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Literature summary extracted from

  • Yakunin, A.F.; Proudfoot, M.; Kuznetsova, E.; Savchenko, A.; Brown, G.; Arrowsmith, C.H.; Edwards, A.M.
    The HD domain of the E. coli tRNA nucleotidyltransferase has 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and phosphatase activities (2004), J. Biol. Chem., 279, 36819-36827.
    View publication on PubMed

Cloned(Commentary)

EC Number Cloned (Comment) Organism
2.7.7.72 recombinant expression of the isolated His-tagged HD domain in Escherichia coli strain BL21 (DE3) Escherichia coli
3.1.4.16
-
 Escherichia coli
3.1.4.37
-
 Escherichia coli
3.1.4.37 tRNA nucleotidyltransferase, EC 2.7.7.25, with its HD domain possessing 2',3'-cyclic phosphodiesterase activity Escherichia coli

Protein Variants

EC Number Protein Variants Comment Organism
3.1.4.37 D21A tRNA nucleotidyltransferase mutant, EC 2.7.7.25, no effect on the 2',3'-cyclic phosphodiesterase activity Escherichia coli
3.1.4.37 D23A tRNA nucleotidyltransferase mutant, EC 2.7.7.25, no effect on the 2',3'-cyclic phosphodiesterase activity Escherichia coli
3.1.4.37 D256A HD domain mutant without detectable 2',3'-cyclic phosphodiesterase activity Escherichia coli
3.1.4.37 D306A HD domain mutant with 2',3'-cyclic phosphodiesterase activity Escherichia coli
3.1.4.37 H225A HD domain mutant without detectable 2',3'-cyclic phosphodiesterase activity Escherichia coli
3.1.4.37 H305A HD domain mutant without detectable 2',3'-cyclic phosphodiesterase activity Escherichia coli

General Stability

EC Number General Stability Organism
3.1.4.16 stable Escherichia coli
3.1.4.37 stable Escherichia coli

Inhibitors

EC Number Inhibitors Comment Organism Structure
3.1.4.16 5'-AMP
-
 Escherichia coli
3.1.4.16 tRNA
-
 Escherichia coli
3.1.4.37 5'-AMP
-
 Escherichia coli
3.1.4.37 Co2+
-
 Escherichia coli
3.1.4.37 Cu2+
-
 Escherichia coli
3.1.4.37 additional information not inhibited by Mg2+, Mn2+, Ca2+ or Ni2+ Escherichia coli
3.1.4.37 tRNA 10 nM, strong competitive inhibition of 2',3'-cyclic phosphodiesterase activity, inhibition is abolished by addition of Mg2+, Mn2+ or Ca2+, but not of Ni2+ Escherichia coli
3.1.4.37 Zn2+
-
 Escherichia coli

KM Value [mM]

EC Number KM Value [mM] KM Value Maximum [mM] Substrate Comment Organism Structure
3.1.4.16 0.1
-
 diphosphate +/- 0.004 Escherichia coli
3.1.4.16 0.13
-
 CTP +/- 0.01 Escherichia coli
3.1.4.16 0.15
-
 NADP +/- 0.02 Escherichia coli
3.1.4.16 0.18
-
 ATP +/- 0.01 Escherichia coli
3.1.4.16 0.19
-
 ADP +/- 0.02 Escherichia coli
3.1.4.16 0.49
-
 2',3'-cAMP +/- 0.04 Escherichia coli
3.1.4.16 0.53
-
 CDP +/- 0.09 Escherichia coli
3.1.4.16 0.76
-
 2'-AMP +/- 0.13 Escherichia coli
3.1.4.16 1.6
-
 2',3'-cGMP +/- 0.22 Escherichia coli
3.1.4.16 6.2
-
 p-nitrophenyl phosphate +/- 0.46 Escherichia coli
3.1.4.37 0.1
-
 diphosphate +/- 0.004 Escherichia coli
3.1.4.37 0.13
-
 CTP +/- 0.01 Escherichia coli
3.1.4.37 0.15
-
 NADP +/- 0.02 Escherichia coli
3.1.4.37 0.18
-
 ATP +/- 0.01 Escherichia coli
3.1.4.37 0.19
-
 ADP +/- 0.02 Escherichia coli
3.1.4.37 0.49
-
 cyclic 2',3'-AMP pH 7, 37°C Escherichia coli
3.1.4.37 0.49
-
 2',3'-cAMP +/- 0.04 Escherichia coli
3.1.4.37 0.53
-
 CDP +/- 0.09 Escherichia coli
3.1.4.37 0.76
-
 2'-AMP +/- 0.13 Escherichia coli
3.1.4.37 1.6
-
 cyclic 2',3'-GMP pH 7, 37°C Escherichia coli
3.1.4.37 1.6
-
 2',3'-cGMP +/- 0.22 Escherichia coli
3.1.4.37 6.2
-
 p-nitrophenyl phosphate +/- 0.46 Escherichia coli

