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Literature summary extracted from

  • Spaeth, B.; Settele, F.; Schilling, O.; DAngelo, I.; Vogel, A.; Feldmann, I.; Meyer-Klaucke, W.; Marchfelder, A.
    Metal requirements and phosphodiesterase activity of tRNase Z enzymes (2007), Biochemistry, 46, 14742-14750.
    View publication on PubMed

Application

EC Number Application Comment Organism
3.1.26.11 analysis comparative studies both bis(p-nitrophenyl)phosphate hydrolysis and pre-tRNA processing of tRNase Z variants Arabidopsis thaliana

Cloned(Commentary)

EC Number Cloned (Comment) Organism
3.1.26.11 expressed in Escherichia coli Drosophila melanogaster
3.1.26.11 expressed in Escherichia coli Saccharomyces cerevisiae
3.1.26.11 expressed in Escherichia coli, prior to electrophoretic mobility shift assay (EMSA) and cross-linking experiments Arabidopsis thaliana

Protein Variants

EC Number Protein Variants Comment Organism
3.1.4.1 C25G 3fold decrease in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 C40G 50% decrease in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 E208A 33% increase in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 F51L 50% decrease in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 G62V 80% decrease in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 P178A 65% increase in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 P64A 75% decrease in ratio kcat/KM value Arabidopsis thaliana
3.1.4.1 R252G 40fold increase in ratio kcat/KM value Arabidopsis thaliana
3.1.26.11 C25G variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 C40G variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 E208A variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 F51L variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 G62V variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 P178A variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 P64A variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana
3.1.26.11 R252G variants of AthTRZ1 wild-type enzyme generated by mutagenesis Arabidopsis thaliana

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.1.26.11 bis(p-nitrophenyl)phosphate pre-tRNA processing inhibited by bis(p-nitrophenyl)phosphate concentrations higher than 10 mM observed Drosophila melanogaster
3.1.26.11 bis(p-nitrophenyl)phosphate pre-tRNA processing inhibited by bis(p-nitrophenyl)phosphate concentrations higher than 10 mM observed Saccharomyces cerevisiae
3.1.26.11 additional information reaction performed with 20 microM bis(p-nitrophenyl)phosphate and 20 microM tRNA, bis(p-nitrophenyl)phosphate does not inhibit tRNA binding Arabidopsis thaliana

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.4.1 1.2
-
 bis(4-nitrophenyl)phosphate mutant P178A, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 1.8
-
 bis(4-nitrophenyl)phosphate mutant R252G, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 3.5
-
 bis(4-nitrophenyl)phosphate mutant E208A, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 6
-
 bis(4-nitrophenyl)phosphate mutant C40G, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 6.5
-
 bis(4-nitrophenyl)phosphate mutant F51L, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 8
-
 bis(4-nitrophenyl)phosphate mutant G62V, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 8.5
-
 bis(4-nitrophenyl)phosphate wild-type, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 13.2
-
 bis(4-nitrophenyl)phosphate mutant C25G, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 22.2
-
 bis(4-nitrophenyl)phosphate mutant P64A, pH 7.4, 37°C Arabidopsis thaliana
3.1.26.11 1.2
-
 bis(p-nitrophenyl)phosphate AthTRZ1-P178A, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 1.8
-
 bis(p-nitrophenyl)phosphate AthTRZ1-R252G, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 3.5
-
 bis(p-nitrophenyl)phosphate AthTRZ1-E208A, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 6
-
 bis(p-nitrophenyl)phosphate AthTRZ1-C40G, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 6.5
-
 bis(p-nitrophenyl)phosphate AthTRZ1-F51L, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 8
-
 bis(p-nitrophenyl)phosphate AthTRZ1-G62V, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 8.5
-
 bis(p-nitrophenyl)phosphate AthTRZ1 wild-type, hydrolysis of phosphodiester bonds of bpNPP, KM value for AthTRZ1 two-fold increased relative to that of the tRNase Z of Escherichia coli Arabidopsis thaliana
3.1.26.11 13.2
-
 bis(p-nitrophenyl)phosphate AthTRZ1-C25G, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana
3.1.26.11 22.2
-
 bis(p-nitrophenyl)phosphate AthTRZ1-P64A, mutant, bis(p-nitrophenyl)phosphate catalysis Arabidopsis thaliana

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.4.1 additional information hydrolysis of bis(4-nitrophenyl)phosphate requires the presence of Zn2+. Pre-5RNa processing by enzyme requires additional metal ions Arabidopsis thaliana
3.1.4.1 Zn2+ high affinity for Zn2+ ions, upon incubation with metal chelators, 0.76 mol Zn2+ ions are retained per mol of enzyme dimer Arabidopsis thaliana
3.1.26.11 Ca2+ requird for in Vitro tRNA processing reaction Arabidopsis thaliana
3.1.26.11 Mg2+ 2 mM, also required for in vitro tRNA processing reactions Arabidopsis thaliana
3.1.26.11 Mn2+ 0.2 mM, addition of Mn2+ ions triples activity, also required for in Vitro tRNA processing reactions Arabidopsis thaliana
3.1.26.11 additional information in contrast to bis(p-nitrophenyl)phosphate hydrolysis, pre-tRNA processing requires additional metal ions, Mn2+ or Mg2+, as Zn2+ ions alone are insufficient, metal dependence of the in vitro processing reaction analyzed, bis(p-nitrophenyl)phosphate activity of the chelator-treated AthTRZ1 without (TRZ-E) and with additional metal ions tested, chelator-treated AthTRZ1 without additional metal ions reveal same activity as the nonchelator-treated AthTRZ1 Arabidopsis thaliana
3.1.26.11 Zn2+ 0.2 mM, addition of Zn2+ ions to the chelator-treated enzyme doubles activity, high affinity to Zn2+ even upon incubation with metal chelators, 0.76 Zn2+ ions retained per dimer Arabidopsis thaliana

