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Information on EC 3.1.21.7 - deoxyribonuclease V and Organism(s) Thermotoga maritima and UniProt Accession Q9X2H9
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3.1.21.7 deoxyribonuclease VSpecify your search results
Word Map
- 3.1.21.7
- nick
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deaminate
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phosphodiester
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beta-polymerase
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deoxyinosine-containing
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3\'-hydroxyl
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proofreading
- biotechnology
- analysis
- molecular biology
- drug development
- medicine
The taxonomic range for the selected organisms is: Thermotoga maritima
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
The expected taxonomic range for this enzyme is: Bacteria, Archaea, Eukaryota
Synonyms
endo v, dnase v, deoxyinosine 3' endonuclease, agtendov, pfuendov, deoxyinosine 3'endonuclease, escherichia coli endodeoxyribonuclease v, 
more
topSYNONYM 
ORGANISM
UNIPROT
COMMENTARY 
LITERATURE
Deoxyinosine 3'endonuclease
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DNase V
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endodeoxyribonuclease V
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Escherichia coli endodeoxyribonuclease V
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REACTION TYPE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
hydrolysis of phosphoric ester
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CAS REGISTRY NUMBER
COMMENTARY
61970-03-4
Previously classified erroneously as EC 3.1.22.3
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
deoxyinosine-containing single-stranded DNA + H2O
?
precursor activity of DNA repair
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-
?
DNA + H2O
5'-phosphoryltermini DNA + 3'-hydroxyltermini DNA
EndoV hydrolyzes the second phosphodiester bond 3' of a deaminated base using Mg2+ as a cofactor
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?
DNA + H2O
?
the enzyme binds A:TT loops with higher affinity than undamaged DNA
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?
DNA + H2O
?
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the enzyme cleaves the second phosphodiester bond 3' to deoxyinosine
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-
?
DNA + H2O
hydrolysed DNA
cleavage of deaminated bases at the second phosphodiester bond 3' downstream to a lesion
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?
DNA + H2O
hydrolysed DNA
hydrolysis of the second phosphodiester bond 3' from a deaminated base lesion including inosine, xanthosine, oxanosine and uridine
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-
?
additional information
?
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EndoV cleaves substrates with base mismatches and helical distortions, such as mismatch loops, hairpins and flap structures, EndoV cleaves mismatched base pairs preferentially at adenine and guanine purines, EndoV binds to cleaved mismatch base pair products with much lower affinity as compared to cleaved deaminated bases
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?
additional information
?
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3'-exonuclease activity in endonuclease V might be preferentially triggered by the specific cleavage event at the inosine site
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?
additional information
?
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endonuclease V is an enzyme that initiates a conserved DNA repair pathway by making an endonucleolytic incision at the 3'-side 1 nt from a deaminated base lesion. But Tma endonuclease V also exhibits inosine-dependent 3'-exonuclease activity and non-specific 5'-exonuclease activity
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?
additional information
?
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cleavage of 50-labeled inosine- and non-inosine-containing substrates
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-
?
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
DNA + H2O
?
the enzyme binds A:TT loops with higher affinity than undamaged DNA
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-
?
DNA + H2O
?
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the enzyme cleaves the second phosphodiester bond 3' to deoxyinosine
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?
additional information
?
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endonuclease V is an enzyme that initiates a conserved DNA repair pathway by making an endonucleolytic incision at the 3'-side 1 nt from a deaminated base lesion. But Tma endonuclease V also exhibits inosine-dependent 3'-exonuclease activity and non-specific 5'-exonuclease activity
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-
?
