Information on EC 3.1.13.3 - oligonucleotidase

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

EC NUMBER
COMMENTARY
3.1.13.3
-
RECOMMENDED NAME
GeneOntology No.
oligonucleotidase
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
REACTION TYPE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
SYNONYMS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
nucleotidase, oligo-
-
-
-
-
oligoribonuclease
-
-
-
-
oligoribonuclease
-
-
phosphodiesterase
-
contains oligonucleotidase activity
small fragment nuclease
-
-
EC 3.1.4.19
-
-
formerly
-
additional information
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
37288-23-6
-
ORGANISM
COMMENTARY
LITERATURE
SEQUENCE CODE
SEQUENCE DB
SOURCE
several mutants
-
-
Manually annotated by BRENDA team
comparative and functional analysis of orn genes carried on an indigenous Pseudomonas plasmid. The plasmid-encoded enzyme is distinct from enzyme encoded by the chromosome of proteobacteria. the plasmid-derived orn gene is plant inducible and widespread among group I plasmids. The donor is unknown
-
-
Manually annotated by BRENDA team
pv. ca,pestris
-
-
Manually annotated by BRENDA team
SUBSTRATE
PRODUCT                      
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3'-phosphoadenosine 5'-phosphate + H2O
AMP + phosphate
show the reaction diagram
-
-
-
-
?
5'-p-nitrophenyl-TMP + H2O
p-nitrophenol + TMP
show the reaction diagram
-
-
-
-
?
CpC + H2O
5'-CMP
show the reaction diagram
-
-
-
-
?
CpU + H2O
5'-CMP + 5'-UMP
show the reaction diagram
-
-
-
-
?
DNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
no activity
-
-
?
DNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
active after dissociation from a ribonucleoprotein
-
-
?
mRNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
required for for degradation of mRNA to mononucleotides
-
-
?
NAD+ + H2O
NMN + AMP
show the reaction diagram
-
-
-
-
?
NAD+ + H2O
NMN + AMP
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
processive degradation, however higher affinity to longer chains
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
exonuclease: 3`to 5'-direction
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
exonuclease: 3`to 5'-direction
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
reaction rate inversely proportional to chain length of substrate
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
hydrolyzes oligodeoxyribonucleotides and oligoribonucleotides
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
hydrolyzes oligodeoxyribonucleotides and oligoribonucleotides
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
P0A784
hydrolyzes oligodeoxyribonucleotides and oligoribonucleotides
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
no base specificity
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
specific for short ribooligonucleotides
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
initial site of attack: 3'-hydroxyl end
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
initial site of attack: 3'-hydroxyl end
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
also hydrolyses NAD+ to NMN and AMP, mechanism
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
has higher affinity to shorter chains, no activity at 3'-phosphate end
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
essential for complete degradation of mRNA
-
-
?
p-nitrophenyl deoxythymidine 5'-phosphate + H2O
p-nitrophenol + 5'-TMP
show the reaction diagram
-
no activity on nitrophenyl deoxythymidine 3'-phosphate
-
-
?
p-nitrophenyl uridine 5'-monophosphate + H2O
p-nitrophenol + 5'-UMP
show the reaction diagram
-
-
-
-
?
p-nitrophenyl-2',3'-isopropyl-5'-UMP + H2O
p-nitrophenol + isopropyl-5'-UMP
show the reaction diagram
-
-
-
-
?
polymer synthesized from NAD+ + H2O
?
show the reaction diagram
-
chain length 27-30
-
-
?
RNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
hydrolyzed very slowly
-
-
?
RNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
active after dissociation from a ribonucleoprotein
-
-
?
RNA + H2O
nucleoside 5'-phosphate + ?
show the reaction diagram
-
degrades RNA oligonucleotides with preference for 3-mers
-
-
?
UpC + H2O
5'-CMP + 5'-UMP
show the reaction diagram
-
-
-
-
?
UpU + H2O
5'-UMP
show the reaction diagram
-
-
-
-
?
DNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
hydrolyzed very slowly, not: ADP, UDP, ATP, UTP
-
-
?
additional information
?
-
-
oligoribonuclease is a common downstream target of lithium-induced pAp accumulation (inhibition of the pAp-degrading enzyme by lithium is widely used to treat bipolar disorders)
-
-
-
additional information
?
-
P0A784
oligoribonuclease is a common downstream target of lithium-induced pAp accumulation (inhibition of the pAp-degrading enzyme by lithium is widely used to treat bipolar disorders)
-
-
-
additional information
?
