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Literature summary for 3.1.3.74 extracted from

  • Tirrell, I.M.; Wall, J.L.; Daley, C.J.; Denial, S.J.; Tennis, F.G.; Galens, K.G.; O'Handley, S.F.
    YZGD from Paenibacillus thiaminolyticus, a pyridoxal phosphatase of the HAD (haloacid dehalogenase) superfamily and a versatile member of the Nudix (nucleoside diphosphate x) hydrolase superfamily (2006), Biochem. J., 394, 665-674.
    View publication on PubMedView publication on EuropePMC
Search for more literature for 3.1.3.74

Application

Application Comment Organism
drug development important in vitamin B6 metabolism Paenibacillus thiaminolyticus

Cloned(Commentary)

Cloned (Comment) Organism
expression in Escherichia coli HMS174(DE3) Paenibacillus thiaminolyticus
yzgd gene subcloned from plasmid pAN13, ligated into plasmid pET11b, transformed into Escherichia coli DH5alpha for storage and Escherichia coli HMS174(DE3) for expression Paenibacillus thiaminolyticus

Protein Variants

Protein Variants Comment Organism
D12N complete loss of activity, the corresponding Asp residue is part of the active site in other HAD superfamily members Paenibacillus thiaminolyticus
D12N complete loss of PLPase activity Paenibacillus thiaminolyticus
E324Q no difference in the expression, solubility or PLPase activity between the mutant or the wild-type enzyme Paenibacillus thiaminolyticus

Inhibitors

Inhibitors Comment Organism Structure
Mn2+ Mn2+ lowers activity of the Co2+-supported phosphatase activity, but does not eliminate it Paenibacillus thiaminolyticus

KM Value [mM]

KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
0.33
-
 pyridoxal 5'-phosphate
-
 Paenibacillus thiaminolyticus
0.33
-
 pyridoxal-5'-phosphate 5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C Paenibacillus thiaminolyticus

Metals/Ions

Metals/Ions Comment Organism Structure
Co2+ highest activity at 5 mM, either Mg2+ or Co2+ required Paenibacillus thiaminolyticus
Co2+ most effective to stimulate activity Paenibacillus thiaminolyticus
Fe2+
-
 Paenibacillus thiaminolyticus
Mg2+
-
 Paenibacillus thiaminolyticus
Mg2+ highest activity at 15 mM, either Mg2+ or Co2+ required Paenibacillus thiaminolyticus
Mn2+ can partially substitute for Co2+ Paenibacillus thiaminolyticus
additional information Ca2+ and Cu2+ do not support activity Paenibacillus thiaminolyticus
Ni2+
-
 Paenibacillus thiaminolyticus
Zn2+ can partially substitute for Co2+ Paenibacillus thiaminolyticus

Molecular Weight [Da]

Molecular Weight [Da] Molecular Weight Maximum [Da] Comment Organism
45000
-
 2 * 45000, SDS-PAGE Paenibacillus thiaminolyticus
45000
-
 2 * 45000, gel filtration compared to deduced molecular weight from sequence Paenibacillus thiaminolyticus
90000
-
 gel filtration Paenibacillus thiaminolyticus

Organism

Organism UniProt Comment Textmining
Paenibacillus thiaminolyticus
-
-
-

Purification (Commentary)

Purification (Comment) Organism
by gel filtration Paenibacillus thiaminolyticus
one chromatography step to homogeneity Paenibacillus thiaminolyticus

Source Tissue

Source Tissue Comment Organism Textmining
cell culture
-
 Paenibacillus thiaminolyticus
-

Specific Activity [micromol/min/mg]

Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
7
-
 purified enzyme Paenibacillus thiaminolyticus
7
-
 5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C Paenibacillus thiaminolyticus
20
-
 5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C Paenibacillus thiaminolyticus

Substrates and Products (Substrate)

Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
additional information pyridoxamine 5-phosphate, casein, serine phosphate, threonine phosphate, tyrosine phosphate, histidine phosphate, arginine phosphate, glycolate 2-phosphate, trehalose 6-phosphate, phosphoethanolamine and phosphocholine are not substrates Paenibacillus thiaminolyticus ?
-
 ?
p-nitrophenyl phosphate + H2O
-
 Paenibacillus thiaminolyticus p-nitrophenol + phosphate
-
 ?
p-nitrophenyl-phosphate + H2O
-
 Paenibacillus thiaminolyticus p-nitrophenol + phosphate
-
 ?
pyridoxal 5'-phosphate + H2O phosphatase activity of YZGD is highly specific on pyridoxal 5’-phosphate Paenibacillus thiaminolyticus pyridoxal + phosphate
-
 ?
pyridoxal-5'-phosphate + H2O
-
 Paenibacillus thiaminolyticus pyridoxal + phosphate
-
 ?

Subunits

Subunits Comment Organism
dimer 2 * 45000, SDS-PAGE Paenibacillus thiaminolyticus
dimer 2 * 45000, gel filtration compared to deduced molecular weight from sequence Paenibacillus thiaminolyticus

Synonyms

Synonyms Comment Organism
PLPase
-
 Paenibacillus thiaminolyticus
pyridoxal phosphatase
-
 Paenibacillus thiaminolyticus
pyridoxal-5'-phosphate phosphatase
-
 Paenibacillus thiaminolyticus
YZGD
-
 Paenibacillus thiaminolyticus

Turnover Number [1/s]

Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
19
-
 pyridoxal-5'-phosphate 5 mM CoCl2, 1 mM dithiothreitol, 50 mM Tris/maleate pH 5.0, 37°C Paenibacillus thiaminolyticus
19.4
-
 pyridoxal 5'-phosphate
-
 Paenibacillus thiaminolyticus

pH Optimum

pH Optimum Minimum pH Optimum Maximum Comment Organism
5
-
-
 Paenibacillus thiaminolyticus

pI Value

Organism Comment pI Value Maximum pI Value
Paenibacillus thiaminolyticus
-
-
 4.9