BRENDA - Enzyme Database

Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5'-monophosphatase

Yang, J.; Wang, F.; Yang, D.; Zhou, K.; Liu, M.; Gao, Z.; Liu, P.; Dong, Y.; Zhang, J.; Liu, Q.; Biochem. Biophys. Res. Commun. 501, 674-681 (2018)

Data extracted from this reference:

Cloned(Commentary)
EC Number
Commentary
Organism
3.1.3.89
expressed in Escherichia coli Rosetta2 cells; expressed in Escherichia coli Rosetta2 cells
Saccharomyces cerevisiae
Crystallization (Commentary)
EC Number
Crystallization
Organism
3.1.3.89
selenomethionine-substituted enzyme, hanging drop vapor diffusion method, using 0.1M sodium acetate trihydrate pH 4.5, 22% (w/v) PEG 3350, 0.01M CdCl2 at 20 C
Saccharomyces cerevisiae
Engineering
EC Number
Amino acid exchange
Commentary
Organism
3.1.3.89
D90A
the mutant shows no activity
Saccharomyces cerevisiae
3.1.3.89
E114A
the mutant shows no activity
Saccharomyces cerevisiae
3.1.3.89
E145A
the mutant shows almost no activity
Saccharomyces cerevisiae
3.1.3.89
E93A
the mutant shows almost no activity
Saccharomyces cerevisiae
3.1.3.89
H111A
the mutant shows slightly reduced activity compared to the wild type enzyme
Saccharomyces cerevisiae
3.1.3.89
H89A
the mutant shows almost no activity
Saccharomyces cerevisiae
Inhibitors
EC Number
Inhibitors
Commentary
Organism
Structure
3.1.3.89
Zn2+
no activity is observed in presence of Zn2+; no activity is observed in presence of Zn2+
Saccharomyces cerevisiae
KM Value [mM]
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
3.1.3.89
0.18
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.23
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.32
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.36
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
5.44
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
Metals/Ions
EC Number
Metals/Ions
Commentary
Organism
Structure
3.1.3.89
Co2+
0.1 mM used in assay conditions; 0.1 mM used in assay conditions
Saccharomyces cerevisiae
3.1.3.89
Mg2+
5 mM used in assay conditions; 5 mM used in assay conditions
Saccharomyces cerevisiae
3.1.3.89
Mn2+
activates; activates
Saccharomyces cerevisiae
Organism
EC Number
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
3.1.3.89
Saccharomyces cerevisiae
P53144
-
-
3.1.3.89
Saccharomyces cerevisiae
-
-
-
Purification (Commentary)
EC Number
Commentary
Organism
3.1.3.89
Ni-NTA bead column chromatography, HiTrap Q column chromatography, and Superdex 200 gel filtration; Ni-NTA bead column chromatography, HiTrap Q column chromatography, and Superdex 200 gel filtration
Saccharomyces cerevisiae
Substrates and Products (Substrate)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.1.3.89
4-nitrophenyl phosphate + H2O
-
749824
Saccharomyces cerevisiae
4-nitrophenol + phosphate
-
-
-
?
3.1.3.89
5'-dAMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxyadenosine + phosphate
-
-
-
?
3.1.3.89
5'-dCMP + H2O
-
749824
Saccharomyces cerevisiae
deoxycytosine + phosphate
-
-
-
?
3.1.3.89
5'-dGMP + H2O
best substrate
749824
Saccharomyces cerevisiae
deoxyguanosine + phosphate
-
-
-
?
3.1.3.89
5'-dTMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxythymidine + phosphate
-
-
-
?
3.1.3.89
AMP + H2O
-
749824
Saccharomyces cerevisiae
adenosine + phosphate
-
-
-
?
3.1.3.89
CMP + H2O
-
749824
Saccharomyces cerevisiae
cytosine + phosphate
-
-
-
?
3.1.3.89
GMP + H2O
-
749824
Saccharomyces cerevisiae
guanosine + phosphate
-
-
-
?
3.1.3.89
additional information
the enzyme prefers purine nucleotides to pyrimidine nucleotides, favors deoxyribonucleotides over ribonucleotides and has no detectable phosphatase activity against nucleoside 5'-triphosphates such as ATP
749824
Saccharomyces cerevisiae
?
-
-
-
-
3.1.3.89
UMP + H2O
-
749824
Saccharomyces cerevisiae
uridine + phosphate
-
-
-
?
Subunits
EC Number
Subunits
Commentary
Organism
3.1.3.89
?
x * 30000, SDS-PAGE; x * 30000, SDS-PAGE
Saccharomyces cerevisiae
Turnover Number [1/s]
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
3.1.3.89
0.28
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
1
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
1.1
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
1.2
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
3.48
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
Cloned(Commentary) (protein specific)
EC Number
Commentary
Organism
3.1.3.89
expressed in Escherichia coli Rosetta2 cells
Saccharomyces cerevisiae