-
-
degradation of RNA oligomers by oligoribonuclease is critical for completion of the Streptomyces coelicolor life cycle, but expression of ornA is not likely to be contigent on bldA-dependent translation of adpA
-
-
-
NATURAL SUBSTRATES
NATURAL PRODUCTS
REACTION DIAGRAM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
(Substrate)
LITERATURE
(Substrate)
COMMENTARY
(Product)
LITERATURE
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
-
-
-
?
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
-
essential for complete degradation of mRNA
-
-
?
additional information
?
-
-
oligoribonuclease is a common downstream target of lithium-induced pAp accumulation (inhibition of the pAp-degrading enzyme by lithium is widely used to treat bipolar disorders)
-
-
-
additional information
?
-
P0A784
oligoribonuclease is a common downstream target of lithium-induced pAp accumulation (inhibition of the pAp-degrading enzyme by lithium is widely used to treat bipolar disorders)
-
-
-
additional information
?
-
-
degradation of RNA oligomers by oligoribonuclease is critical for completion of the Streptomyces coelicolor life cycle, but expression of ornA is not likely to be contigent on bldA-dependent translation of adpA
-
-
-
METALS and IONS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
Ca2+
-
activation
Ca2+
-
no stimulation
Co2+
-
activation
K+
-
activates at high concentration
K+
-
no effect
Mg2+
-
activation
Mg2+
-
activation
Mg2+
-
one magnesium ion, coordinating well with the DEDDh active site carboxylate groups of Asp15, Glu17, Asp166, and the oxygen atom of U51Op group
Mn2+
-
strong stimulation
Na+
-
activates at high concentration
INHIBITORS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
3'-phosphoadenosine 5'-phosphate
-
inhibits YtqI-catalyzed degradation of nanoRNA. At 0.1, 0.2 or 0.5 mM, the activity of YtqI based on the conversion of 5-mer into monomers in 30 min dropps to 28, 4 and 1%, respectively
beta-mercaptoethanol
-
slight
Ni2+
-
effective competitive inhibitor
p-chloromercuribenzoate
-
slight
KM VALUE [mM]
KM VALUE [mM] Maximum
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.25
-
(Ap)2
-
-
0.05
-
(Ap)3
-
-
0.021
-
(Ap)4
-
-
0.017
-
(Ap)6
-
-
0.27
-
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
0.28
-
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
0.46
-
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
0.54
-
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
0.85
-
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
1.9
-
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
0.41
-
p-nitrophenyl uridine 5'-monophosphate
-
-
TURNOVER NUMBER [1/s]
TURNOVER NUMBER MAXIMUM[1/s]
SUBSTRATE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.03
0.55
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
0.04
1.97
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
0.04
1.97
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
0.057
0.65
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
2.15
-
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
2.3
-
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
7.417
-
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
8.767
-
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
9.317
-
5'-p-nitrophenyl-TMP
-
in the presence of 3 mM Mn2+
10.88
-
5'-p-nitrophenyl-TMP
-
in the presence of 1 mM Mn2+
Ki VALUE [mM]
Ki VALUE [mM] Maximum
INHIBITOR
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
IMAGE
0.022
-
Ni2+
-
-
0.039
-
Ni2+
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
SPECIFIC ACTIVITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
1.2
-
-
p-nitrophenyl uridine 5'-monophosphate
1.77
-
-
purified enzyme
7.1
-
-
purified enzyme
10.75
-
-
-
14.9
-
-
purified enzyme
pH OPTIMUM
pH MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
10.1
-
-
nitrophenyl uridine 5'-monophosphate
10.5
-
-
NAD
pH RANGE
pH RANGE MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
7
9.5
-
pH 7.0: 50% of maximum activity, pH 9.5: 70% of maximum activity
8
10
-
nitrophenyl uridine 5'-monphosphate, pH 8: about 15% of maximum activity, pH 10: about 10% of maximum activity
additional information
-
-
active site highly acidic and substrate binding site highly basic
TEMPERATURE OPTIMUM
TEMPERATURE OPTIMUM MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
-
supernatant fraction
Manually annotated by BRENDA team
MOLECULAR WEIGHT
MOLECULAR WEIGHT MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
38000
-
-
gel filtration
SUBUNITS
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
dimer
-
2 * 20000, amino acid analysis, SDS-PAGE
dimer
-
crystals grown in presence of Mn2+, crystallization data
