboundUnboundUnbound
1ubpC01UnboundUnbound UnboundUnboundUnboundUnbound
2ubpC01UnboundUnbound UnboundUnboundUnboundUnbound
3ubpC01UnboundUnbound UnboundUnboundUnboundUnbound
4ubpC01UnboundUnbound UnboundUnboundUnboundUnbound
1a5kC02UnboundUnbound UnboundUnboundUnboundUnbound
1a5lC02UnboundUnbound UnboundUnboundUnboundUnbound
1a5mC02UnboundUnbound UnboundUnboundUnboundUnbound
1a5nC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1a5oC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ef2A02Analogue:2x_MNUnbound UnboundUnboundUnboundUnbound
1ejrC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ejsC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ejtC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ejuC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ejvC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ejwC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1ejxC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fwaC02Bound:2x_NIUnbound UnboundUnboundUnboundIntermediate-analogue:CO3
1fwbC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fwcC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fwdC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fweC02Bound:2x_NIUnbound UnboundUnboundUnboundIntermediate-analogue:HAE
1fwfC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fwgC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fwhC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1fwiC02Bound:_NIUnbound UnboundUnboundUnboundUnbound
1fwjC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1kauC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1kraC02UnboundUnbound UnboundUnboundUnboundUnbound
1krbC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
1krcC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
2kauC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
3kauC02UnboundUnbound UnboundUnboundUnboundUnbound
1ie7C02Bound:2x_NIUnbound UnboundUnboundTransition-state-analogue:PO4Unbound
1s3tC02Bound:2x_NIAnalogue:BO3Bound:HOH 604UnboundUnboundUnboundUnbound
1ubpC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
2ubpC02Bound:2x_NIUnbound UnboundUnboundUnboundUnbound
3ubpC02Bound:2x_NIUnbound UnboundUnboundTransition-state-analogue:2PAUnbound
4ubpC02Bound:2x_NIUnbound UnboundUnboundUnboundIntermediate-analogue:HAE
1a5kBUnboundUnbound UnboundUnboundUnboundUnbound
1a5lBUnboundUnbound UnboundUnboundUnboundUnbound
1a5mBUnboundUnbound UnboundUnboundUnboundUnbound
1a5nBUnboundUnbound UnboundUnboundUnboundUnbound
1a5oBUnboundUnbound UnboundUnboundUnboundUnbound
1ef2BUnboundUnbound UnboundUnboundUnboundUnbound
1ejrBUnboundUnbound UnboundUnboundUnboundUnbound
1ejsBUnboundUnbound UnboundUnboundUnboundUnbound
1ejtBUnboundUnbound UnboundUnboundUnboundUnbound
1ejuBUnboundUnbound UnboundUnboundUnboundUnbound
1ejvBUnboundUnbound UnboundUnboundUnboundUnbound
1ejwBUnboundUnbound UnboundUnboundUnboundUnbound
1ejxBUnboundUnbound UnboundUnboundUnboundUnbound
1fwaBUnboundUnbound UnboundUnboundUnboundUnbound
1fwbBUnboundUnbound UnboundUnboundUnboundUnbound
1fwcBUnboundUnbound UnboundUnboundUnboundUnbound
1fwdBUnboundUnbound UnboundUnboundUnboundUnbound
1fweBUnboundUnbound UnboundUnboundUnboundUnbound
1fwfBUnboundUnbound UnboundUnboundUnboundUnbound
1fwgBUnboundUnbound UnboundUnboundUnboundUnbound
1fwhBUnboundUnbound UnboundUnboundUnboundUnbound
1fwiBUnboundUnbound UnboundUnboundUnboundUnbound
1fwjBUnboundUnbound UnboundUnboundUnboundUnbound
1kauBUnboundUnbound UnboundUnboundUnboundUnbound
1kraBUnboundUnbound UnboundUnboundUnboundUnbound
1krbBUnboundUnbound UnboundUnboundUnboundUnbound
1krcBUnboundUnbound UnboundUnboundUnboundUnbound
2kauBUnboundUnbound UnboundUnboundUnboundUnbound
3kauBUnboundUnbound UnboundUnboundUnboundUnbound
1ie7BUnboundUnbound UnboundUnboundUnboundUnbound
1s3tBUnboundUnbound UnboundUnboundUnboundUnbound
1ubpBUnboundUnbound UnboundUnboundUnboundUnbound
2ubpBUnboundUnbound UnboundUnboundUnboundUnbound
3ubpBUnboundUnbound UnboundUnboundUnboundUnbound
4ubpBUnboundUnbound UnboundUnboundUnboundUnbound
1a5kAUnboundUnbound UnboundUnboundUnboundUnbound
1a5lAUnboundUnbound UnboundUnboundUnboundUnbound
1a5mAUnboundUnbound UnboundUnboundUnboundUnbound
1a5nAUnboundUnbound UnboundUnboundUnboundUnbound
1a5oAUnboundUnbound UnboundUnboundUnboundUnbound
1ef2CUnboundUnbound UnboundUnboundUnboundUnbound
1ejrAUnboundUnbound UnboundUnboundUnboundUnbound
1ejsAUnboundUnbound UnboundUnboundUnboundUnbound
1ejtAUnboundUnbound UnboundUnboundUnboundUnbound
1ejuAUnboundUnbound UnboundUnboundUnboundUnbound
1ejvAUnboundUnbound UnboundUnboundUnboundUnbound
1ejwAUnboundUnbound UnboundUnboundUnboundUnbound
1ejxAUnboundUnbound UnboundUnboundUnboundUnbound
1fwaAUnboundUnbound UnboundUnboundUnboundUnbound
1fwbAUnboundUnbound UnboundUnboundUnboundUnbound
1fwcAUnboundUnbound UnboundUnboundUnboundUnbound
1fwdAUnboundUnbound UnboundUnboundUnboundUnbound
1fweAUnboundUnbound UnboundUnboundUnboundUnbound
1fwfAUnboundUnbound UnboundUnboundUnboundUnbound
1fwgAUnboundUnbound UnboundUnboundUnboundUnbound
1fwhAUnboundUnbound UnboundUnboundUnboundUnbound
1fwiAUnboundUnbound UnboundUnboundUnboundUnbound
1fwjAUnboundUnbound UnboundUnboundUnboundUnbound
1kauAUnboundUnbound UnboundUnboundUnboundUnbound
1kraAUnboundUnbound UnboundUnboundUnboundUnbound
1krbAUnboundUnbound UnboundUnboundUnboundUnbound
1krcAUnboundUnbound UnboundUnboundUnboundUnbound
2kauAUnboundUnbound UnboundUnboundUnboundUnbound
3kauAUnboundUnbound UnboundUnboundUnboundUnbound
1ie7AUnboundUnbound UnboundUnboundUnboundUnbound
1s3tAUnboundUnbound UnboundUnboundUnboundUnbound
1ubpAUnboundUnbound UnboundUnboundUnboundUnbound
2ubpAUnboundUnbound UnboundUnboundUnboundUnbound
3ubpAUnboundUnbound UnboundUnboundUnboundUnbound
4ubpAUnboundUnbound UnboundUnboundUnboundUnbound
2fvhAUnboundUnbound UnboundUnboundUnboundUnbound
2fvhBUnboundUnbound UnboundUnboundUnboundUnbound
2fvhCUnboundUnbound UnboundUnboundUnboundUnbound