Organism

EC Number Organism UniProt Comment Textmining
3.1.4.1 Arabidopsis thaliana
-
 endonuclease tRNase Z also has phosphodiesterase activity
-
3.1.26.11 Arabidopsis thaliana
-
 AthTRZ1, wild-type and mutant variants studied
-
3.1.26.11 Drosophila melanogaster
-
-
-
3.1.26.11 Saccharomyces cerevisiae P36159 long tRNase Z enzyme
-

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.1.26.11 additional information
-
 in vitro tRNA processing assays, bis(p-nitrophenyl)phosphate hydrolysis assay described, in contrast to the short tRNase Z enzyme AthTRZ1 of Arabidopsis thaliana, long tRNase Z enzymes do not have bis(p-nitrophenyl)phosphate hydrolysis activity Saccharomyces cerevisiae
3.1.26.11 additional information
-
 in vitro tRNA processing assays, bis(p-nitrophenyl)phosphate hydrolysis assay described, kinetic analysis shown, AthTRZ1 effective catalyst of bpNPP hydrolysis, AthTRZ1-R252G reveals ten times higher activity compared to the wild-type enzyme, in contrast to the short tRNase Z enzyme AthTRZ1, long tRNase Z enzymes do not have bis(p-nitrophenyl)phosphate hydrolysis activity Arabidopsis thaliana
3.1.26.11 additional information
-
 in vitro tRNA processing assays, bpNPP hydrolysis assay described, in contrast to the short tRNase Z enzyme AthTRZ1 of Arabidopsis thaliana, long tRNase Z enzymes do not have bis(p-nitrophenyl)phosphate hydrolysis activity Drosophila melanogaster

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
3.1.4.1 bis(4-nitrophenyl)phosphate + H2O
-
 Arabidopsis thaliana 4-nitrophenyl phosphate + 4-nitrophenol
-
 ?
3.1.26.11 bis(p-nitrophenyl)phosphate + H2O differentiation of tRNase Z variants by 3'-processing activity and their ability to hydrolyze the phosphodiester bond in the chromogenic phosphodiester bis(p-nitrophenyl)phosphate (bpNPP), smallest known tRNase Z substrate, fourteen variants lost ability to hydrolyze bpNPP, seven variants reveal reduced activity Arabidopsis thaliana p-nitrophenol + p-nitrophenyl phosphate
-
 ?
3.1.26.11 bis(p-nitrophenyl)phosphate + H2O no hydrolysis of the the chromogenic phosphodiester bis(p-nitrophenyl)phosphate (bpNPP) observed Drosophila melanogaster p-nitrophenol + p-nitrophenyl phosphate
-
 ?
3.1.26.11 bis(p-nitrophenyl)phosphate + H2O no hydrolysis of the the chromogenic phosphodiester bis(p-nitrophenyl)phosphate (bpNPP) observed Saccharomyces cerevisiae p-nitrophenol + p-nitrophenyl phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
3.1.26.11 dimer
-
 Arabidopsis thaliana

Synonyms

EC Number Synonyms Comment Organism
3.1.4.1 tRNase Z
-
 Arabidopsis thaliana
3.1.26.11 AthTrz1
-
 Arabidopsis thaliana
3.1.26.11 tRNase Z
-
 Drosophila melanogaster
3.1.26.11 tRNase Z
-
 Arabidopsis thaliana
3.1.26.11 tRNase Z
-
 Saccharomyces cerevisiae

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.4.1 0.8
-
 bis(4-nitrophenyl)phosphate mutant G62V, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 1.8
-
 bis(4-nitrophenyl)phosphate mutant P178A, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 2.3
-
 bis(4-nitrophenyl)phosphate mutant F51L, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 3.1
-
 bis(4-nitrophenyl)phosphate mutant C40G, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 3.9
-
 bis(4-nitrophenyl)phosphate mutant C25G, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 4
-
 bis(4-nitrophenyl)phosphate mutant E208A, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 4.6
-
 bis(4-nitrophenyl)phosphate mutant P64A, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 7.4
-
 bis(4-nitrophenyl)phosphate wild-type, pH 7.4, 37°C Arabidopsis thaliana
3.1.4.1 68.5
-
 bis(4-nitrophenyl)phosphate mutant R252G, pH 7.4, 37°C Arabidopsis thaliana
3.1.26.11 additional information
-
 additional information turnover rate of AthTRZ1 eight-fold reduced if compared to tRNAse Z of Escherichia coli Arabidopsis thaliana