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Literature summary for 3.5.2.2 extracted from

  • Martinez-Rodriguez, S.; Martinez-Gomez, A.I.; Clemente-Jimenez, J.M.; Rodriguez-Vico, F.; Garcia-Ruiz, J.M.; Las Heras-Vazquez, F.J.; Gavira, J.A.
    Structure of dihydropyrimidinase from Sinorhizobium meliloti CECT4114: new features in an amidohydrolase family member (2010), J. Struct. Biol., 169, 200-208.
    View publication on PubMed

Activating Compound

Activating Compound Comment Organism Structure
2-mercaptoethanol 10 mM, 108% of initial activity Sinorhizobium meliloti
dithiothreitol 10 mM, 111% of initial activity Sinorhizobium meliloti

Cloned(Commentary)

Cloned (Comment) Organism
-
Sinorhizobium meliloti

Crystallization (Commentary)

Crystallization (Comment) Organism
to 1.85 A resolution. Enzyme consists of two domains, an (alpha/beta)8 TIM-like barrel domain, where the catalytic centre is located, and a smaller beta-sheet sandwich domain of unknown function. The C-terminal tails of each subunit extend toward another monomer in a swapping-like manner, creating a hydrogen bond network which suggests its implication in protein oligomerisation. Mutational and structural evidence suggest the involvement of a conserved tyrosine in the reaction mechanism of the enzyme Sinorhizobium meliloti

Inhibitors

Inhibitors Comment Organism Structure
EDTA 10 mM, 90% residual activity Sinorhizobium meliloti
Hg2+ 2 mM, 0% residual activity Sinorhizobium meliloti
additional information not inhibitory: iodoacetamide Sinorhizobium meliloti

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
1
-
DL-5-methyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
3
-
dihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
5
-
D-5-benzylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
10
-
D-5-isobutylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
14
-
D-5-butylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
18
-
D-5-ethylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
20
-
DL-5-(p-hydroxyphenyl)hydantoin pH 8.0, 40°C Sinorhizobium meliloti
26
-
D-5-propylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
44
-
D-5-isopropylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
66
-
D-5-methyl-thio-ethylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
72
-
D-5-methylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
81
-
DL-6-isopropyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
111
-
DL-6-methyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
125
-
hydantoin pH 8.0, 40°C Sinorhizobium meliloti

Metals/Ions

Metals/Ions Comment Organism Structure
Co2+ 2 mM, 331% of initial activity Sinorhizobium meliloti
Cu2+ 2 mM, 150% of initial activity Sinorhizobium meliloti
Mg2+ 2 mM, 121% of initial activity Sinorhizobium meliloti
Mn2+ 2 mM, 407% of initial activity Sinorhizobium meliloti
Ni2+ 2 mM, 346% of initial activity Sinorhizobium meliloti
Zn2+ 2 mM, 432% of initial activity Sinorhizobium meliloti

Organism

Organism UniProt Comment Textmining
Sinorhizobium meliloti
-
strain CECT4114
-

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
D-5-benzylhydantoin + H2O
-
Sinorhizobium meliloti N-carbamoyl-D-phenylalanine
-
?
D-5-butylhydantoin + H2O
-
Sinorhizobium meliloti ?
-
?
D-5-ethylhydantoin + H2O
-
Sinorhizobium meliloti ?
-
?
D-5-isobutylhydantoin + H2O
-
Sinorhizobium meliloti ?
-
?
D-5-isopropylhydantoin + H2O
-
Sinorhizobium meliloti ?
-
?
D-5-methyl-thio-ethylhydantoin + H2O
-
Sinorhizobium meliloti ?
-
?
D-5-methylhydantoin + H2O
-
Sinorhizobium meliloti N-carbamoyl-D-alanine
-
?
D-5-propylhydantoin + H2O
-
Sinorhizobium meliloti ?
-
?
dihydrouracil + H2O
-
Sinorhizobium meliloti ureidopropionate
-
?
DL-5-(p-hydroxyphenyl)hydantoin + H2O
-
Sinorhizobium meliloti N-carbamoyl-p-hydroxyphenylglycine
-
?
DL-5-methyldihydrouracil + H2O
-
Sinorhizobium meliloti ?
-
?
DL-6-isopropyldihydrouracil + H2O
-
Sinorhizobium meliloti ?
-
?
DL-6-methyldihydrouracil + H2O
-
Sinorhizobium meliloti ?
-
?
hydantoin + H2O
-
Sinorhizobium meliloti N-carbamoyl glycine
-
?
additional information enzyme presents both hydantoinase and dihydropyrimidinase activities, with higher affinity for the natural six-membered ring substrates. For the five-membered ring substrates, affinity is greater for those with aliphatic and apolar groups in the 5th carbon atom, with the highest rates of hydrolysis for D-5-methyl and D-5-ethyl hydantoin. Enzyme is enantioselective for the D-isomer of monosubstituted 5-hydantoins. Activity with substrate analogues such as allantoin, 5,5-dimethylhydantoin, 5-benzyl,5-methyl-hydantoin, succinimide, rodamine or tiazoledione is not detected under the conditions assayed Sinorhizobium meliloti ?
-
?

Temperature Optimum [°C]

Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
60
-
-
Sinorhizobium meliloti

Temperature Stability [°C]

Temperature Stability Minimum [°C] Temperature Stability Maximum [°C] Comment Organism
60
-
6 h, 95% residual activity Sinorhizobium meliloti
70
-
30 min, 25% residual activity Sinorhizobium meliloti

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
1
-
DL-5-(p-hydroxyphenyl)hydantoin pH 8.0, 40°C Sinorhizobium meliloti
1
-
DL-5-methyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
1
-
DL-6-isopropyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
2
-
dihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
2
-
D-5-isobutylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
2
-
D-5-benzylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
3
-
D-5-butylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
5
-
D-5-isopropylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
6
-
D-5-propylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
8
-
DL-6-methyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
12
-
hydantoin pH 8.0, 40°C Sinorhizobium meliloti
17
-
D-5-ethylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
18
-
D-5-methyl-thio-ethylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
197
-
D-5-methylhydantoin pH 8.0, 40°C Sinorhizobium meliloti

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
8
-
-
Sinorhizobium meliloti

kcat/KM [mM/s]

kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
0.012
-
DL-6-isopropyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
0.05
-
DL-5-(p-hydroxyphenyl)hydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.072
-
DL-6-methyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
0.096
-
hydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.114
-
D-5-isopropylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.2
-
D-5-isobutylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.214
-
D-5-butylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.231
-
D-5-propylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.273
-
D-5-methyl-thio-ethylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.4
-
D-5-benzylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
0.667
-
dihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
0.944
-
D-5-ethylhydantoin pH 8.0, 40°C Sinorhizobium meliloti
1
-
DL-5-methyldihydrouracil pH 8.0, 40°C Sinorhizobium meliloti
2.736
-
D-5-methylhydantoin pH 8.0, 40°C Sinorhizobium meliloti