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IUBMB Comments Prefers CC sites in double-stranded circular and linear DNA. Greater affinity for double-stranded than single-stranded DNA. Produces nicks, generating double-stranded fragments with 5′- and/or 3′-protruding single-stranded tails. Requires magnesium ions for activity. The endonuclease from Chlorella -like green algae infected with NYs-1 virus 4 may be the same enzyme.
Reaction Schemes
Endonucleolytic cleavage to give 5'-phosphooligonucleotide end-products, with a preference for cleavage within the sequence CC
Synonyms
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DNA-adenine-transferase
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EC 3.1.4.30
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related
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endodeoxyribonuclease
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Escherichia coli endonuclease II
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Nuclease, endodeoxyribo-
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Redoxyendonuclease
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Streptomyces glaucescens exocytoplasmic dodeoxyribonuclease
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VirD1/D2 endonuclease
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Deoxyriboendonuclease
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Deoxyriboendonuclease
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Endonucleolytic cleavage to give 5'-phosphooligonucleotide end-products, with a preference for cleavage within the sequence CC
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hydrolysis of phosphoric ester
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37211-67-9
not distinguished from EC 3.1.21.2
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28S rDNA + H2O
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Substrates: R1Bm EN cleaves both strands of the 28S rDNA sequence at the target site, 5'-A(G/C)(A/T)!(A/G)T-3' is the consensus sequence, thus cleavage site
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covalently closed circular DNA pUC18 + H2O
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Substrates: -
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Lambda DNA
Double-stranded fragments between 7 and 24 bases with 5' and/or 3'-protruding single-stranded tails
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Substrates: -
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lambda DNA + H2O
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Substrates: -
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pBR322 DNA + H2O
DNA fragments carrying phosphate groups at 5' ends and hydroxyl group at the 3' ends, respectively
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Substrates: -
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additional information
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double-stranded DNA
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Substrates: preferably binds to the dinucleotide 5'-CC-3' and nicks DNA between both cytosines
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double-stranded DNA
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Virus NYs-1
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Substrates: the enzyme recognizes the sequence 5'-CC-3' and cleaves 5' to the first C. It cleaves 5'-CIIIC-3' sequences but not 5'-IIICC-3' sequences. The enzyme creates breaks in dsDNA whenever two 5-CC-3' sequences on opposite strands are close enough for the two strands to separate. When the 5'-CC-3' sequence on opposite strands are further apart only a portion of the strands separate
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additional information
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Substrates: catalyzes the endonucleolytic cleavage of both the double- as well as the single-strand DNA non-specifically
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additional information
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Virus NYs-1
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Substrates: the enzyme does not cleave ssDNA and definitely does not cleave ssRNA or dsRNA
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Mn2+
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can replace Mg2+ showing better activity
Mg2+
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required for activity, maximum activity at 2.5 mM
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EDTA
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chelates Mg2+, increasing Mg2+ concentrations can restore the activity of the enzyme
additional information
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not inhibited by Na+
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additional information
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cytosine methylation does not inhibit
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Infections
Nuclear disruption after infection of Escherichia coli with a bacteriophage T4 mutant unable to induce endonuclease II.
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9444
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521fold purified enzyme
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mc26 culture
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Virus NYs-1
dsDNA-containing virus
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additional information
Virus NYs-1
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Chlorella sp. strain NC64A cell infected with the dsDNA-containing virus NYs-1
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Highest Expressing Human Cell Lines
Filter by:
Cell Line Links
Gene Links
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by hanging drop vapor diffusion method, to 2.0 A resolution, belongs to space group P321 with unit cell parameters a = b = 141.3 A, c = 37.5 A, alpha = beta = 90°, gamma = 120°, has a beta-hairpin region (residues 176-183) at the edge of the DNA binding surface
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D19A
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relative activity of bottom-strand cleavage is less than half that of top-strand cleavage, whereas activity of top-strand cleavage is more than 80% that of the wild-type
E147A
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does not exhibit a significant reduction in nicking activity, compared with that of the wild-type
E18A
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relative activity of bottom-strand cleavage is less than half that of top-strand cleavage, whereas activity of top-strand cleavage is more than 80% that of the wild-type
H130A
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moderately decreased nicking activity
H140A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
H209A
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exhibits no detectable cleavage activity on the top or bottom strand of the oligonucleotide substrate
H54A
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relative activity of bottom-strand cleavage is less than half that of top-strand cleavage, whereas activity of top-strand cleavage is more than 80% that of the wild-type
H78A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
K56A
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moderately decreased nicking activity
N180A
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altered cleavage patterns, shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
Q97A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
R139A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
R144A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
S206A
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relative activity of bottom-strand cleavage is less than half that of top-strand cleavage, whereas activity of top-strand cleavage is more than 80% that of the wild-type
S43A
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does not exhibit a significant reduction in nicking activity, compared with that of the wild-type
S99A
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does not exhibit a significant reduction in nicking activity, compared with that of the wild-type
T178A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
Y42A
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shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
Y98A
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altered cleavage patterns, shows less than 20% of the wild-type activity for the cleavage of both strands, amounts of cleavage products are less than 1% of the total substrates
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0°C, Tris-HCl buffer, pH 7.4, 10 mM EDTA, 10% glycerol, stable for at least 15 days
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by nickel chelation chromatography and by gel filtration
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to near homogeneity, 521fold by gel filtration
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plasmid pR1EN and its mutant derivatives were transformed into Escherichia coli BL21(DE3)/pLysS strain
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additional information
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important role of residues Y98 and N180 for the sequence recognition of R1Bm EN
additional information
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deoxyribonuclease is an endonuclease, but is not a restriction endonuclease
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Aparicio, J.F.; Freije, J.M.P.; Lopez-Otin, C.; Cal, S.; Sanchez, J.
A Streptomyces glaucens endodeoxyribonuclease which shows a strong preference for CC dinucleotide
Eur. J. Biochem.
205
695-699
1992
Streptomyces glaucescens
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Xia, Y.; Morgan, R.; Schildkraut, I.; van Etten, J.L.
A site-specific single strand endonuclease activity induced by NYs-1 virus infection of a Chlorella-like green alga
Nucleic Acids Res.
16
9477-9487
1988
Virus NYs-1
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Mandal, P.; Chakraborty, P.; Sau, S.; Mandal, N.C.
Purification and characterization of a deoxyriboendonuclease from Mycobacterium smegmatis
J. Biochem. Mol. Biol.
39
140-144
2006
Mycolicibacterium smegmatis
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Maita, N.; Aoyagi, H.; Osanai, M.; Shirakawa, M.; Fujiwara, H.
Characterization of the sequence specificity of the R1Bm endonuclease domain by structural and biochemical studies
Nucleic Acids Res.
35
3918-3927
2007
Bombyx mori
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