Metals/Ions

EC Number Metals/Ions Comment Organism Structure
3.1.4.16 Mg2+ activataes with 2'-AMP, KD: 0.24 +/- 0.1 mM Escherichia coli
3.1.4.16 Mg2+ activates with 2',3'-cAMP, KD: 0.49 +/- 0.1 mM Escherichia coli
3.1.4.16 Mg2+ activates with ATP, KD ~ 0.1 mM Escherichia coli
3.1.4.16 Ni2+ activates with diphosphate, KD: 1.06 +/- 0.1 uM Escherichia coli
3.1.4.16 Ni2+ activates with p-nitrophenyl phosphate, KD: 6.0 +/- 0.7 uM Escherichia coli
3.1.4.37 Mg2+ activataes with 2'-AMP, KD: 0.24 +/- 0.1 mM Escherichia coli
3.1.4.37 Mg2+ activates with 2',3'-cAMP, KD: 0.49 +/- 0.1 mM Escherichia coli
3.1.4.37 Mg2+ activates with ATP, KD ~ 0.1 mM Escherichia coli
3.1.4.37 additional information metal-independent 2',3'-cyclic phosphodiesterase activity Escherichia coli
3.1.4.37 Ni2+ hydrolysis of bis-p-nitrophenyl phosphate is strongly dependent on Ni2+ Escherichia coli
3.1.4.37 Ni2+ activates with p-nitrophenyl phosphate, KD: 6.0 +/- 0.7 uM Escherichia coli
3.1.4.37 Ni2+ activates with PPi, KD: 1.06 +/- 0.1 uM Escherichia coli

Natural Substrates/ Products (Substrates)

EC Number Natural Substrates Organism Comment (Nat. Sub.) Natural Products Comment (Nat. Pro.) Rev. Reac.
2.7.7.72 additional information Escherichia coli the HD domain of the enzyme also exhibits 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and Ni2+-dependent phosphatase activities, overview ?
-
 ?
3.1.4.37 cyclic 2',3'-AMP + H2O Escherichia coli natural substrate, the 2',3'-cyclic phosphodiesterase activity of the C-terminal HD domain of tRNA nucleotidyltransferase, EC 2.7.7.25, is involved in the repair of the 3’-CCA end of tRNA 2'-AMP
-
 ?