Active-site residues
resource
Swiss-prot;P18314, P41020, P69996 & literature [17], [22], [31]
pdbCatalytic residuesCofactor-binding residuesModified residuescomment
            
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 
 
 
 
1a5kC02HIS  219;ASP  221;HIS  320;ARG  336
                       ;HIS  246;HIS  272(Nickel-1);HIS  134;HIS  136;ASP  360(Nickel-2)
                          
mutant K217E
1a5lC02HIS  219;ASP  221;        ;        
                       ;HIS  246;HIS  272(Nickel-1);HIS  134;HIS  136;ASP  360(Nickel-2)
                          
mutant K217C, C319A, invisible 309-338
1a5mC02HIS  219;ASP  221;HIS  320;ARG  336
                       ;HIS  246;HIS  272(Nickel-1);HIS  134;HIS  136;ASP  360(Nickel-2)
                          
mutant K217A
1a5nC02HIS  219;ASP  221;        ;ARG  336
                       ;HIS  246;HIS  272(Nickel-1);HIS  134;HIS  136;ASP  360(Nickel-2)
                          
mutant K217A, invisible 316-330
1a5oC02HIS  219;ASP  221;HIS  320;ARG  336
                       ;HIS  246;HIS  272(Nickel-1);HIS  134;HIS  136;ASP  360(Nickel-2)
                          
mutant K217C, C319A
1ef2A02HIS 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)
 
1ejrC02HIS 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
1ejuC02HIS 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
1ejvC02HIS 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
1ejwC02HIS 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)
 
1ejxC02HIS 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
1fwaC02HIS  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
1fwbC02HIS  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
1fwcC02HIS  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
1fwdC02HIS  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
1fweC02HIS  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
1fwfC02HIS  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
1fwgC02HIS  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
1fwhC02HIS  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
1fwiC02HIS  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
1fwjC02HIS  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)
 
1kauC02HIS  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)
 
1kraC02HIS  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
1krcC02HIS  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
2kauC02HIS  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)
 
3kauC02HIS  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)
                          
 
1ie7C02HIS  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)
 
1s3tC02HIS  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)
 
1ubpC02HIS  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)
 
2ubpC02HIS  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)
 
3ubpC02HIS  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)
 
4ubpC02HIS  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
ReferencesSectionsNo. 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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[9]
CommentsX-ray crystallography
PubMed ID8702515
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Related PDB1fwi
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CommentsX-ray crystallography
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[14]
CommentsX-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
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[15]
CommentsX-ray crystallography
JournalJ Biol Inorg Chem
Year1998
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[16]
CommentsX-RAY CRYSTALLOGRAPHY (2.5 ANGSTROMS).
PubMed ID10555581
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Related UniProtKBP18314,P18315,P18316
[17]
CommentsX-RAY CRYSTALLOGRAPHY (1.65 ANGSTROMS).
Medline ID99148127
PubMed ID10368287
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TitleA 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.
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Related UniProtKBP41020,P41021,P41022
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Year2000
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Pages8575-84
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[21]
CommentsX-ray crystallography
PubMed ID10766443
JournalJ Biol Inorg Chem
Year2000
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PubMed ID10798524
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Year2000
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comments
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])
(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.

createdupdated
2005-10-182012-03-23


Copyright: Nozomi Nagano, JST & CBRC-AIST
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Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2005 - March 2006)
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Funded by BIRD/Japan Science and Technology Corporation (JST) (September 2005 - September 2008)
Funded by BIRD/Japan Science and Technology Corporation (JST) (October 2007 - September 2010)
Funded by Grant-in-Aid for Publication of Scientific Research Results/Japan Society for the Promotion of Science (JSPS) (April 2011 - March 2012)
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