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Information on EC 3.1.11.1 - exodeoxyribonuclease I and Organism(s) Escherichia coli and UniProt Accession P04995
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3.1.11.1 exodeoxyribonuclease ISpecify your search results
Word Map
- 3.1.11.1
- camp
- cyclase
- adenylate
- monophosphate
- agonist
- forskolin
- ibmx
- cardiac
- arterial
- theophylline
- pulmonary
- rolipram
- ventricular
- calmodulin
- prostaglandin
-
inotropic
- guanosine
- 3-isobutyl-1-methylxanthine
- milrinone
-
vasodilator
- isoproterenol
-
klenow
-
camp-dependent
-
contractile
- polymerases
-
adenylyl
- sildenafil
- isobutylmethylxanthine
-
guanylate
-
dibutyryl
- papaverine
-
beta-adrenergic
-
erectile
-
hemodynamic
-
calmodulin-dependent
- prostacyclin
- rhodopsin
-
guanylyl
-
beta-adrenoceptor
-
3',5'-monophosphate
- pentoxifylline
- isoprenaline
- dipyridamole
- dntp
- drug development
- transducin
- molecular biology
- tadalafil
-
phototransduction
-
chronotropic
-
bronchodilator
- analysis
- dobutamine
The taxonomic range for the selected organisms is: Escherichia coli
The enzyme appears in selected viruses and cellular organisms
The enzyme appears in selected viruses and cellular organisms
Synonyms
phosphodiesterase, dna polymerase i, exonuclease i, exonuclease 1, exo i, hexo1, polb1, 3'-to-5' exonuclease, sbcb15, drpase, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
3'5' exonuclease
-
-
-
-
DNA deoxyribophosphodiesterase
-
-
-
-
dRPase
-
-
-
-
E. coli exonuclease I
-
-
-
-
Escherichia coli exonuclease I
-
-
-
-
exonuclease I
exonuclease I
-
-
-
-
REACTION
REACTION DIAGRAM
COMMENTARY
ORGANISM
UNIPROT
LITERATURE
Exonucleolytic cleavage in the 3'- to 5'- direction to yield nucleoside 5'-phosphates
mechanism
-
REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
-
-
-
-
CAS REGISTRY NUMBER
COMMENTARY
9037-46-1
-
SUBSTRATE
PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
Reversibility
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
quadruplex-forming and a non-quadruplex-forming oligomer as substrates.The formation of quadruplex in the oligomer inhibits its hydrolysis and quadruplex stabilization enhances the inhibition
-
-
?
3'-sticky-ended double-strand DNA + H2O
3'-blunt-ended double-strand DNA + nucleoside 5'-monophosphate
-
-
-
?
pdTpS-dApdTpS-dA + H2O
?
-
catalyzes the hydrolysis of chiral phosphothioate diesters with inversion of configuration at phosphorus
-
?
single-stranded methylphosphonate 13-oligodeoxythymidylate + H2O
single-stranded methylphosphonate 13-oligodeoxythymidylate + thymidine 5'-monophosphate
-
-
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
single-stranded oligodeoxycytidylate + H2O
single-stranded oligodeoxycytidylate + cytidyl 5'-monophosphate
-
-
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
single-stranded oligodeoxythymidylate + H2O
single-stranded oligodeoxythymidylate + thymidine 5'-monophosphate
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
single-stranded DNA + H2O
?
-
the enzyme continuously degrades its substrate so that the DNA does not extend on both sides of the groove
-
?
single-stranded oligodeoxyadenylate + H2O
single-stranded oligodeoxyadenylate + adenosine 5'-monophosphate
-
-
mainly degraded to 9-mers
?
single-stranded oligodeoxyadenylate + H2O
single-stranded oligodeoxyadenylate + adenosine 5'-monophosphate
-
(dA)16-mers
degradation of (dA)16-mers from 15-mers to 6-mers, mainly degraded to 9-mers
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
degradation of p(dNT)18-mers from 10-mers to 7-mers
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
nucleic acid binding requires two distinct recognition sites in oligodeoxyribonucleotides
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
nucleic acid binding requires two distinct recognition sites in oligodeoxyribonucleotides
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
E. coli exonuclease I, III and V are required for stable maintenance of ColE1-related plasmids
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
inactivation of exonuclease I diverts most of plasmid replication activity from circular monomer production to synthesis of linear multimers
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
implicated in DNA repair and recombination pathways
-
?
single-stranded oligodeoxythymidylate + H2O
single-stranded oligodeoxythymidylate + thymidine 5'-monophosphate
-
-
mainly degraded to 9-mers
?
single-stranded oligodeoxythymidylate + H2O
single-stranded oligodeoxythymidylate + thymidine 5'-monophosphate
-
(dT)16-mers
degradation of (dT)16-mers from 15-mers to 4-mers, mainly degraded to 9-mers
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
additional information
?