Organism

EC Number Organism UniProt Comment Textmining
2.7.7.72 Escherichia coli P06961
-
-
3.1.4.16 Escherichia coli P06961
-
-
3.1.4.37 Escherichia coli
-
 2',3'-cyclic phosphodiesterase activity of the C-terminal HD domain of the multifunctional enzyme tRNA nucleotidyltransferase, EC 2.7.7.25
-
3.1.4.37 Escherichia coli P06961
-
-

Purification (Commentary)

EC Number Purification (Comment) Organism
2.7.7.72 recombinant His-tagged HD domain from Escherichia coli strain BL21 (DE3) by nickel affinity chromatography Escherichia coli
3.1.4.37 recombinant tRNA nucleotidyltransferase, EC 2.7.7.25, with its HD domain possessing 2',3'-cyclic phosphodiesterase activity Escherichia coli

Specific Activity [micromol/min/mg]

EC Number Specific Activity Minimum [µmol/min/mg] Specific Activity Maximum [µmol/min/mg] Comment Organism
3.1.4.16 1.49
-
 +/- 0.08, ADP Escherichia coli
3.1.4.16 2.36
-
 +/- 0.10, 2',3'-cGMP Escherichia coli
3.1.4.16 3.01
-
 +/- 0.06, diphosphate Escherichia coli
3.1.4.16 3.21
-
 +/- 0.1, 2',3'-cAMP Escherichia coli
3.1.4.16 3.71
-
 +/- 0.17, 2'-CMP Escherichia coli
3.1.4.16 4.03
-
 +/- 0.20, CTP Escherichia coli
3.1.4.16 4.53
-
 +/- 0.14, ATP Escherichia coli
3.1.4.16 5.8
-
 +/- 0.47, CDP Escherichia coli
3.1.4.16 12.4
-
 +/- 0.34, p-nitrophenyl phosphate Escherichia coli
3.1.4.16 17.9
-
 +/- 0.6, NADP Escherichia coli
3.1.4.37 1.49
-
 +/- 0.08, ADP Escherichia coli
3.1.4.37 2.36
-
 +/- 0.10, 2',3'-cGMP Escherichia coli
3.1.4.37 3.01
-
 +/- 0.06, diphosphate Escherichia coli
3.1.4.37 3.21
-
 +/- 0.1, 2',3'-cAMP Escherichia coli
3.1.4.37 3.71
-
 +/- 0.17, 2'-CMP Escherichia coli
3.1.4.37 4.03
-
 +/- 0.20, CTP Escherichia coli
3.1.4.37 4.53
-
 +/- 0.14, ATP Escherichia coli
3.1.4.37 5.8
-
 +/- 0.47, CDP Escherichia coli
3.1.4.37 12.4
-
 +/- 0.34, p-nitrophenyl phosphate Escherichia coli
3.1.4.37 17.9
-
 +/- 0.6, NADP Escherichia coli

Storage Stability

EC Number Storage Stability Organism
3.1.4.16 4°C, 5% glycerol, 0.5 M NaCl, pH 7.5, no loss in activity after several months Escherichia coli
3.1.4.37 4°C, 5% glycerol, 0.5 M NaCl, pH 7.5, no loss in activity after several months Escherichia coli

Substrates and Products (Substrate)

