Literature summary for 3.1.4.37 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.

Search for more literature for 3.1.4.37

Cloned(Commentary)

Cloned (Comment)	Organism
-	Escherichia coli
tRNA nucleotidyltransferase, EC 2.7.7.25, with its HD domain possessing 2',3'-cyclic phosphodiesterase activity	Escherichia coli

Protein Variants

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

General Stability

General Stability	Organism
stable	Escherichia coli

Inhibitors

Inhibitors	Comment	Organism	Structure
5'-AMP	-	Escherichia coli
Co2+	-	Escherichia coli
Cu2+	-	Escherichia coli
additional information	not inhibited by Mg2+, Mn2+, Ca2+ or Ni2+	Escherichia coli
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
Zn2+	-	Escherichia coli

KM Value [mM]

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

Metals/Ions

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

Natural Substrates/ Products (Substrates)

Natural Substrates	Organism	Comment (Nat. Sub.)	Natural Products	Comment (Nat. Pro.)	Rev.	Reac.
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

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

Purification (Commentary)

Purification (Comment)	Organism
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]

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

Storage Stability

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

Substrates and Products (Substrate)

Substrates	Comment Substrates	Organism	Products	Comment (Products)	Rev.	Reac.
2',3'-cAMP + H2O	-	Escherichia coli	2'-AMP + 3'-AMP	-	?
2',3'-cGMP + H2O	-	Escherichia coli	2'-GMP + 3'-GMP	-	?
2'-AMP + H2O	-	Escherichia coli	adenosine + phosphate	-	?
ADP + H2O	-	Escherichia coli	AMP + phosphate	-	?
ATP + H2O	-	Escherichia coli	ADP + phosphate	-	?
bis-p-nitrophenyl phosphate + H2O	-	Escherichia coli	?	-	?
CDP + H2O	-	Escherichia coli	CMP + phosphate	-	?
CTP + H2O	-	Escherichia coli	CDP + phosphate	-	?
cyclic 2',3'-AMP + H2O	best substrate	Escherichia coli	2'-AMP	-	?
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	-	?
cyclic 2',3'-CMP + H2O	low activity	Escherichia coli	2'-CMP	-	?
cyclic 2',3'-GMP + H2O	high activity	Escherichia coli	2'-GMP	-	?
diphosphate + H2O	-	Escherichia coli	2 phosphate	-	?
additional information	not: nucleoside 3',5'-cyclic phosphate	Escherichia coli	?	-	?
NADP+ + H2O	-	Escherichia coli	NAD+ + phosphate	-	?
nucleoside 2',3'-cyclic phosphate + H2O	-	Escherichia coli	nucleoside 2'-phosphate	-	?
p-nitrophenyl phosphate + H2O	-	Escherichia coli	p-nitrophenol + phosphate	-	?

Subunits

Subunits	Comment	Organism
dimer	-	Escherichia coli
monomer	predominantly	Escherichia coli
oligomer	-	Escherichia coli

Temperature Optimum [°C]

Temperature Optimum [°C]	Temperature Optimum Maximum [°C]	Comment	Organism
37	-	assay at	Escherichia coli

Turnover Number [1/s]

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

pH Optimum

pH Optimum Minimum	pH Optimum Maximum	Comment	Organism
7	-	-	Escherichia coli

Ki Value [mM]

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

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Release 2023.1 (January 2023)