BRENDA - Enzyme Database
show all sequences of 3.1.3.89

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)
Commentary
Organism
expressed in Escherichia coli Rosetta2 cells; expressed in Escherichia coli Rosetta2 cells
Saccharomyces cerevisiae
Crystallization (Commentary)
Crystallization
Organism
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
Amino acid exchange
Commentary
Organism
D90A
the mutant shows no activity
Saccharomyces cerevisiae
E114A
the mutant shows no activity
Saccharomyces cerevisiae
E145A
the mutant shows almost no activity
Saccharomyces cerevisiae
E93A
the mutant shows almost no activity
Saccharomyces cerevisiae
H111A
the mutant shows slightly reduced activity compared to the wild type enzyme
Saccharomyces cerevisiae
H89A
the mutant shows almost no activity
Saccharomyces cerevisiae
Inhibitors
Inhibitors
Commentary
Organism
Structure
Zn2+
no activity is observed in presence of Zn2+; no activity is observed in presence of Zn2+
Saccharomyces cerevisiae
KM Value [mM]
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.18
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.23
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.32
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.36
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
5.44
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
Metals/Ions
Metals/Ions
Commentary
Organism
Structure
Co2+
0.1 mM used in assay conditions; 0.1 mM used in assay conditions
Saccharomyces cerevisiae
Mg2+
5 mM used in assay conditions; 5 mM used in assay conditions
Saccharomyces cerevisiae
Mn2+
activates; activates
Saccharomyces cerevisiae
Organism
Organism
Primary Accession No. (UniProt)
Commentary
Textmining
Saccharomyces cerevisiae
P53144
-
-
Saccharomyces cerevisiae
-
-
-
Purification (Commentary)
Commentary
Organism
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)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4-nitrophenyl phosphate + H2O
-
749824
Saccharomyces cerevisiae
4-nitrophenol + phosphate
-
-
-
?
5'-dAMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxyadenosine + phosphate
-
-
-
?
5'-dCMP + H2O
-
749824
Saccharomyces cerevisiae
deoxycytosine + phosphate
-
-
-
?
5'-dGMP + H2O
best substrate
749824
Saccharomyces cerevisiae
deoxyguanosine + phosphate
-
-
-
?
5'-dTMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxythymidine + phosphate
-
-
-
?
AMP + H2O
-
749824
Saccharomyces cerevisiae
adenosine + phosphate
-
-
-
?
CMP + H2O
-
749824
Saccharomyces cerevisiae
cytosine + phosphate
-
-
-
?
GMP + H2O
-
749824
Saccharomyces cerevisiae
guanosine + phosphate
-
-
-
?
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
?
-
-
-
-
UMP + H2O
-
749824
Saccharomyces cerevisiae
uridine + phosphate
-
-
-
?
Subunits
Subunits
Commentary
Organism
?
x * 30000, SDS-PAGE; x * 30000, SDS-PAGE
Saccharomyces cerevisiae
Turnover Number [1/s]
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.28
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
1
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
1.1
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
1.2
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
3.48
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
Cloned(Commentary) (protein specific)
Commentary
Organism
expressed in Escherichia coli Rosetta2 cells
Saccharomyces cerevisiae
Crystallization (Commentary) (protein specific)
Crystallization
Organism
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)
Amino acid exchange
Commentary
Organism
D90A
the mutant shows no activity
Saccharomyces cerevisiae
E114A
the mutant shows no activity
Saccharomyces cerevisiae
E145A
the mutant shows almost no activity
Saccharomyces cerevisiae
E93A
the mutant shows almost no activity
Saccharomyces cerevisiae
H111A
the mutant shows slightly reduced activity compared to the wild type enzyme
Saccharomyces cerevisiae
H89A
the mutant shows almost no activity
Saccharomyces cerevisiae
Inhibitors (protein specific)
Inhibitors
Commentary
Organism
Structure
Zn2+
no activity is observed in presence of Zn2+
Saccharomyces cerevisiae
KM Value [mM] (protein specific)
KM Value [mM]
KM Value Maximum [mM]
Substrate
Commentary
Organism
Structure
0.18
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.23
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.32
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.36
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
5.44
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
Metals/Ions (protein specific)
Metals/Ions
Commentary
Organism
Structure
Co2+
0.1 mM used in assay conditions
Saccharomyces cerevisiae
Mg2+
5 mM used in assay conditions
Saccharomyces cerevisiae
Mn2+
activates
Saccharomyces cerevisiae
Purification (Commentary) (protein specific)
Commentary
Organism
Ni-NTA bead column chromatography, HiTrap Q column chromatography, and Superdex 200 gel filtration
Saccharomyces cerevisiae
Substrates and Products (Substrate) (protein specific)
Substrates
Commentary Substrates
Literature (Substrates)
Organism
Products
Commentary (Products)
Literature (Products)
Organism (Products)
Reversibility
4-nitrophenyl phosphate + H2O
-
749824
Saccharomyces cerevisiae
4-nitrophenol + phosphate
-
-
-
?
5'-dAMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxyadenosine + phosphate
-
-
-
?
5'-dCMP + H2O
-
749824
Saccharomyces cerevisiae
deoxycytosine + phosphate
-
-
-
?
5'-dGMP + H2O
best substrate
749824
Saccharomyces cerevisiae
deoxyguanosine + phosphate
-
-
-
?
