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 hide
3.1.13.3
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RECOMMENDED NAME
GeneOntology No.
oligonucleotidase
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
exonucleolytic cleavage of oligonucleotides to yield nucleoside 5'-phosphates
show the reaction diagram
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
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CAS REGISTRY NUMBER
COMMENTARY hide
37288-23-6
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ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
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Manually annotated by BRENDA team
mushroom
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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
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Manually annotated by BRENDA team
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Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
physiological function
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
24mer RNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
3'-phosphoadenosine 5'-phosphate + H2O
AMP + phosphate
show the reaction diagram
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-
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?
5'-p-nitrophenyl-TMP + H2O
p-nitrophenol + TMP
show the reaction diagram
5'Cy5-AAA3' + H2O
nucleoside 5'-phosphates
show the reaction diagram
5'Cy5-AAAAA3' + H2O
nucleoside 5'-phosphates
show the reaction diagram
5'Cy5-CCC3' + H2O
nucleoside 5'-phosphates
show the reaction diagram
5'Cy5-CCCCC3' + H2O
nucleoside 5'-phosphates
show the reaction diagram
5'Cy5-AAAAA3' is a better substrate than 5'Cy5-CCCCC3'
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?
CpC + H2O
5'-CMP
show the reaction diagram
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?
CpU + H2O
5'-CMP + 5'-UMP
show the reaction diagram
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-
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?
DNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
mRNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
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required for for degradation of mRNA to mononucleotides
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?
NAD+ + H2O
NMN + AMP
show the reaction diagram
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
p-nitrophenyl deoxythymidine 5'-phosphate + H2O
p-nitrophenol + 5'-TMP
show the reaction diagram
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no activity on nitrophenyl deoxythymidine 3'-phosphate
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?
p-nitrophenyl uridine 5'-monophosphate + H2O
p-nitrophenol + 5'-UMP
show the reaction diagram
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?
p-nitrophenyl-2',3'-isopropyl-5'-UMP + H2O
p-nitrophenol + isopropyl-5'-UMP
show the reaction diagram
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?
polymer synthesized from NAD+ + H2O
?
show the reaction diagram
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chain length 27-30
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?
RNA + H2O
nucleoside 5'-phosphate + ?
show the reaction diagram
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degrades RNA oligonucleotides with preference for 3-mers
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?
RNA + H2O
nucleoside 5'-phosphates
show the reaction diagram
UpC + H2O
5'-CMP + 5'-UMP
show the reaction diagram
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?
UpU + H2O
5'-UMP
show the reaction diagram
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?
additional information
?
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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
oligonucleotides + H2O
nucleoside 5'-phosphates
show the reaction diagram
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
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activation
Na+
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activates at high concentration
additional information
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3'-AMP
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slight
3'-phosphoadenosine 5'-phosphate
5'-AMP
beta-mercaptoethanol
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slight
CuCl2
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slight
p-chloromercuribenzoate
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slight
UTP
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slight
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.25 - 0.66
(Ap)2
2.47
(Ap)2A
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0.05
(Ap)3
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3.03
(Ap)3A
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0.021
(Ap)4
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0.017
(Ap)6
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0.27 - 1.9
5'-p-nitrophenyl-TMP
0.41
p-nitrophenyl uridine 5'-monophosphate
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.03 - 10.88
5'-p-nitrophenyl-TMP
Ki VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.022 - 0.24
Ni2+
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
1.2
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p-nitrophenyl uridine 5'-monophosphate
1.77
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purified enzyme
7.1
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purified enzyme
14.9
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purified enzyme
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
10.1
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nitrophenyl uridine 5'-monophosphate
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7 - 9.5
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pH 7.0: 50% of maximum activity, pH 9.5: 70% of maximum activity
8 - 10
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nitrophenyl uridine 5'-monphosphate, pH 8: about 15% of maximum activity, pH 10: about 10% of maximum activity
additional information
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active site highly acidic and substrate binding site highly basic
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
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supernatant fraction
Manually annotated by BRENDA team
dual cellular localization being present both in cytosolic and mitochondrial fractions
Manually annotated by BRENDA team
dual cellular localization being present both in cytosolic and mitochondrial fractions. The mitochondrial form localizes to both the intermembrane space and the matrix
Manually annotated by BRENDA team
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
38000
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gel filtration
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
tetramer
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crystallization data
Crystallization/COMMENTARY
ORGANISM
UNIPROT
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
both native and selenomethionine-labeled enzyme
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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
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
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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
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TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
65
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half-life: 10 min
100
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half-life: 2.5 min
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-25°C, 50% glycerol
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
copurifies with polynucleotide phosphorylase
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more than 99% pure
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on Ni-NTA column and by gel filtration, more than 95% pure
to homogeneity
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
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
expression in Escherichia coli
expression of his-tagged YtqI under control of the arabinose-inducible promoter Para
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into pMCSG7 vector
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overexpression of the orn gene in Escherichia coli
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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)
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D130A
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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
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
additional information