Information on EC 3.1.11.2 - exodeoxyribonuclease III

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

EC NUMBER
COMMENTARY hide
3.1.11.2
-
RECOMMENDED NAME
GeneOntology No.
exodeoxyribonuclease III
REACTION
REACTION DIAGRAM
COMMENTARY hide
ORGANISM
UNIPROT
LITERATURE
Exonucleolytic cleavage in the 3'- to 5'- direction to yield nucleoside 5'-phosphates
show the reaction diagram
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY hide
9037-44-9
-
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
double-stranded DNA + H2O
?
show the reaction diagram
double-stranded DNA + H2O
deoxynucleoside 5'-phosphate
show the reaction diagram
double-stranded DNA + H2O
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
double-stranded DNA + H2O
?
show the reaction diagram
additional information
?
-
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
Mn2+
-
at concentrations above 5 mM
NaCl
-
no activity above 300 mM
p-chloromercuribenzoate
-
50% inhibition of DNA phosphatase activity, 90% loss of exonuclease activity
PNA
-
anti-parallel complementary PNA suppresses the degradation of double-stranded DNA by enzyme and the suppression is dependent on the amount and concentration of the PNA
ZnCl2
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2-mercaptoethanol
-
required
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
3.5
apurinic DNA
-
-
-
0.05 - 0.75
PUC18 DNA, PstI
-
9.5
Urea-containing DNA
-
-
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
0.27
-
exonuclease activity
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.7 - 8.4
pH RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
6 - 8
-
-
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22
-
exonuclease III digestion
22 - 30
-
assay at 30C or at room temperature
25
-
assay at
TEMPERATURE RANGE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
22 - 37
-
low activity at 37C
22 - 46
-
between 22C and 46C the activity doubles every 6C
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Bacillus subtilis (strain 168)
Escherichia coli (strain K12)
Methanosarcina mazei (strain ATCC BAA-159 / DSM 3647 / Goe1 / Go1 / JCM 11833 / OCM 88)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Methanothermobacter thermautotrophicus (strain ATCC 29096 / DSM 1053 / JCM 10044 / NBRC 100330 / Delta H)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
Neisseria meningitidis serogroup B (strain MC58)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25500 - 26000
-
gel filtration
29000
-
2 * 29000, SDS-PAGE, wild-type and mutant enzymes E117Q and E117D
58000
-
SDS-PAGE
95000
-
determined by SDS-PAGE
100000
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
homodimer
-
2 * 29000, SDS-PAGE, wild-type and mutant enzymes E117Q and E117D
monomer
additional information
-
investigation of the structure of the recombinant enzyme in the free and DNA-bound states by limited proteolysis experiments and fluorescence quenching measurements
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
TEMPERATURE STABILITY
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
37
-
30 min, in absence of Mg2+ or substrate, 93% loss of activity
46
-
heat inactivation above
70
-
20 min, inactivation
75
-
10 min, inactivation
additional information
-
in presence of Mg2+, exonuclease III exists in two temperature-dependent conformations. The transition temperature for the conformation change occurs at 25C
STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
-20C, 6 months, less than 10% loss of activity
-
Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
mutant enzymes are purified as (His)6-tagged species
-
recombinant fusion protein
-
using a glutathione-Sepharose column
-
Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
expression as a GST-fusion protein in Saccharomyces cerevisiae
-
into the Gateway entry vector pENTR3C, for expressing Ape2 proteins in the yeast strain BJ5464, the cDNAs are cloned in fusion with GST using the plasmid pBJ842
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the enzyme containing the mitochondrial targeting signal of manganese superoxide dismutase is expressed in a human malignant breast epithelial cell line, MDA-MB-231, this expression results in a decrease in cell viability following exposure to oxidative stress
-
ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
E58A
-
altered Mg2+-binding properties, 3'-diesterase activity is reduced when compared to the native enzyme
E117D
-
mutant is unable to cleave substrate in vitro without affecting substrate binding, substitution of Mn2+ for Mg2+ increases the activity
E117Q
-
mutant is unable to cleave substrate in vitro but can bind substrate, substitution of Mn2+ for Mg2+ does not increase the activity
D277A
-
mutant lacking all enzymatic activities
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
medicine
synthesis
-
enzyme is used for purification of eucaryotic extrachromosomal circular DNAs using exonuclease III
additional information
-
using the cleavage function of exonuclease III on double-stranded DNA, design of an amplified DNA detection scheme employing a stem-loop DNA molecular beacon as the signaling probe. Exonuclease III used to recycle target molecules, thus leading to improved sensitivity relative to traditional molecular beacons without any significant restriction in the choice of target sequences
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