Information on EC 3.1.11.1 - exodeoxyribonuclease I

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

EC NUMBER
COMMENTARY hide
3.1.11.1
-
RECOMMENDED NAME
GeneOntology No.
exodeoxyribonuclease I
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
9037-46-1
-
ORGANISM
COMMENTARY hide
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
strains FC29, FC40, SMR4608, SMR593, SMR868, SS778, LMM1001, LMM997, CGSC8563 and MDF01-MDF11
-
-
Manually annotated by BRENDA team
C57BL/6J mice
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-
Manually annotated by BRENDA team
L. cv. Nipponbare
UniProt
Manually annotated by BRENDA team
diverse genotypes, overview
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-
Manually annotated by BRENDA team
strain HB8
UniProt
Manually annotated by BRENDA team
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
evolution
malfunction
physiological function
additional information
SUBSTRATE
PRODUCT                       
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate) hide
LITERATURE
(Substrate)
COMMENTARY
(Product) hide
LITERATURE
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
3'-end-labeled dsDNA + H2O
?
show the reaction diagram
-
-
-
-
?
3'-sticky-ended double-strand DNA + H2O
3'-blunt-ended double-strand DNA + nucleoside 5'-monophosphate
show the reaction diagram
-
-
-
?
5'-end-labeled dsDNA + H2O
?
show the reaction diagram
-
-
-
-
?
5'-fluorescein-TTTTTTTTTTTTTTTTTTTTTTTTT-3' + H2O
?
show the reaction diagram
5'-strand DNA + H2O
?
show the reaction diagram
-
-
-
-
?
biotinylated single-stranded 56mer polynucleotide + H2O
?
show the reaction diagram
-
3'-fluorescent-labeled substrate attached to streptavidin-coated reaction microspheres via a biotin linker
-
-
?
damaged DNA + H2O
?
show the reaction diagram
DNA containing mismatches + H2O
?
show the reaction diagram
dsDNA + H2O
-
show the reaction diagram
mismatched DNA + H2O
?
show the reaction diagram
-
the enzyme shows 5' to 3' exonuclease activity
-
-
-
nicked DNA containing mismatches
?
show the reaction diagram
pdTpS-dApdTpS-dA + H2O
?
show the reaction diagram
-
catalyzes the hydrolysis of chiral phosphothioate diesters with inversion of configuration at phosphorus
-
?
single-stranded DNA + H2O
?
show the reaction diagram
single-stranded methylphosphonate 13-oligodeoxythymidylate + H2O
single-stranded methylphosphonate 13-oligodeoxythymidylate + thymidine 5'-monophosphate
show the reaction diagram
-
-
degradation of methylphosphonate 13-(dT)16-mers from 15-mers to 6-mers, mainly yielded to 9-mers
?
single-stranded oligodeoxyadenylate + H2O
single-stranded oligodeoxyadenylate + adenosine 5'-monophosphate
show the reaction diagram
single-stranded oligodeoxycytidylate + H2O
single-stranded oligodeoxycytidylate + cytidyl 5'-monophosphate
show the reaction diagram
-
-
degradation of p(dC) polymers to products from 10-mers to 6-mers, mainly degraded to 8-mers
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
show the reaction diagram
single-stranded oligodeoxythymidylate + H2O
single-stranded oligodeoxythymidylate + thymidine 5'-monophosphate
show the reaction diagram
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
show the reaction diagram
ssDNA + H2O
?
show the reaction diagram
ssDNA 10 mer + H2O
?
show the reaction diagram
-
-
-
?
ssDNA 21 mer + H2O
?
show the reaction diagram
-
-
-
?
ssDNA 28 mer + H2O
?
show the reaction diagram
-
-
-
?
ssDNA 40 mer + H2O
?
show the reaction diagram
-
-
-
?
ssDNA 50 mer + H2O
?
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
3'-sticky-ended double-strand DNA + H2O
3'-blunt-ended double-strand DNA + nucleoside 5'-monophosphate
show the reaction diagram
-
-
-
?
damaged DNA + H2O
?
show the reaction diagram
-
requirement of the Mre11 complex and exonuclease 1, playing overlapping roles, for activation of the Mec1 signaling pathway, Mre11 and Exo1 collaborate in producing long single-stranded DNA tails at double-strand breaks of DNA and promote Mec1 association with the double-strand break, Mre11 and Exo1 contribute to the activation of the replication checkpoint pathway, modeling of complex activity
-
-
?