homodimer
-
2 * 21638, electrospray ionisation mass spectrometry
homodimer
-
2 * 24576, electrospray ionisation mass spectrometry
homodimer
-
2 * 24637, electrospray ionisation mass spectrometry
homodimer
-
crystallography
homodimer
P30014
crystallography
homodimer
Q9HY82
crystallography
tetramer
-
crystallization data
Crystallization/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
belongs to space group I422, with unit cell parameters a = 213.1, b = 213.1, c = 149.2, 90.0, 90.0, 90.0, to 30.0-3.1 A resolution, opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer
P30014
both native and selenomethionine-labeled enzyme
-
belongs to space group P21, with unit cell parameters a = 49.9, b = 76.6, c = 61.7, 90.0, 93.55, 90.0, to 19.97-2.09 A resolution, opposing dimeric arrangement, with the catalytic DEDD residues from one monomer closely juxtaposed with a large basic patch on the other monomer
Q9HY82
by sitting-drop vapor diffusion method, to a resolution of 2.1 A, orn monomer comprises 9 alpha-helices and 5 beta-strands, helix H is oriented opposingly from similar helices in all reported 3'-5' DNases discovered so far, possibly to prevent steric hindrance of accommodating oligoribonucleotide substrates. Amino acids Leu135, Leu143, Ile140, and Leu174 form a hydrophobic cluster, side chains of Glu142/Arg133 and Thr139/Asp136 form salt bridges and H-bonds in the dimer interface, while side chains of Arg145, and Lys157 interact with the ribose 2'-OH or phosphate oxygen atoms of U5 substrates
-
sitting-drop vapour-diffusion method, 2.1 A resolution, crystals are tetragonal and belong to space group P4(3)2(1)2 with unit cell parameters a = b = 67.5 A, c = 89.8 A. One molecule is present per asymmetric unit
-
TEMPERATURE STABILITY
TEMPERATURE STABILITY MAXIMUM
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
65
-
-
half-life: 10 min
70
-
-
pH 7.3, 5 min, complete loss of activity
70
-
-
half-life: 10 min
100
-
-
half-life: 2.5 min
STORAGE STABILITY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
-25°C, 50% glycerol
-
Purification/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
copurifies with polynucleotide phosphorylase
-
on Ni-NTA column and by gel filtration, more than 95% pure
-
to homogeneity
-
on Ni-NTA column and by gel filtration, more than 95% pure
-
more than 99% pure
-
Cloned/COMMENTARY
ORGANISM
UNIPROT ACCESSION NO.
LITERATURE
expression of his-tagged YtqI under control of the arabinose-inducible promoter Para
-
expressed as N-terminal His6-tagged ORN enzyme under control of the bacteriophage T7 promoter in Escherichia coli BL21(kDE3)/pLysS using derivatives of the expression vector pETMCSI
-
overexpression of the orn gene in Escherichia coli
-
expressed as N-terminal His6-tagged ORN enzyme under control of the bacteriophage T7 promoter in Escherichia coli BL21(kDE3)/pLysS using derivatives of the expression vector pETMCSI
-
wild-type ornA and the ornA (D130A) point mutant are placed under the control of the strong, constitutive ermE promoter in the hygromycin-resistant, attP-integrative vector pIJ10275. The resultant plasmids (pJS93 and pJS94) introduced into Streptomyces coelicolor J3411 (DELTAornA::apr) by conjugation with Escherichia coli strain ET12567 (pUZ8002) to yield Streptomyces coelicolor J3411 (pJS93) and Streptomyces coelicolor J3411 (pJS94)
-
expression in Escherichia coli
-
into pMCSG7 vector
-
ENGINEERING
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
ytqI mutant, shows impairment of growth in the absence of cysteine
additional information
-
ORN mutant, shows growth defect, YtqI from Bacillus subtilis is able to complement the mutant
D130A
-
pJS94, encoding the catalytically inactive point mutant OrnA D130A does not suppress the phenotype of the Streptomyces coelicolor J3411 (DELTAornA::apr) null mutant
additional information
-
oligoribonuclease null mutant J3411 (DELTAornA::apr), reveals a conditional defect in morphological differentiation that is reminiscent of bldA. PpJS93, containing ornA under the control of a constitutive promoter, completely suppresses the phenotype of Streptomyces coelicolor J3411 (DELTAornA::apr), but pJS94 (encoding catalytically inactive OrnA D130A) does not
APPLICATION
ORGANISM
UNIPROT ACCESSION NO.
COMMENTARY
LITERATURE
additional information
-
YtqI, in addition to oligoribonuclease activity, has 3'-phosphoadenosine 5'-phosphate-phosphatase activity in vitro. YtqI is able to complement both orn and cysQ mutants in Escherichia coli
additional information
P30014
requirement of dimerization for RNase T action
additional information
Q9HY82
requirement of dimerization for RNase T action