METALS and IONS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
Ca2+
Mg2+
Mn2+
Ca2+
protein binding, D43, E89, D110, and H214 have been identified as active site residues that are involved in metal coordination
Mg2+
DNA cleavage, D43, E89, D110, and H214 have been identified as active site residues that are involved in metal coordination
Mg2+
contains one Mg2+ ion in the active site, which is required for activity
Mn2+
in the presence of Mn2+, 3'-exonuclease activity is pronounced in wild type and mutant enzymes E89D, D110C, H214C, H214E, and H214D, while reduced activity is detected in D110A, D110H, and D110E
ACTIVATING COMPOUND
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
IMAGE
additional information
high pH, metal cofactor Mn2+, using excess enzyme, and/or solvents such as dimethyl sulfoxide and betaine, lead to cleavage of most mismatched DNA base pairs
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additional information
-
high pH, metal cofactor Mn2+, using excess enzyme, and/or solvents such as dimethyl sulfoxide and betaine, lead to cleavage of most mismatched DNA base pairs
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pH RANGE
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
TEMPERATURE OPTIMUM
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
ORGANISM
COMMENTARY
LITERATURE
UNIPROT
SEQUENCE DB
SOURCE
GENERAL INFORMATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
physiological function
physiological function
-
endonuclease V is an enzyme that initiates a conserved DNA repair pathway by making an endonucleolytic incision at the 3'-side 1 nt from a deaminated base lesion
physiological function
the DNA repair enzyme recognizes and cleaves DNA at deaminated adenine lesions (hypoxanthine) In addition, the enzyme cleaves DNA containing various helical distortions such as loops, hairpins, and flaps
physiological function
EndoV is a single-conformation and single-binding-site protein that switches between three distinct DNA scanning modes, each with a clear range of activation energy barriers. It is involved in the repair pathways for removing DNA damage
PDB
SCOP
CATH
UNIPROT
ORGANISM
SUBUNIT
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
CRYSTALLIZATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
EndoV in complex with a hypoxanthine lesion substrate and with product DNA, hanging drop vapour diffusion method, in 6-12% (w/v) MPEG 2k in 200 mM imidazole-matate buffer, pH 5.8-7.4
in complex with DNA containing one nucleotide A:TT loop, vapor diffusion method, using 15% (w/v) polyethylene glycol 400 and 100 mM MES, pH 6.3
PROTEIN VARIANTS
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
D43A
H214D
Y80A
Y80F
Y80H
the mutant is severely compromised in its ability to bind to DNA base lesions and the corresponding nicked product
A123I
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levels of oxanosine and uridine cleavage are reduced by more than 90%
A86M
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fully active in inosine and xanthosine substrates, significant loss in the level of oxanosine and uridine cleavage
F46A
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mutation reduces the levels of oxanosine and uridine cleavage to less than 40%
F87A
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mutant essentially maintains wild-type level activity towards inosine, xanthosine, oxanosine and uridine substrates
G111V
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levels of oxanosine and uridine cleavage are reduced by more than 90%, level of cleavage of the T/I substrate is reduced by 40%
G113V
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levels of oxanosine and uridine cleavage are reduced by more than 90%, level of cleavage of the T/I substrate is reduced by 50%
G121V
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levels of oxanosine and uridine cleavage are reduced by more than 90%, level of cleavage of the T/I substrate is reduced by 10%
G127V
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levels of oxanosine and uridine cleavage are reduced by more than 90%, level of cleavage of the T/I substrate is reduced by 70%
G41V
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mutation reduces the levels of oxanosine and uridine cleavage to less than 40%
G83V
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fully active in inosine and xanthosine substrates, significant loss in the level of oxanosine and uridine cleavage
I81A
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mutant essentially maintains wild-type level activity towards inosine, xanthosine and uridine substrates, 40% less active towards oxanosine substrates
L85V
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fully active in inosine and xanthosine substrates, significant loss in the level of oxanosine and uridine cleavage
P79A
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mutant essentially maintains wild-type level activity towards inosine, xanthosine, oxanosine and uridine substrates
P82A
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mutant essentially maintains wild-type level activity towards inosine, xanthosine, oxanosine and uridine substrates, 70% less active towards oxanosine substrates
R88E
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fully active in inosine and xanthosine substrates, significant loss in the level of oxanosine and uridine cleavage
R99Q
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fully active in inosine and xanthosine substrates, significant loss in the level of oxanosine and uridine cleavage
Y80A
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mutant is fully active towards inosine and xanthosine substrates but is minimally active on oxanosine and uridine substrates
Y80F
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mutant is fully active towards inosine and xanthosine substrates but is minimally active on oxanosine and uridine substrates, partially active on G/U substrate
Y80H
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mutant is fully active towards inosine and xanthosine substrates but is minimally active on oxanosine and uridine substrates
additional information
-
construction of enzyme mutants defective in DNA binding and Mn2+ as a metal cofactor. The majority of the binding defective mutants show varying degrees of non-specific activities
H214D
little change in substrate specificity or DNA cleavage kinetics
Y80A
the mutant is severely compromised in its ability to bind to DNA base lesions and the corresponding nicked product
Y80F
the mutant is similar to the wild type EndoV in its ability to bind to DNA base lesions and the corresponding nicked product
PURIFICATION (Commentary)
ORGANISM
UNIPROT
LITERATURE
CLONED (Commentary)
ORGANISM
UNIPROT
LITERATURE
APPLICATION
ORGANISM
UNIPROT
COMMENTARY
LITERATURE
biotechnology
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method of linear amplification of DNA, allows 100fold amplification of target molecules
REF.