DNA containing mismatches + H2O
?
show the reaction diagram
-
the enzyme is involved in mismatch repair and participates directly in somatic hypermutation and class-switch recombination
-
-
?
nicked DNA containing mismatches
?
show the reaction diagram
-
the enzyme is part of the mismatch repair machinery, MMR, the replication factors PCNA and RFC, and Ku70/80 modulate the directionality of the enzyme-mediated excision in DNA mismatch repair, complex components and reaction process, overview
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-
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single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
show the reaction diagram
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
show the reaction diagram
ssDNA + H2O
?
show the reaction diagram
Q53VZ1
TTHB178 possesses 3'5'-ssExo activity that degrades ssDNAs containing deaminated and methylated bases, but not ssDNA containing oxidized bases or abasic sites. The enzyme functions in various DNA repair systems in cooperation with or independently of RecJ
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-
?
additional information
?
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METALS and IONS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
Co2+
activity requires divalent cations
additional information
-
wild-type enzyme structures in complex with Mn2+ or Ba2+, binding structures, anomalous scattering, overview
INHIBITORS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
5'-thiophosphorylated oligonucleotide
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camptothecin
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on exposure to camptothecin, depletion of EXO1 in CtIP-deficient cells increases the frequency of DNA-PK-dependent radial chromosome formation
EDTA
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activity 88% reduced in the presence of Mg2+
endonuclease CtIP
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inhibitory effect of CtIP on EXO1 activity using either a radiolabelled DNA oligonucleotide substrate or a linearized plasmid both containing 3'-overhangs
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fullerene-oligonucleotide conjugate
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increasing the amount of cDNA template reduces the inhibitory effect
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NTP
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the strong 3'-5' exonuclease activity of polB1 is inhibited by 50% in the presence of 0.002 mM dNTPs, but remains measurable at up to 0.6 mM dNTPs
single-stranded DNA-binding protein
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deleting the N-terminal most Met from the C-terminus of single-stranded DNA-binding protein sequence has a negligible effect on apparent binding to ExoI. The C-terminus of single-stranded DNA-binding proteins abrogate single-stranded DNA-binding protein stimulation of ExoI activity through a competitive inhibition mechanism, the peptides can disrupt ExoI/single-stranded DNA-binding protein/single-stranded DNA ternary complexes. C-terminus of single-stranded DNA-binding protein inhibition is dose-dependent, requiring ca. 0.001 mM peptide to achieve 50% inhibition and ca. 0.01 mM to reduce ExoI activity to C-terminus of single-stranded DNA-binding protein-free levels. Addition of up to 0.1 mM of C-terminus of single-stranded DNA-binding protein does not inhibit ExoI activity to levels below that of ExoI with free single-stranded DNA, and addition of the peptide to single-stranded DNA-binding-protein free reactions has no measurable effect on ExoI nuclease activity
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additional information
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ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
E. coli single-stranded binding protein
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four molecules bind to exonuclease, carboxy terminus is the recognition site for the exonuclease, binds ssDNA to establish a conformation suitable for replication, recombination and repair
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additional information
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KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.1
p(dA)4
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inverse dependence with polymer size
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0.04
pdTpdApdTpdA
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0.016
single-stranded DNA
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at 37C, in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 3 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 10% (v/v) glycerol, 5% (v/v) dimethyl sulfoxide
0.28 - 0.48
ssDNA 10 mer
-
0.35 - 0.44
ssDNA 21 mer
-
0.26 - 0.29
ssDNA 28 mer
-
0.24 - 0.32
ssDNA 40 mer
-
0.13 - 0.16
ssDNA 50 mer
-
additional information
additional information
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kinetics of the enzyme located in streptavidin-coated microspheres with biotinylated DNA substrate and Mg2+ cofactor
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TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
115.5
single-stranded DNA
Escherichia coli
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at 37C, in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 3 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 10% (v/v) glycerol, 5% (v/v) dimethyl sulfoxide
0.71 - 7.5
ssDNA 10 mer
-
0.4 - 5.3
ssDNA 21 mer
-
0.23 - 1.9
ssDNA 28 mer
-
0.17 - 2.3
ssDNA 40 mer
-
0.19 - 1
ssDNA 50 mer
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kcat/KM VALUE [1/mMs-1]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
2.6 - 16
ssDNA 10 mer
19240
1.1 - 12
ssDNA 21 mer
19241
0.83 - 7
ssDNA 28 mer
19242
0.72 - 7.5
ssDNA 40 mer
19243
1.7 - 6.4
ssDNA 50 mer
19244
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
IMAGE
0.0043 - 1
single-stranded DNA-binding protein
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SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
7.6
-
assay at
8.5
-
assay at
9.2 - 9.8
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TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
60
the kcat/KM value is 4-fold to 10-fold higher at 60C than at 37C
74
-
assay at
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
SOURCE
-
Burkitt's lymphoma cell line
Manually annotated by BRENDA team
yound leaves and mature leaves, weak expression
Manually annotated by BRENDA team
strong expression
Manually annotated by BRENDA team
weak expression
Manually annotated by BRENDA team
moderate expression
Manually annotated by BRENDA team
strong expression
Manually annotated by BRENDA team
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY hide
GeneOntology No.
