Information on EC 3.1.4.16 - 2',3'-cyclic-nucleotide 2'-phosphodiesterase

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The expected taxonomic range for this enzyme is: Bacteria, Eukaryota

EC NUMBER
COMMENTARY hide
3.1.4.16
-
RECOMMENDED NAME
GeneOntology No.
2',3'-cyclic-nucleotide 2'-phosphodiesterase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
nucleoside 2',3'-cyclic phosphate + H2O = nucleoside 3'-phosphate
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
PATHWAY
BRENDA Link
KEGG Link
MetaCyc Link
Purine metabolism
-
-
Pyrimidine metabolism
-
-
SYSTEMATIC NAME
IUBMB Comments
nucleoside-2',3'-cyclic-phosphate 3'-nucleotidohydrolase
Also hydrolyses 3'-nucleoside monophosphates and bis-4-nitrophenyl phosphate, but not 3'-deoxynucleotides. Similar reactions are carried out by EC 3.1.27.3 (ribonuclease T1) and EC 3.1.27.5 (pancreatic ribonuclease).
CAS REGISTRY NUMBER
COMMENTARY hide
9037-18-7
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strain A-40-2
-
-
Manually annotated by BRENDA team
Bacillus sp. A-40-2
strain A-40-2
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
activity towards 2',3'-cyclic nucleotides and 3',5'-cyclic nucleotides are associated with the same protein molecule
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
CECT 2148
-
-
Manually annotated by BRENDA team
CECT 2148
-
-
Manually annotated by BRENDA team
strain 6746, activity towards 2',3'-cyclic nucleotides and 3',5'-cyclic nucleotides are associated with the same protein molecule
-
-
Manually annotated by BRENDA team
strain 6746, activity towards 2',3'-cyclic nucleotides and 3',5'-cyclic nucleotides are associated with the same protein molecule
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
-
-
-
Manually annotated by BRENDA team
cv. Lukullus
-
-
Manually annotated by BRENDA team
O:8 strains WA-C and WA-314
SwissProt
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
2',3'-cAMP + H2O
2'-AMP + 3'-AMP
show the reaction diagram
-
-
-
-
2',3'-cGMP + H2O
2'-GMP + 3'-GMP
show the reaction diagram
-
-
-
-
2'-AMP + H2O
adenosine + phosphate
show the reaction diagram
-
-
-
-
3'-AMP + H2O
adenosine + phosphate
show the reaction diagram
3'-CMP + H2O
cytidine + phosphate
show the reaction diagram
3'-GMP + H2O
guanosine + phosphate
show the reaction diagram
3'-UMP + H2O
uridine + phosphate
show the reaction diagram
5'-dTMP p-nitrophenyl ester
?
show the reaction diagram
-
-
-
?
5'-UMP + H2O
uridine + phosphate
show the reaction diagram
-
weak activity
-
-
?
ADP + H2O
AMP + phosphate
show the reaction diagram
-
-
-
-
alpha-naphthyl phosphate + H2O
alpha-naphthol + phosphate
show the reaction diagram
-
-
-
-
?
ATP + H2O
ADP + phosphate
show the reaction diagram
-
-
-
-
bis-p-nitrophenyl phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
show the reaction diagram
CDP + H2O
CMP + phosphate
show the reaction diagram
-
-
-
-
CTP + H2O
CDP + phosphate
show the reaction diagram
-
-
-
-
cyclic 2',3'-AMP + H2O
3'-AMP
show the reaction diagram
cyclic 2',3'-CMP + H2O
3'-CMP
show the reaction diagram
cyclic 2',3'-GMP + H2O
3'-GMP
show the reaction diagram
cyclic 2',3'-UMP + H2O
3'-UMP
show the reaction diagram
cyclic 3',5'-AMP + H2O
3'-AMP
show the reaction diagram
-
-
mixture of 3-AMP and 5-AMP in a ratio of 6:1, no further hydrolysis to nucleoside and phosphate
?
cyclic 3',5'-AMP + H2O
5'-AMP
show the reaction diagram
cyclic 3',5'-CMP + H2O
3'-CMP
show the reaction diagram
-
-
mixture of 3-CMP and 5-CMP in a ratio of 6:1, no further hydrolysis to nucleoside and phosphate
?
