Literature summary for 3.1.3.89 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 .

Search for more literature for 3.1.3.89

Cloned(Commentary)

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

Crystallization (Commentary)

Crystallization (Comment)	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

Protein Variants

Protein Variants	Comment	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	Comment	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	Comment	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	Comment	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

Organism

Organism	UniProt	Comment	Textmining
Saccharomyces cerevisiae	-	-	-
Saccharomyces cerevisiae	P53144	-	-

Purification (Commentary)

Purification (Comment)	Organism
Ni-NTA bead column chromatography, HiTrap Q column chromatography, and Superdex 200 gel filtration	Saccharomyces cerevisiae

Substrates and Products (Substrate)

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

Subunits

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

Synonyms

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

Turnover Number [1/s]

Turnover Number Minimum [1/s]	Turnover Number Maximum [1/s]	Substrate	Comment	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	Comment	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

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Release 2023.1 (January 2023)