LITERATURE
SOURCE
PDB
SCOP
CATH
ORGANISM
UNIPROT
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
Escherichia coli (strain K12)
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
25596
3 * 25596, calculated from sequence
43000
-
gel filtration
53170
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calculation from sequence of cDNA
54000
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SDS-PAGE
70000
-
2 * 70000, native PAGE
72000
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glycerol gradient centrifugation, SDS-PAGE
73400
gel filtration
75000
-
gel filtration
92200
x * 92200, calculated from sequence
140000
-
native PAGE and SDS-PAGE, 85% of activity migrated as dimer, 15% as monomer
SUBUNITS
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
?
x * 92200, calculated from sequence
dimer
-
2 * 70000, native PAGE
homotrimer
monomer
trimer
3 * 25596, calculated from sequence
additional information
POSTTRANSLATIONAL MODIFICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
phosphoprotein
Crystallization/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
by hanging-drop vapor-diffusion method, unbound ExoI, to 1.7 resolution. ExoI bound to the C terminus of ssDNA-binding protein, at 2.7 A resolution. Two C terminus ssDNA-binding proteins bind to adjacent sites on ExoI
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hanging-drop vapour-diffusion method at room temperature, structure of ExoI in complex with a nucleotide product, thymidine 5'-monophosphate; in complex with thymidine 5'-monophosphate, hanging drop vapour diffusion method, using 200 mM NaCl, 100 mM Tris-HCl pH 8.5, and 20% (w/v) PEG 8000
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purified enzyme in complex with four different ssDNA substrates, 5'-Cy5-dT13, 5'-Cy5-dA13, dA16 and dT13, hanging drop vapor diffusion, 0.002 ml of 10 mg/ml enzyme in 20 mM Tris, 1 mM DTT, 10 mM EDTA, pH 8.0, with a 1.2 molar excess of oligonucleotide, is mixed with 0.002 ml of reservoir solution containing 0.9-1.5M ammonium sulfate, 3.756.0% 2-propanol and 25% glycerol, 1 week, X-ray diffraction structure determination and analysis at 2.0-3.7 A resolution
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X-ray structure determination
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crystallization of recombinant wild-type native and selenomethionine-labeled enzyme, and of recombinant mutant D173A enzyme in complex with metal ions, X-ray diffraction structure determination and analysis at 2.5-3.4 A resolution, modelling
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solubilization of the inclusion bodies is performed by the high-pressure refolding method and highly purified protein is subjected to crystallization by the sitting-drop vapour-diffusion method at 20C. A crystal of PhoExo I is obtained in a reservoir solution consisting of 0.1 M Tris-HCl pH 8.9, 27% PEG 6000 and diffracts X-rays to 1.52 A resolution. The crystal of PhoExo I belong to space group H32, with unit-cell parameters a = b = 112.07, c = 202.28 A. The crystal contains two PhoExo I molecules in the asymmetric unit
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GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
30% loss of activity after sonification and storage for one day at 0C
-
50% loss of activity within one month when stored at 0C or at -12C
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STORAGE STABILITY
ORGANISM
UNIPROT
LITERATURE
on ice, 0.02 M Tris-HCl pH 7.4, 1 mM beta-mercaptoethanol, 1 mM EDTA, 10% glycerol, 30% polyethylene glycol, 2 months
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Purification/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
near homogeneity by chromatography steps
-
Ni-NTA agarose resin column chromatography
-
overexpression in Escherichia coli, chromatography techniques, near homogeneity
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recombinant His-tagged enzyme from Escherichia coli strain BL21(AI) by nickel affinity chromatography and ultrafiltration
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to homogeneitiy by affinity chromatography
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to homogeneity by chromatography steps
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Cloned/COMMENTARY
ORGANISM
UNIPROT
LITERATURE
construction of a fusion gene encoding OsEXO1-sGFP fusion protein whose expression is regulated by the cauliflower mosaic virus 35S promoter. The fusion gene is transferred into onion epidermal cells by particle bombardment. When it is transiently expressed in onion cells, the green fluorescence is localized exclusively to the nucleus
deletion mutants of sbcB, xthA and recBrecC genes
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expressed in insect Sf9 cells
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expression in Escherichia coli
expression of hEXO1 in Spodoptera frugiperda Sf9 insect cells using the baculovirus vector system
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into plasmid pcDNA3.1A(-), expressing a COOH-terminal His-Myc-tagged EXO1 protein
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murine NIH3T3 cells are transiently cotransfected with plasmids expressing CFP-PCNA and YFP-hEXO1, expression of wild-type and mutant N-terminal YFP-tagged hEXO1 fusion proteins in Escherichia coli strain BL21(DE3), in vitro transcription translation of hEXO1, plasmid pcDNA3.1A/myc-His(-)A-hEXO1 expressing COOH-terminal his6 and myc epitope tagged hEXO1