Crystallization (Commentary) (protein specific)
EC Number
Crystallization
Organism
3.1.3.89
selenomethionine-substituted enzyme, hanging drop vapor diffusion method, using 0.1M sodium acetate trihydrate pH 4.5, 22% (w/v) PEG 3350, 0.01M CdCl2 at 20 C
Saccharomyces cerevisiae
Engineering (protein specific)
EC Number
Amino acid exchange
Commentary
Organism
3.1.3.89
D90A
the mutant shows no activity
Saccharomyces cerevisiae
3.1.3.89
E114A
the mutant shows no activity
Saccharomyces cerevisiae
3.1.3.89
E145A
the mutant shows almost no activity
Saccharomyces cerevisiae
3.1.3.89
E93A
the mutant shows almost no activity
Saccharomyces cerevisiae
3.1.3.89
H111A
the mutant shows slightly reduced activity compared to the wild type enzyme
Saccharomyces cerevisiae
3.1.3.89
H89A
the mutant shows almost no activity
Saccharomyces cerevisiae
Inhibitors (protein specific)
EC Number
Inhibitors
Commentary
Organism
Structure
3.1.3.89
Zn2+
no activity is observed in presence of Zn2+
Saccharomyces cerevisiae
KM Value [mM] (protein specific)
EC Number
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
3.1.3.89
0.18
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.23
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.32
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.36
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
5.44
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
Metals/Ions (protein specific)
EC Number
Metals/Ions
Commentary
Organism
Structure
3.1.3.89
Co2+
0.1 mM used in assay conditions
Saccharomyces cerevisiae
3.1.3.89
Mg2+
5 mM used in assay conditions
Saccharomyces cerevisiae
3.1.3.89
Mn2+
activates
Saccharomyces cerevisiae
Purification (Commentary) (protein specific)
EC Number
Commentary
Organism
3.1.3.89
Ni-NTA bead column chromatography, HiTrap Q column chromatography, and Superdex 200 gel filtration
Saccharomyces cerevisiae
Substrates and Products (Substrate) (protein specific)
EC Number
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
3.1.3.89
4-nitrophenyl phosphate + H2O
-
749824
Saccharomyces cerevisiae
4-nitrophenol + phosphate
-
-
-
?
3.1.3.89
5'-dAMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxyadenosine + phosphate
-
-
-
?
3.1.3.89
5'-dCMP + H2O
-
749824
Saccharomyces cerevisiae
deoxycytosine + phosphate
-
-
-
?
3.1.3.89
5'-dGMP + H2O
best substrate
749824
Saccharomyces cerevisiae
deoxyguanosine + phosphate
-
-
-
?
3.1.3.89
5'-dTMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxythymidine + phosphate
-
-
-
?
3.1.3.89
AMP + H2O
-
749824
Saccharomyces cerevisiae
adenosine + phosphate
-
-
-
?
3.1.3.89
CMP + H2O
-
749824
Saccharomyces cerevisiae
cytosine + phosphate
-
-
-
?
3.1.3.89
GMP + H2O
-
749824
Saccharomyces cerevisiae
guanosine + phosphate
-
-
-
?
3.1.3.89
additional information
the enzyme prefers purine nucleotides to pyrimidine nucleotides, favors deoxyribonucleotides over ribonucleotides and has no detectable phosphatase activity against nucleoside 5'-triphosphates such as ATP
749824
Saccharomyces cerevisiae
?
-
-
-
-
3.1.3.89
UMP + H2O
-
749824
Saccharomyces cerevisiae
uridine + phosphate
-
-
-
?
Subunits (protein specific)
EC Number
Subunits
Commentary
Organism
3.1.3.89
?
x * 30000, SDS-PAGE
Saccharomyces cerevisiae
Turnover Number [1/s] (protein specific)
EC Number
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
3.1.3.89
0.28
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
1
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
1.1
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
1.2
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
3.48
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
KCat/KM [mM/s]
EC Number
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
3.1.3.89
0.64
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.78
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
3.12
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
4.78
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
6.67
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
KCat/KM [mM/s] (protein specific)
EC Number
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
3.1.3.89
0.64
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
0.78
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
3.12
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
4.78
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae
3.1.3.89
6.67
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30C
Saccharomyces cerevisiae