AUTHORS
TITLE
JOURNAL
VOL.
PAGES
YEAR
ORGANISM (UNIPROT)
PUBMED ID
SOURCE
Feng, H.; Dong, L.; Klutz, A.M.; Aghaebrahim, N.; Cao, W.
Defining amino acid residues involved in DNA-protein interactions and revelation of 3'-exonuclease activity in endonuclease V
Biochemistry
44
11486-11495
2005
Thermotoga maritima
Turner, D.J.; Pingle, M.R.; Barany, F.
Harnessing asymmetrical substrate recognition by thermostable EndoV to achieve balanced linear amplification in multiplexed SNP typing
Biochem. Cell Biol.
84
232-242
2006
Thermotoga maritima
Feng, H.; Dong, L.; Cao, W.
Catalytic Mechanism of Endonuclease V: A Catalytic and Regulatory Two-Metal Model
Biochemistry
45
10251-10259
2006
Thermotoga maritima (Q9X2H9)
Lin, J.; Gao, H.; Schallhorn, K.A.; Harris, R.M.; Cao, W.; Ke, P.C.
Lesion Recognition and Cleavage by Endonuclease V: A Single-Molecule Study
Biochemistry
46
7132-7137
2007
Thermotoga maritima (Q9X2H9)
Gao, H.; Huang, J.; Barany, F.; Cao, W.
Switching base preferences of mismatch cleavage in endonuclease V: an improved method for scanning point mutations
Nucleic Acids Res.
35
e2/1-e2/6
2007
Thermotoga maritima (Q9X2H9)
-
Dalhus, B.; Arvai, A.S.; Rosnes, I.; Olsen, O.E.; Backe, P.H.; Alseth, I.; Gao, H.; Cao, W.; Tainer, J.A.; Bjoras, M.
Structures of endonuclease V with DNA reveal initiation of deaminated adenine repair
Nat. Struct. Mol. Biol.
16
138-143
2009
Thermotoga maritima (Q9X2H9)
Mi, R.; Abole, A.; Cao, W.
Dissecting endonuclease and exonuclease activities in endonuclease V from Thermotoga maritima
Nucleic Acids Res.
39
536-544
2011
Thermotoga maritima
Baumann, T.; Arndt, K.; Mueller, K.
Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
BMC Biotechnol.
13
81
2013
Escherichia coli, Thermotoga maritima
Rosnes, I.; Rowe, A.D.; Vik, E.S.; Forstrom, R.J.; Alseth, I.; Bjoras, M.; Dalhus, B.
Structural basis of DNA loop recognition by endonuclease V
Structure
21
257-265
2013
Thermotoga maritima (Q9X2H9)
Ahmadi, A.; Rosnes, I.; Blicher, P.; Diekmann, R.; Schuettpelz, M.; Glette, K.; Torresen, J.; Bjoras, M.; Dalhus, B.; Rowe, A.D.
Breaking the speed limit with multimode fast scanning of DNA by endonuclease V
Nat. Commun.
9
5381
2018
Thermotoga maritima (Q9X2H9), Thermotoga maritima ATCC 43589 (Q9X2H9)
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