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mutation of the xon gene leads to a temperature sensitive enzyme
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overexpression in Escherichia coli
overexpression of Escherichia coli exonuclease I in Deinococcus inhibits DNA double-strand break repair; transgenic Deinococcus cells expressing exonuclease I functions of Escherichia coli show significant reduction in gamma radiation radioresistance, while the resistance to far-UV and hydrogen peroxide remains unaffected. The overexpression of Escherichia coli exonuclease I in Deinococcus inhibits DNA double-strand break repair
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produced as inclusion bodies in Escherichia coli
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recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(AI)
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stable expression of GFP-tagged EXO1 in U2OS cells
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ENGINEERING
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
D319A
-
does not alter the secondary structure significantly. 2-fold binding defect to the C terminus of ssDNA-binding protein relative to wild-type ExoI
E150A
-
does not alter the secondary structure significantly. 2fold enhanced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
E318A
-
does not alter the secondary structure significantly. 2fold enhanced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
K227A
-
does not alter the secondary structure significantly. Displays a 3fold binding defect to the C terminus of ssDNA-binding protein relative to wild-type ExoI
L331A
-
does not alter the secondary structure significantly. Reduced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
Q311A
-
does not alter the secondary structure significantly. Displays modest 2fold binding defect to the C terminus of ssDNA-binding protein relative to wild-type ExoI
R148A
-
does not alter the secondary structure significantly. Displays dramatically reduced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
R316A
-
does not alter the secondary structure significantly. Displays dramatically reduced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
R327A
-
does not alter the secondary structure significantly. Reduced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
R338A
-
does not alter the secondary structure significantly. Displays a 3fold binding defect to the C terminus of ssDNA-binding protein relative to wild-type ExoI
Y207A
-
does not alter the secondary structure significantly. Displays dramatically reduced binding to the C terminus of ssDNA-binding protein relative to wild-type ExoI
F506A
-
substitution on the Mlh1 interacting protein box significantly weakens the interaction with MLH1 and has no impact on the interaction with MSH2 proteins
F506A/F507A
F507A
-
substitution on the Mlh1 interacting protein box significantly weakens the interaction with MLH1 and has no impact on the interaction with MSH2 proteins
Q154A/Y157A
-
site-directed mutagenesis, the expression of the mutant interferes with S-phase distribution
Q285A/F288A
-
site-directed mutagenesis, the expression of the mutant interferes with S-phase distribution
S504A
-
substitution on the Mlh1 interacting protein box significantly weakens the interaction with MLH1 and has no impact on the interaction with MSH2 proteins
D405A
-
mutant enzyme loses 99.8% of DNA polymerizing activity and 90% of 3'->5' exonucleolytic activity
D405E
-
mutant enzyme loses 95.8% of DNA polymerizing activity and 90% of 3'->5' exonucleolytic activity
DELTAH672-S775
-
mutant enzyme loses 99% of DNA polymerizing activity and 97% of 3'->5' exonucleolytic activity
DELTAL717-S775
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mutant enzyme loses 97% of DNA polymerizing activity and 97% of 3'->5' exonucleolytic activity
DELTAL746-S775
-
mutant protein has DNA polymerizing activity with 2.3fold higher specific activity than that of the wild-type but retains only 10% of the 3'->5' exonucleolytic activity of the wild-type
D173A
-
site-directed mutagenesis, the exo1-D173A mutant defective in nuclease activity is able to maintain crossing-over at wild-type levels in a number of genetic intervals. Exo1-D173A cells are able to maintain crossing-over despite reducedhDNAformation
F447A
-
abolishes binding to human MLH1
F448A
-
abolishes binding to human MLH1
S445A
-
abolishes binding to human MLH1
D173A
-
site-directed mutagenesis, the exo1-D173A mutant defective in nuclease activity is able to maintain crossing-over at wild-type levels in a number of genetic intervals. Exo1-D173A cells are able to maintain crossing-over despite reducedhDNAformation
-
additional information
APPLICATION
ORGANISM
UNIPROT
COMMENTARY hide
LITERATURE
analysis
-
an exonuclease I hydrolysis assay for evaluating G-quadruplex stabilization by small molecules
drug development
-
inhibition of a newly synthesized fullerene-oligonucleotide conjugate against PCR-amplification of targeted DNA and the enzymatic activity of an engineered DNA enzyme, Exo I
molecular biology
additional information
Show AA Sequence (2765 entries)
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