EC Number Substrates Comment Substrates Organism Products Comment (Products) Rev. Reac.
2.7.7.72 additional information the HD domain of the enzyme also exhibits 2',3'-cyclic phosphodiesterase, 2'-nucleotidase, and Ni2+-dependent phosphatase activities, overview Escherichia coli ?
-
 ?
3.1.4.16 2',3'-cAMP + H2O
-
 Escherichia coli 2'-AMP + 3'-AMP
-
 ?
3.1.4.16 2',3'-cGMP + H2O
-
 Escherichia coli 2'-GMP + 3'-GMP
-
 ?
3.1.4.16 2'-AMP + H2O
-
 Escherichia coli adenosine + phosphate
-
 ?
3.1.4.16 ADP + H2O
-
 Escherichia coli AMP + phosphate
-
 ?
3.1.4.16 ATP + H2O
-
 Escherichia coli ADP + phosphate
-
 ?
3.1.4.16 CDP + H2O
-
 Escherichia coli CMP + phosphate
-
 ?
3.1.4.16 CTP + H2O
-
 Escherichia coli CDP + phosphate
-
 ?
3.1.4.16 diphosphate + H2O
-
 Escherichia coli 2 phosphate
-
 ?
3.1.4.16 NADP+ + H2O
-
 Escherichia coli NAD+ + phosphate
-
 ?
3.1.4.16 p-nitrophenyl phosphate + H2O
-
 Escherichia coli p-nitrophenol + phosphate
-
 ?
3.1.4.37 2',3'-cAMP + H2O
-
 Escherichia coli 2'-AMP + 3'-AMP
-
 ?
3.1.4.37 2',3'-cGMP + H2O
-
 Escherichia coli 2'-GMP + 3'-GMP
-
 ?
3.1.4.37 2'-AMP + H2O
-
 Escherichia coli adenosine + phosphate
-
 ?
3.1.4.37 ADP + H2O
-
 Escherichia coli AMP + phosphate
-
 ?
3.1.4.37 ATP + H2O
-
 Escherichia coli ADP + phosphate
-
 ?
3.1.4.37 bis-p-nitrophenyl phosphate + H2O
-
 Escherichia coli ?
-
 ?
3.1.4.37 CDP + H2O
-
 Escherichia coli CMP + phosphate
-
 ?
3.1.4.37 CTP + H2O
-
 Escherichia coli CDP + phosphate
-
 ?
3.1.4.37 cyclic 2',3'-AMP + H2O best substrate Escherichia coli 2'-AMP
-
 ?
3.1.4.37 cyclic 2',3'-AMP + H2O natural substrate, the 2',3'-cyclic phosphodiesterase activity of the C-terminal HD domain of tRNA nucleotidyltransferase, EC 2.7.7.25, is involved in the repair of the 3’-CCA end of tRNA Escherichia coli 2'-AMP
-
 ?
3.1.4.37 cyclic 2',3'-CMP + H2O low activity Escherichia coli 2'-CMP
-
 ?
3.1.4.37 cyclic 2',3'-GMP + H2O high activity Escherichia coli 2'-GMP
-
 ?
3.1.4.37 diphosphate + H2O
-
 Escherichia coli 2 phosphate
-
 ?
3.1.4.37 additional information not: nucleoside 3',5'-cyclic phosphate Escherichia coli ?
-
 ?
3.1.4.37 NADP+ + H2O
-
 Escherichia coli NAD+ + phosphate
-
 ?
3.1.4.37 nucleoside 2',3'-cyclic phosphate + H2O
-
 Escherichia coli nucleoside 2'-phosphate
-
 ?
3.1.4.37 p-nitrophenyl phosphate + H2O
-
 Escherichia coli p-nitrophenol + phosphate
-
 ?

Subunits

EC Number Subunits Comment Organism
2.7.7.72 More the enzyme comprises two domains: an N-terminal domain containing the nucleotidyltransferase activity and a C-terminal HD domain Escherichia coli
3.1.4.16 dimer
-
 Escherichia coli
3.1.4.16 monomer predominantly Escherichia coli
3.1.4.16 oligomer
-
 Escherichia coli
3.1.4.37 dimer
-
 Escherichia coli
3.1.4.37 monomer predominantly Escherichia coli
3.1.4.37 oligomer
-
 Escherichia coli

Synonyms

EC Number Synonyms Comment Organism
2.7.7.72 ATP(CTP):tRNA nucleotidyltransferase
-
 Escherichia coli
2.7.7.72 tRNA nucleotidyltransferase
-
 Escherichia coli
2.7.7.72 tRNA-NT
-
 Escherichia coli

Temperature Optimum [°C]

EC Number Temperature Optimum [°C] Temperature Optimum Maximum [°C] Comment Organism
2.7.7.72 37
-
 assay at Escherichia coli
3.1.4.37 37
-
 assay at Escherichia coli

Turnover Number [1/s]