-
ssDNA-binding protein stimulates ExoI by recruiting the enzyme to its substrate and provides a structural paradigm for understanding ssDNA-binding protein's organizational role in genome maintenance
-
-
?
additional information
?
-
-
ssDNA-binding protein stimulates ExoI by recruiting the enzyme to its substrate and provides a structural paradigm for understanding ssDNA-binding protein's organizational role in genome maintenance
-
-
?
additional information
?
-
exonuclease I digests single-stranded DNA in the 3'-5' direction in a highly processive manner. The interactions at the anchor site, which involve all three domains of the enzyme protein and three consecutive nucleotides of the ssDNA
-
-
?
additional information
?
-
-
exonuclease I digests single-stranded DNA in the 3'-5' direction in a highly processive manner. The interactions at the anchor site, which involve all three domains of the enzyme protein and three consecutive nucleotides of the ssDNA
-
-
?
additional information
?
-
-
the enzyme is part of the mismatch repair machinery, MMR, the replication factors PCNA and RFC modulate the directionality of the enzyme-mediated excision in DNA mismatch repair, complex components and reaction process, overview
-
-
?
additional information
?
-
-
role for the single-stranded exonuclease in guarding the genome against mutagenesis by removing excess single-stranded DNA that, if left, leads to SOS induction and PolIV-dependent mutagenesis
-
-
?
additional information
?
-
-
self-assembling peptide EAK-oligodeoxynucleotide aggregates generated with EAK16IV at pH 4 are not degraded by exonuclease I even after 90 min. Fl-dC16-Rh complexed with EAK16IV at pH 4 shows significant nuclease resistance against exonuclease I. Aggregates prepared with EAK16IV and Fl-dC16-Rh at pH 4 protect Fl-dC16-Rh against nuclease degradation even after being incubated at pH 9.5 for 2 h. Centrifuging the EAK16IV-oligodeoxynucleotide solution immediately after sample preparation results in the loss of this nuclease protection. If the solution of EAK-oligodeoxynucleotide aggregates is centrifuged 24 h after sample preparation, the nuclease protection afforded by the EAK16IVoligodeoxynucleotide aggregates to the oligodeoxynucleotide is maintained even after being subject to a 10fold dilution and up to 4 rounds of centrifugation over 4 days
-
-
?
NATURAL SUBSTRATE
NATURAL PRODUCT
REACTION DIAGRAM
ORGANISM
UNIPROT
COMMENTARY
(Substrate)
(Substrate)
LITERATURE
(Substrate)
(Substrate)
COMMENTARY
(Product)
(Product)
LITERATURE
(Product)
(Product)
REVERSIBILITY
r=reversible
ir=irreversible
?=not specified
r=reversible
ir=irreversible
?=not specified
3'-sticky-ended double-strand DNA + H2O
3'-blunt-ended double-strand DNA + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
nucleic acid binding requires two distinct recognition sites in oligodeoxyribonucleotides
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
nucleic acid binding requires two distinct recognition sites in oligodeoxyribonucleotides
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
E. coli exonuclease I, III and V are required for stable maintenance of ColE1-related plasmids
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
inactivation of exonuclease I diverts most of plasmid replication activity from circular monomer production to synthesis of linear multimers
-
?
single-stranded oligodeoxyribonucleotide + H2O
single-stranded oligodeoxyribonucleotide + nucleoside 5'-monophosphate
-
implicated in DNA repair and recombination pathways
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
single-stranded polydeoxyribonucleotide + H2O
single-stranded oligodeoxynucleotide + nucleoside 5'-monophosphate
-
-
-
?
additional information
?