cyclic 3',5'-GMP + H2O
3'-GMP
show the reaction diagram
-
-
mixture of 3-GMP and 5-GMP in a ratio of 6:1, no further hydrolysis to nucleoside and phosphate
?
cyclic 3',5'-GMP + H2O
5'-GMP
show the reaction diagram
cyclic 3',5'-UMP + H2O
3'-UMP
show the reaction diagram
-
-
mixture of 3-UMP and 5-UMP in a ratio of 6:1, no further hydrolysis to nucleoside and phosphate
?
cyclic 3',5'-UMP + H2O
5'-UMP
show the reaction diagram
di(p-nitrophenyl) phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
show the reaction diagram
di-p-nitrophenyl phosphate + H2O
p-nitrophenol + p-nitrophenyl phosphate
show the reaction diagram
diphosphate + H2O
2 phosphate
show the reaction diagram
NADP+ + H2O
NAD+ + phosphate
show the reaction diagram
-
-
-
-
nucleoside 2',3'-cyclic phosphate + H2O
nucleoside 3'-phosphate
show the reaction diagram
nucleoside 3',5'-cyclic phosphate + H2O
nucleoside 3'-phosphate
show the reaction diagram
-
no apparent base specificity, 2fold higher specific activity with nucleoside 2',3'-cyclic phosphate than with the 3',5'-cyclic isomers
mixture of nucleoside 3'-phosphate and nucleoside 5'-phosphate in a ratio of 6:1, no further hydrolysis to nucleoside and phosphate
?
p-nitrophenyl phenylphosphonate + H2O
?
show the reaction diagram
-
-
-
-
?
p-nitrophenyl phosphate + H2O
p-nitrophenol + phosphate
show the reaction diagram
p-nitrophenyl phosphorylcholine + H2O
?
show the reaction diagram
-
-
?
thymidine p-nitrophenyl phosphate + H2O
thymidine + p-nitrophenyl phosphate
show the reaction diagram
-
-
-
-
?
additional information
?
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
nucleoside 2',3'-cyclic phosphate + H2O
nucleoside 3'-phosphate
show the reaction diagram
-
RNA degradation, enzyme functions as an accessory ribonucleolytic activity that effectively hydrolyzes the primary products of RNase LE, a phosphate starvation-inducible ribonuclease generating 2,3-cyclic nucleoside monophosphates, to substrates for phosphate starvation-inducible phospomonoesterases
-
?
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Ba2+
-
activates
KCN
-
slight activation of cyclic phosphodiesterase
Mo6+
-
activates
Ni2+
activates with diphosphate, KD: 1.06 +/- 0.1 uM; activates with p-nitrophenyl phosphate, KD: 6.0 +/- 0.7 uM
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Ba2+
-
-
Co2+
-
0.1 mM, 80% inhibition
MgCl2
-
maximal inhibition at 20 mM
MgSO4
-
slight inhibition
Na2SO4
-
slight inhibition
phosphate
additional information
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2'-AMP
-
2',3'-cyclic nucleotide phosphodiesterase activity
3',5'-cAMP
-
2',3'-cyclic nucleotide phosphodiesterase activity
3'-AMP
-
cleavage of 2',3'-cyclic nucleotides
5'-ADP
-
2',3'-cyclic nucleotide phosphodiesterase activity
5'-AMP
-
2',3'-cyclic nucleotide phosphodiesterase activity
5'-ATP
-
2',3'-cyclic nucleotide phosphodiesterase activity
5'-CMP
-
2',3'-cyclic nucleotide phosphodiesterase activity
5'-GMP
-
2',3'-cyclic nucleotide phosphodiesterase activity
5'-UMP
-
2',3'-cyclic nucleotide phosphodiesterase activity
adenosine
-
2',3'-cyclic nucleotide phosphodiesterase activity
Br-
-
activates hydrolysis of 3'-nucleotides and di-p-dinitrophenyl phosphate
Calmodulin
-
stimulates activity towards 2',3'-cyclic nucleotides and 3',5'-cyclic nucleotides
CH3COO-
-
activates hydrolysis of 3'-nucleotides and di-p-dinitrophenyl phosphate
cytidine
-
2',3'-cyclic nucleotide phosphodiesterase activity
guanosine
-
2',3'-cyclic nucleotide phosphodiesterase activity
HCOO-
-
