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Literature summary extracted from

  • Yang, J.; Wang, F.; Yang, D.; Zhou, K.; Liu, M.; Gao, Z.; Liu, P.; Dong, Y.; Zhang, J.; Liu, Q.
    Structural and biochemical characterization of the yeast HD domain containing protein YGK1 reveals a metal-dependent nucleoside 5'-monophosphatase (2018), Biochem. Biophys. Res. Commun., 501, 674-681 .
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.1.3.89 expressed in Escherichia coli Rosetta2 cells Saccharomyces cerevisiae

Crystallization (Commentary)

EC Number Crystallization (Comment) 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

Protein Variants

EC Number Protein Variants Comment 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 Comment 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 Comment Organism Structure
3.1.3.89 0.18
-
 5'-dGMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 0.23
-
 5'-dTMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 0.32
-
 5'-dAMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 0.36
-
 5'-dCMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 5.44
-
 4-nitrophenyl phosphate wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae

Metals/Ions

EC Number Metals/Ions Comment 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

Organism

EC Number Organism UniProt Comment Textmining
3.1.3.89 Saccharomyces cerevisiae
-
-
-
3.1.3.89 Saccharomyces cerevisiae P53144
-
-

Purification (Commentary)

EC Number Purification (Comment) 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)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.3.89 4-nitrophenyl phosphate + H2O
-
 Saccharomyces cerevisiae 4-nitrophenol + phosphate
-
 ?
3.1.3.89 5'-dAMP + H2O high activity Saccharomyces cerevisiae deoxyadenosine + phosphate
-
 ?
3.1.3.89 5'-dCMP + H2O
-
 Saccharomyces cerevisiae deoxycytidine + phosphate
-
 ?
3.1.3.89 5'-dGMP + H2O best substrate Saccharomyces cerevisiae deoxyguanosine + phosphate
-
 ?
3.1.3.89 5'-dTMP + H2O high activity Saccharomyces cerevisiae deoxythymidine + phosphate
-
 ?
3.1.3.89 AMP + H2O
-
 Saccharomyces cerevisiae adenosine + phosphate
-
 ?
3.1.3.89 CMP + H2O
-
 Saccharomyces cerevisiae cytosine + phosphate
-
 ?
3.1.3.89 GMP + H2O
-
 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 Saccharomyces cerevisiae ?
-
 ?
3.1.3.89 UMP + H2O
-
 Saccharomyces cerevisiae uridine + phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
3.1.3.89 ? x * 30000, SDS-PAGE Saccharomyces cerevisiae

Synonyms

EC Number Synonyms Comment Organism
3.1.3.89 deoxyribonucleoside 5'-monophosphatase
-
 Saccharomyces cerevisiae
3.1.3.89 YB92
-
 Saccharomyces cerevisiae
3.1.3.89 YBR242W
-
 Saccharomyces cerevisiae
3.1.3.89 YGK1
-
 Saccharomyces cerevisiae
3.1.3.89 YGL101W
-
 Saccharomyces cerevisiae

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.3.89 0.28
-
 5'-dCMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 1
-
 5'-dAMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 1.1
-
 5'-dTMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 1.2
-
 5'-dGMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 3.48
-
 4-nitrophenyl phosphate wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae

kcat/KM [mM/s]

EC Number kcat/KM Value [1/mMs-1] kcat/KM Value Maximum [1/mMs-1] Substrate Comment Organism Structure
3.1.3.89 0.64
-
 4-nitrophenyl phosphate wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 0.78
-
 5'-dCMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 3.12
-
 5'-dAMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 4.78
-
 5'-dTMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae
3.1.3.89 6.67
-
 5'-dGMP wild type enzyme, at pH 8.0 and 30°C Saccharomyces cerevisiae