-
ssDNA-binding protein stimulates ExoI by recruiting the enzyme to its substrate and provides a structural paradigm for understanding ssDNA-binding protein's organizational role in genome maintenance
-
-
?
additional information
?
-
-
ssDNA-binding protein stimulates ExoI by recruiting the enzyme to its substrate and provides a structural paradigm for understanding ssDNA-binding protein's organizational role in genome maintenance
-
-
?
additional information
?
-
-
the enzyme is part of the mismatch repair machinery, MMR, the replication factors PCNA and RFC modulate the directionality of the enzyme-mediated excision in DNA mismatch repair, complex components and reaction process, overview
-
-
?
additional information
?
-
-
role for the single-stranded exonuclease in guarding the genome against mutagenesis by removing excess single-stranded DNA that, if left, leads to SOS induction and PolIV-dependent mutagenesis
-
-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Mg2+
Mg2+
Mg2+
Arg-316 rotamer position allows a nonactive site Mg2+ ion to bind to an acidic pocket formed by Glu-150, Glu-318, and Asp-319
Mg2+
required, binds at the active site, the Mg2+ ion is coordinated with near octahedral geometry to the scissile phosphate, the carboxylate of Asp15 and three water molecules
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
fullerene-oligonucleotide conjugate
-
increasing the amount of cDNA template reduces the inhibitory effect
-
single-stranded DNA-binding protein
-
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
-
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
E. coli single-stranded binding protein
-
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
-
additional information
ssDNA-binding protein stimulates ExoI by recruiting the enzyme. ExoI/ssDNA-binding protein complex formation is necessary, but not sufficient for ssDNA-binding protein stimulation of ExoI activity
-
additional information
-
ssDNA-binding protein stimulates ExoI by recruiting the enzyme. ExoI/ssDNA-binding protein complex formation is necessary, but not sufficient for ssDNA-binding protein stimulation of ExoI activity
-
additional information
-
ExoI enzymatic activity is stimulated by single-stranded DNA-binding protein, whereby the hydrophobic C-terminal residues play critical roles in ExoI binding
-
KM VALUE [mM]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.016
single-stranded DNA
-
at 37°C, 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
TURNOVER NUMBER [1/s]
SUBSTRATE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
115.5
single-stranded DNA
-
at 37°C, 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
IC50 VALUE [mM]
INHIBITOR
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
0.0043
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with N-terminal truncation WDFDDDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0052
single-stranded DNA-binding protein
Escherichia coli
-
wild type peptide inhibitor, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0067
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with neutralizing modification WMDFDADIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0085
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with neutralizing modification WMDFADDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0093
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with neutralizing modification WMDFDDAIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0116
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with neutralizing modification WMAFDDDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0121
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with N-terminal truncation WFDDDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0253
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with N-terminal truncation WDDDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0335
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with N-terminal truncation WDDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0529
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with C-terminal modification/truncation WMDFDDDISF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.0791
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with N-terminal truncation WDIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.169
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with neutralizing modification WMAFAAAIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.252
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with N-terminal truncation WIPF, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
0.382
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with C-terminal modification/truncation WMDFDDDIPY, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
1
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with C-terminal modification/truncation WMDFDDD, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
1
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with C-terminal modification/truncation WMDFDDDI, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
1
single-stranded DNA-binding protein
Escherichia coli
-
peptide inhibitor with C-terminal modification/truncation WMDFDDDIP, at 22°C in 20 mM Tris-HCl buffer, pH 8.0, 100 mM NaCl, 1 mM MgCl2, 1 mM 2-mercaptoethanol, 0.1 g/l bovine serum albumin, 4% (v/v) glycerol, 1% (v/v) dimethyl sulfoxide
-
SPECIFIC ACTIVITY [µmol/min/mg]
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
pH OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
SOURCE TISSUE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
SOURCE
LOCALIZATION
ORGANISM
UNIPROT
COMMENTARY
GeneOntology No.