activates hydrolysis of 3'-nucleotides and di-p-dinitrophenyl phosphate
I-
-
activates hydrolysis of 3'-nucleotides and di-p-dinitrophenyl phosphate
NO3-
-
activates hydrolysis of 3'-nucleotides and di-p-dinitrophenyl phosphate
uridine
-
2',3'-cyclic nucleotide phosphodiesterase activity
additional information
-
monovalent cations activate in the order of decreasing effectiveness: Cl-, Br-/I-, NO3-, HCOO-, CH3COO-
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.49
2',3'-cAMP
+/- 0.04
1.6
2',3'-cGMP
+/- 0.22
0.76
2'-AMP
+/- 0.13
0.022 - 0.08
3'-AMP
0.01
3'-CMP
-
-
0.1
3'-GMP
-
-
0.022 - 0.07
3'-UMP
0.19
ADP
+/- 0.02
0.18
ATP
+/- 0.01
0.022 - 1.2
bis(p-nitrophenyl)phosphate
0.9 - 9.3
bis-p-nitrophenyl phosphate
0.53
CDP
+/- 0.09
0.13
CTP
+/- 0.01
0.0052 - 35
cyclic 2',3'-AMP
0.1 - 0.6
cyclic 2',3'-CMP
0.02 - 2
cyclic 2',3'-UMP
0.2 - 0.45
di-p-nitrophenyl phosphate
0.1
diphosphate
+/- 0.004
0.15
NADP
+/- 0.02
0.033
p-Nitrophenyl phenylphosphonate
-
-
1.7 - 6.2
p-nitrophenyl phosphate
0.167
thymidine p-nitrophenyl phosphate
-
-
additional information
additional information
-
-
-
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
7.63
2',3'-cAMP
Escherichia coli
P06961
+/- 0.48
1.97
2',3'-cGMP
Escherichia coli
P06961
+/- 0.08
3.09
2'-AMP
Escherichia coli
P06961
+/- 0.14
1.24
ADP
Escherichia coli
P06961
+/- 0.07
3.78
ATP
Escherichia coli
P06961
+/- 0.12
12.4 - 72
bis-p-nitrophenyl phosphate
4.83
CDP
Escherichia coli
P06961
+/- 0.39
3.36
CTP
Escherichia coli
P06961
+/- 0.17
0.0006 - 2.95
cyclic 2',3'-AMP
2.51
diphosphate
Escherichia coli
P06961
+/- 0.05
14.9
NADP
Escherichia coli
P06961
+/- 0.5
0.55 - 10.3
p-nitrophenyl phosphate
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.29 - 1.68
tRNA
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.5
phosphate
Escherichia coli
P67095
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.025
-
pH 7.5, 30C, crude extract
1.49
+/- 0.08, ADP
2.36
+/- 0.10, 2',3'-cGMP
3.01
+/- 0.06, diphosphate
3.21
+/- 0.1, 2',3'-cAMP
3.71
+/- 0.17, 2'-CMP
4.03
+/- 0.20, CTP
4.53
+/- 0.14, ATP
5.8
+/- 0.47, CDP
12.4
+/- 0.34, p-nitrophenyl phosphate
12.93
-
-
17.9
+/- 0.6, NADP
100
-
about, pH 6, 37C, di(p-nitrophenyl) phosphate hydrolysis
additional information
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 6.5
-
hydrolysis of di-p-nitrophenyl phosphate
5.6 - 6.4
-
hydrolysis of di-p-nitrophenyl phosphate
7.2 - 8
-
-
7.2 - 7.8
-
hydrolysis of 3'-AMP
7.4 - 8
-
hydrolysis of 2',3'-cyclic AMP, 2',3'-GMP, 2',3'-CMP and 2',3'-UMP
7.5 - 8
-
-
7.5 - 8.5
-
PdeB has slightly alkaline pH optimum (pH 7.5-8.5) for 3',5'-cAMP with 0.1 M Tris-HCl buffer
7.6 - 8.3
-
-
7.6
-
hydrolysis of 3'-UMP
8.1
-
hydrolysis of 3'-GMP
8.2
-
hydrolysis of 3',5'-cyclic AMP
8.3
-
hydrolysis of 3'-AMP or di-p-nitrophenyl phosphate
8.4
-
cyclic phosphodiesterase activity with cyclic 2',3'-phosphate
8.6
-
cyclic phosphodiesterase activity with cyclic 2',3'-phosphate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5 - 7.5
-
pH 5.0: about 40% of maximal activity, pH 9.0: 70-80% of maximal activity
6 - 9
-
about 55% of maximal activity at pH 6 and at pH 9
7.2 - 9
-
pH 7.2: about 45% of maximal activity, pH 9.0: about 70% of maximal activity, hydrolysis of 3'-GMP
8
-
at pH-values greater than 8 activity declines sharply
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
30
-
assay at
40 - 45
-
-
45
-
hydrolysis of 2',3'-cyclic AMP
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
50 - 55
-
heat treatment at 50 or 55C for 5 min slightly activates the phosphodiesterase activity of PdeB against 3',5'-cAMP by about 1.2fold