5'-dTMP + H2O
high activity
749824
Saccharomyces cerevisiae
deoxythymidine + phosphate
-
-
-
?
AMP + H2O
-
749824
Saccharomyces cerevisiae
adenosine + phosphate
-
-
-
?
CMP + H2O
-
749824
Saccharomyces cerevisiae
cytosine + phosphate
-
-
-
?
GMP + H2O
-
749824
Saccharomyces cerevisiae
guanosine + phosphate
-
-
-
?
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
?
-
-
-
-
UMP + H2O
-
749824
Saccharomyces cerevisiae
uridine + phosphate
-
-
-
?
Subunits (protein specific)
Subunits
Commentary
Organism
?
x * 30000, SDS-PAGE
Saccharomyces cerevisiae
Turnover Number [1/s] (protein specific)
Turnover Number Minimum [1/s]
Turnover Number Maximum [1/s]
Substrate
Commentary
Organism
Structure
0.28
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
1
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
1.1
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
1.2
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
3.48
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
KCat/KM [mM/s]
kcat/KM Value [1/mMs-1]
kcat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.64
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.78
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
3.12
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
4.78
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
6.67
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
KCat/KM [mM/s] (protein specific)
KCat/KM Value [1/mMs-1]
KCat/KM Value Maximum [1/mMs-1]
Substrate
Commentary
Organism
Structure
0.64
-
4-nitrophenyl phosphate
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
0.78
-
5'-dCMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
3.12
-
5'-dAMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
4.78
-
5'-dTMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
6.67
-
5'-dGMP
wild type enzyme, at pH 8.0 and 30°C
Saccharomyces cerevisiae
Other publictions for EC 3.1.3.89
No.
1st author
Pub Med
title
organims
journal
volume
pages
year
Activating Compound
Application
Cloned(Commentary)
Crystallization (Commentary)
Engineering
General Stability
Inhibitors
KM Value [mM]
Localization
Metals/Ions
Molecular Weight [Da]
Natural Substrates/ Products (Substrates)
Organic Solvent Stability
Organism
Oxidation Stability
Posttranslational Modification
Purification (Commentary)
Reaction
Renatured (Commentary)
Source Tissue
Specific Activity [micromol/min/mg]
Storage Stability
Substrates and Products (Substrate)
Subunits
Temperature Optimum [°C]
Temperature Range [°C]
Temperature Stability [°C]
Turnover Number [1/s]
pH Optimum
pH Range
pH Stability
Cofactor
Ki Value [mM]
pI Value
IC50 Value
Activating Compound (protein specific)
Application (protein specific)
Cloned(Commentary) (protein specific)
Cofactor (protein specific)
Crystallization (Commentary) (protein specific)
Engineering (protein specific)
General Stability (protein specific)
IC50 Value (protein specific)
Inhibitors (protein specific)
Ki Value [mM] (protein specific)
KM Value [mM] (protein specific)
Localization (protein specific)
Metals/Ions (protein specific)
Molecular Weight [Da] (protein specific)
Natural Substrates/ Products (Substrates) (protein specific)
Organic Solvent Stability (protein specific)
Oxidation Stability (protein specific)
Posttranslational Modification (protein specific)
Purification (Commentary) (protein specific)
Renatured (Commentary) (protein specific)
Source Tissue (protein specific)
Specific Activity [micromol/min/mg] (protein specific)
Storage Stability (protein specific)
Substrates and Products (Substrate) (protein specific)
Subunits (protein specific)
Temperature Optimum [°C] (protein specific)
Temperature Range [°C] (protein specific)
Temperature Stability [°C] (protein specific)
Turnover Number [1/s] (protein specific)
pH Optimum (protein specific)
pH Range (protein specific)
pH Stability (protein specific)
pI Value (protein specific)
Expression
General Information
General Information (protein specific)
Expression (protein specific)
KCat/KM [mM/s]
KCat/KM [mM/s] (protein specific)
749824
Yang
Structural and biochemical ch ...
Saccharomyces cerevisiae
Biochem. Biophys. Res. Commun.
501
674-681
2018
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1
1
6
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1
5
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3
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3
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1
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20
1
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5
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2
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1
6
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2
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5
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6
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2
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20
2
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5
-
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5
5
750203
Terakawa
Bacillus subtilis 5'-nucleoti ...
no activity in Bacillus subtilis
BMC Microbiol.
16
1-13
2016
-
-
-
-
-
-
-
-
-
-
-
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1
-
-
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-
-
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-
-
-
-
-
-
-
722956
Zimmerman
Structural insight into the me ...
Escherichia coli
J. Mol. Biol.
378
215-226
2008
-
-
1
1
10
-
-
4
-
-
-
-
-
1
-
-
-
-
-
-
-
-
1
-
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4
-
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1
-
1
10
-
-
-
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4
-
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-
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-
-
-
-
-
-
-
1
-
-
-
-
4
-
-
-
-
-
-
-
-
4
4
656266
Proudfoot
General Enzymatic Screens Iden ...
Escherichia coli
J. Biol. Chem.
279
54687-54694
2004
-
-
-
-
-
-
11
7
-
3
3
-
-
1
-
-
-
-
-
-
-
-
8
2
-
-
-
7
-
1
-
-
-
-
-
-
-
-
-
-
-
-
-
11
-
7
-
3
3
-
-
-
-
-
-
-
-
-
8
2
-
-
-
7
-
1
-
-
-
-
-
-
7
7