LITERATURE
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
additional information
additional information
the enzyme crystal structure, in the absence of DNA, shows a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Analysis of the active site structure of enzyme with bound ssDNA nucleotides, overview
additional information
-
the enzyme crystal structure, in the absence of DNA, shows a C-shaped molecule with three domains that form a central positively charged groove. The active site is at the bottom of the groove, while an extended loop, proposed to encircle the DNA, crosses over the groove. Analysis of the active site structure of enzyme with bound ssDNA nucleotides, overview
PDB
SCOP
CATH
UNIPROT
ORGANISM
MOLECULAR WEIGHT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
140000
-
native PAGE and SDS-PAGE, 85% of activity migrated as dimer, 15% as monomer
55000
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
monomer
additional information
-
the enzymes are component of the mismatch repair machinery, composition and function, overview
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
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
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
hanging-drop vapour-diffusion method at room temperature, structure of ExoI in complex with a nucleotide product, thymidine 5'-monophosphate
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
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
additional information
additional information
-
mutant lacking RecJ, ExoI, ExoVII and ExoX exonucleases abolishes normal mismatch repair in vitro but confers only a modest increase in mutation rate
additional information
-
the quadruple mutant lacking RecJ, ExoI, ExoVII and ExoX exonucleases and the triple mutant lacking RecJ, ExoI and ExoVII are characterized by sensitivity to the base analogous 2-aminopurine. The quadruple mutant displays a cold-sensitive phenotype and is unable to form colonies at 30°C on rich medium
GENERAL STABILITY
ORGANISM
UNIPROT
LITERATURE
50% loss of activity within one month when stored at 0°C or at -12°C
-
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
-
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant His-tagged enzyme from Escherichia coli strain BL21(AI) by nickel affinity chromatography and ultrafiltration
overexpression in Escherichia coli, chromatography techniques, near homogeneity
-
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
recombinant expression of the His-tagged enzyme in Escherichia coli strain BL21(AI)
expression 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
-
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
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
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Brody, R.S.
Nucleotide positions responsible for the processivity of the reaction of exonuclease I with oligodeoxyribonucleotides
Biochemistry
30
7072-7080
1991
Escherichia coli
Phillips, G.J.; Prasher, D.C.; Kushner, S.R.
Physical and biochemical characterization of cloned sbcB and xonA mutations from Escherichia coli K-12
J. Bacteriol.
170
2089-2094
1988
Escherichia coli
Phillips, G.J.; Kushner, S.R.
Determination of the nucleotide sequence for the exonuclease I structural gene (sbcB) of Escherichia coli K12
J. Biol. Chem.
262
455-459
1987
Escherichia coli
Genschel, J.; Curth, U.; Urbanke, C.
Interaction of E. coli single-stranded DNA binding protein (SSB) with exonuclease I. The carboxy-terminus of SSB is the recognition site for the nuclease
Biol. Chem.
381
183-192
2000
Escherichia coli
Silberstein, Z.; Cohen, A.
Synthesis of linear multimers of OriC and pBR322 derivatives in Escherichia coli K-12: Role of recombination and replication functions
J. Bacteriol.
169
3131-3137
1987
Escherichia coli
Brody, R.S.; Doherty, K.G.; Zimmermann, P.D.
Processivity and kinetics of the reaction of exonuclease I from Escherichia coli with polydeoxyribonucleotides
J. Biol. Chem.
261
7136-7143
1986
Escherichia coli
Brody, R.S.; Doherty, K.G.
Stereochemical course of hydrolysis of DNA by exonuclease I from Escherichia coli
Biochemistry
24
2072-2076
1985
Escherichia coli
Bassett, C.L.; Kushner, S.R.
Exonucleases I, III, and V are required for stability of ColE1-related plasmids in Escherichia coli
J. Bacteriol.
157
661-664
1984
Escherichia coli
Prasher, D.C.; Conarro L.; Kushner, S.R.
Amplification and purification of exonuclease I from Escherichia coli
J. Biol. Chem.
2558
6340-6343
1983
Escherichia coli
Mackay, V.; Linn, S.
Molecular structure of exonuclease I from Escherichia coli B
Biochim. Biophys. Acta
349
131-134
1974
Escherichia coli
Ray, R.K.; Reuben, R.; Molineux, I.; Gefter, M.
The purification of exonuclease I from Escherichia coli by affinity chromatography
J. Biol. Chem.
249
5379-5381
1974
Escherichia coli
Yajko, D.M.; Valentine, M.C.; Weiss, B.
Mutants of Escherichia coli with altered deoxyribonucleases. II. Isolation and characterization of mutants for exonuclease I
J. Mol. Biol.
85
323-342
1974
Escherichia coli
Lehman, I.R.