EC Number Turnover Number Minimum [1/s] Turnover Number Maximum [1/s] Substrate Comment Organism Structure
3.1.4.16 1.24
-
 ADP +/- 0.07 Escherichia coli
3.1.4.16 1.97
-
 2',3'-cGMP +/- 0.08 Escherichia coli
3.1.4.16 2.51
-
 diphosphate +/- 0.05 Escherichia coli
3.1.4.16 3.09
-
 2'-AMP +/- 0.14 Escherichia coli
3.1.4.16 3.36
-
 CTP +/- 0.17 Escherichia coli
3.1.4.16 3.78
-
 ATP +/- 0.12 Escherichia coli
3.1.4.16 4.83
-
 CDP +/- 0.39 Escherichia coli
3.1.4.16 7.63
-
 2',3'-cAMP +/- 0.48 Escherichia coli
3.1.4.16 10.3
-
 p-nitrophenyl phosphate +/- 0.28 Escherichia coli
3.1.4.16 14.9
-
 NADP +/- 0.5 Escherichia coli
3.1.4.37 0.031 0.51 cyclic 2',3'-AMP pH 7, 37°C Escherichia coli
3.1.4.37 1.24
-
 ADP +/- 0.07 Escherichia coli
3.1.4.37 1.97
-
 cyclic 2',3'-GMP pH 7, 37°C Escherichia coli
3.1.4.37 1.97
-
 2',3'-cGMP +/- 0.08 Escherichia coli
3.1.4.37 2.51
-
 diphosphate +/- 0.05 Escherichia coli
3.1.4.37 2.94
-
 cyclic 2',3'-GMP pH 7, 37°C Escherichia coli
3.1.4.37 3.09
-
 2'-AMP +/- 0.14 Escherichia coli
3.1.4.37 3.36
-
 CTP +/- 0.17 Escherichia coli
3.1.4.37 3.78
-
 ATP +/- 0.12 Escherichia coli
3.1.4.37 4.83
-
 CDP +/- 0.39 Escherichia coli
3.1.4.37 7.63
-
 cyclic 2',3'-AMP pH 7, 37°C Escherichia coli
3.1.4.37 7.63
-
 2',3'-cAMP +/- 0.48 Escherichia coli
3.1.4.37 10.3
-
 p-nitrophenyl phosphate +/- 0.28 Escherichia coli
3.1.4.37 14.9
-
 NADP +/- 0.5 Escherichia coli

pH Optimum

EC Number pH Optimum Minimum pH Optimum Maximum Comment Organism
3.1.4.16 7
-
-
 Escherichia coli
3.1.4.37 7
-
-
 Escherichia coli

Ki Value [mM]

EC Number Ki Value [mM] Ki Value maximum [mM] Inhibitor Comment Organism Structure
3.1.4.16 0.29
-
 tRNA with ATP Escherichia coli
3.1.4.16 0.59
-
 5'-AMP
-
 Escherichia coli
3.1.4.16 1.08
-
 tRNA with 2'-AMP Escherichia coli
3.1.4.16 1.68
-
 tRNA with 2',3'-cAMP Escherichia coli
3.1.4.37 0.00000168
-
 tRNA hydrolysis of cyclic 2',3'-AMP Escherichia coli
3.1.4.37 0.29
-
 tRNA with ATP Escherichia coli
3.1.4.37 0.59
-
 5'-AMP
-
 Escherichia coli
3.1.4.37 1.08
-
 tRNA with 2'-AMP Escherichia coli
3.1.4.37 1.68
-
 tRNA with 2',3'-cAMP Escherichia coli

General Information

EC Number General Information Comment Organism
2.7.7.72 physiological function in all mature tRNAs, the 3'-terminal CCA sequence is synthesized or repaired by the template-independent nucleotidyltransferase ATP(CTP):tRNA nucleotidyltransferase. The phosphohydrolase activities of the HD domain of the tRNA nucleotidyltransferase are involved in the repair of the 3'-CCA end of tRNA, modeling, overview Escherichia coli