pI VALUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
8.1
-
chromatofocusing
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
phosphate-starved cells
Manually annotated by BRENDA team
-
-
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
additional information
-
results might indicate a surface localization
-
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
34000
-
SDS-PAGE
65000
-
gel filtration
75000
-
gel filtration
79000
-
gel filtration
122000
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 71958, CpdB including the N-terminal signal sequence, calculated from the amino acid sequence, x * 68000, mature peptide without the signal sequence, SDS-PAGE
monomer
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
proteolytic modification
contains an N-terminal signal sequence of 25 amino acids
pH STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
5
-
37C, loss of activity below
135200
7 - 11
-
40C, 15 min, fairly stable
135205
12
-
40C, 15 min, 80% loss of activity
135205
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
40 - 80
-
very stable to heat, medium concentrate of enzyme, 5 min, stable
50
-
denaturation above
60
-
half-life: 12.2 min
65
-
partial inactivation
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
activity is not affected by several cycles of freezing and thawing
-
chymotrypsin, 10 min at 37C, 80% loss of phosphodiesterase activity and 3'-nucleotidase activity
-
trypsin, 10 min at 37C, 50% loss of phosphodiesterase activity
-
urea, 6.4 M, 53% loss of activity after 10 min, 20% loss of activity after 20 min
-
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, pH 8.0, 20 mM Tris buffer, stable for at least 6 months
-
-20C, several weeks, stable
-
2-4C, pH 7.4-7.6, Tris buffer, 20-30% loss of activity after 2 months
-
4C or -12C, stable
-
4C, 5% glycerol, 0.5 M NaCl, pH 7.5, no loss in activity after several months
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
from the spent culture medium of phosphate-starved cells, 15fold
-
Ni-NTA agarose column chromatography
partial, activity towards 2',3'-cyclic nucleotides and 3',5'-cyclic nucleotides are associated with the same protein molecule
-
Talon affinity column chromatography
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
cpdB gene, overexpression in Escherichia coli HB101, characterization of the gene
expressed in Escherichia coli BL21 cells
-
expressed in Escherichia coli strain BL21(DE3)
genetic mapping of the cpdB locus
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
H98A
the mutation suppresses the 2',3'-cAMP phosphodiesterase activity of Rv0805 without adversely affecting hydrolysis of bis-p-nitrophenyl phosphate
H98D
the mutation suppresses the 2',3'-cAMP phosphodiesterase activity of Rv0805 without adversely affecting hydrolysis of bis-p-nitrophenyl phosphate
H98N
the mutation suppresses the 2',3'-cAMP phosphodiesterase specific activity to one-fifth the level of wild type Rv0805
H98A
-
the mutation suppresses the 2',3'-cAMP phosphodiesterase activity of Rv0805 without adversely affecting hydrolysis of bis-p-nitrophenyl phosphate
H98D
-
the mutation suppresses the 2',3'-cAMP phosphodiesterase activity of Rv0805 without adversely affecting hydrolysis of bis-p-nitrophenyl phosphate
H98N
-
the mutation suppresses the 2',3'-cAMP phosphodiesterase specific activity to one-fifth the level of wild type Rv0805
additional information
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