Exonuclease I (phosphodiesterase) (I) from Escherichia coli
Procedures in Nucleic Acid Research (Cantoni, G. L. , Davies, D. R. , eds. )
203-211
1966
Escherichia coli
-
Lehman, I.R.; Nussbaum, A.L.
The deoxyribonucleases of Escherichia coli. V. On the specificity of exonuclease I (phosphodiesterase)
J. Biol. Chem.
239
2628-2636
1964
Escherichia coli
Viswanathan, M.; Burdett, V.; Baitinger, C.; Modrich, P.; Lovett, S.T.
Redundant exonuclease involvement in Escherichia coli methyl-directed mismatch repair
J. Biol. Chem.
276
31053-31058
2001
Escherichia coli
Breyer, W.A.; Matthews, B.W.
Structure of Escherichia coli exonuclease I suggests how processivity is achieved
Nat. Struct. Biol.
7
1125-1128
2000
Escherichia coli
Feschenko, V.V.; Rajman, L.A.; Lovett, S.T.
Stabilization of perfect and imperfect tandem repeats by single-strand DNA exonucleases
Proc. Natl. Acad. Sci. USA
100
1134-1139
2003
Escherichia coli
Burdett, V.; Baitinger, C.; Viswanathan, M.; Lovett, S.T.; Modrich, P.
In vivo requirement for RecJ, ExoVII, ExoI, and ExoX in methyl-directed mismatch repair
Proc. Natl. Acad. Sci. USA
98
6765-6770
2001
Escherichia coli
Surtees, J.A.; Alani, E.
Replication factors license exonuclease I in mismatch repair
Mol. Cell
15
164-166
2004
Escherichia coli, Homo sapiens
Busam, R.D.
Structure of Escherichia coli exonuclease I in complex with thymidine 5-monophosphate
Acta Crystallogr. Sect. D
64
206-210
2008
Escherichia coli, Escherichia coli (P04995)
Hersh, M.N.; Morales, L.D.; Ross, K.J.; Rosenberg, S.M.
Single-strand-specific exonucleases prevent frameshift mutagenesis by suppressing SOS induction and the action of DinB/DNA polymerase IV in growing cells
J. Bacteriol.
188
2336-2342
2006
Escherichia coli
Misra, H.S.; Khairnar, N.P.; Kota, S.; Shrivastava, S.; Joshi, V.P.; Apte, S.K.
An exonuclease I-sensitive DNA repair pathway in Deinococcus radiodurans: a major determinant of radiation resistance
Mol. Microbiol.
59
1308-1316
2006
Escherichia coli
Yao, Y.; Wang, Q.; Hao, Y.; Tan, Z.
An exonuclease I hydrolysis assay for evaluating G-quadruplex stabilization by small molecules
Nucleic Acids Res.
35
e68/1-e68/9
2007
Escherichia coli (P04995)
Yang, X.; Meng, X.; Li, B.; Chen, Z.; Zhao, D.; Tan, X.; Yu, Q.
Inhibition of in vitro amplification of targeted DNA fragment and activity of exonuclease I by a fullerene-oligonucleotide conjugate
Biologicals
36
223-226
2008
Escherichia coli
Wang, M.; Adikane, H.V.; Duhamel, J.; Chen, P.
Protection of oligodeoxynucleotides against nuclease degradation through association with self-assembling peptides
Biomaterials
29
1099-1108
2008
Escherichia coli
Lu, D.; Keck, J.L.
Structural basis of Escherichia coli single-stranded DNA-binding protein stimulation of exonuclease I
Proc. Natl. Acad. Sci. USA
105
9169-9174
2008
Escherichia coli (P04995), Escherichia coli
Lu, D.; Windsor, M.A.; Gellman, S.H.; Keck, J.L.
Peptide inhibitors identify roles for SSB C-terminal residues in SSB/exonuclease I complex formation
Biochemistry
48
6764-6771
2009
Escherichia coli
Korada, S.K.; Johns, T.D.; Smith, C.E.; Jones, N.D.; McCabe, K.A.; Bell, C.E.
Crystal structures of Escherichia coli exonuclease I in complex with single-stranded DNA provide insights into the mechanism of processive digestion
Nucleic Acids Res.
41
5887-5897
2013
Escherichia coli (P04995), Escherichia coli
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