EC 3.1.21.1     
Accepted name: deoxyribonuclease I
Reaction: Endonucleolytic cleavage to 5′-phosphodinucleotide and 5′-phosphooligonucleotide end-products
Other name(s): pancreatic DNase; DNase; thymonuclease, dornase; dornava; dornavac; pancreatic deoxyribonuclease; pancreatic dornase; deoxyribonuclease (pancreatic); pancreatic DNase; DNAase; deoxyribonucleic phosphatase; DNase I; alkaline deoxyribonuclease; alkaline DNase; endodeoxyribonuclease I; DNA depolymerase; Escherichia coli endonuclease I; deoxyribonuclease A; DNA endonuclease; DNA nuclease
Comments: Preference for double-stranded DNA.
References:
1.  Privat de Garilhe, M. and Laskowski, M. Study of the enzymatic degradation of deoxyribonucleic acid by two different deoxyribonucleodepolymerases. J. Biol. Chem. 215 (1955) 269–276. [PMID: 14392161]
2.  Kunitz, M. Isolation of crystalline deoxyribonuclease from beef pancreas. Science 108 (1948) 19–20. [PMID: 17809290]
3.  Laskowski, M. , Sr. Venom exonuclease. In: Boyer, P.D. (Ed.), The Enzymes, 3rd edn, vol. 4, Academic Press, New York, 1971, pp. 313–328.
[EC 3.1.21.1 created 1961 as EC 3.1.4.5, transferred 1978 to EC 3.1.21.1, modified 1981]
 
 
EC 3.1.21.2     
Accepted name: deoxyribonuclease IV
Reaction: Endonucleolytic cleavage of ssDNA at apurinic/apyrimidinic sites to 5′-phosphooligonucleotide end-products
Other name(s): deoxyribonuclease IV (phage-T4-induced) (misleading); endodeoxyribonuclease IV (phage T4-induced) (misleading); E. coli endonuclease IV; endodeoxyribonuclease (misleading); redoxyendonuclease; deoxriboendonuclease (misleading); endonuclease II; endonuclease IV; DNA-adenine-transferase; nfo (gene name)
Comments: The enzyme is an apurinic/apyrimidinic (AP) site endonuclease that primes DNA repair synthesis at AP sites. It specifically cleaves the DNA backbone at AP sites and also removes 3′ DNA-blocking groups such as 3′ phosphates, 3′ phosphoglycolates, and 3′ α,β-unsaturated aldehydes that arise from oxidative base damage and the activity of combined glycosylase/lyase enzymes. It is also the only known repair enzyme that is able to cleave the DNA backbone 5′ of the oxidative lesion α-deoxyadenosine. The enzyme has a strong preference for single-stranded DNA.
References:
1.  Friedberg, E.C. and Goldthwait, D.A. Endonuclease II of E. coli. I. Isolation and purification. Proc. Natl. Acad. Sci. USA 62 (1969) 934–940. [PMID: 4895219]
2.  Friedberg, E.C., Hadi, S.-M. and Goldthwait, D.A. Endonuclease II of Escherichia coli. II. Enzyme properties and studies on the degradation of alkylated and native deoxyribonucleic acid. J. Biol. Chem. 244 (1969) 5879–5889. [PMID: 4981786]
3.  Hadi, S.M. and Goldthwait, D.A. Endonuclease II of Escherichia coli. Degradation of partially depurinated deoxyribonucleic acid. Biochemistry 10 (1971) 4986–4993. [PMID: 4944066]
4.  Cunningham, R.P., Saporito, S.M., Spitzer, S.G. and Weiss, B. Endonuclease IV (nfo) mutant of Escherichia coli. J. Bacteriol. 168 (1986) 1120–1127. [PMID: 2430946]
5.  Ide, H., Tedzuka, K., Shimzu, H., Kimura, Y., Purmal, A.A., Wallace, S.S. and Kow, Y.W. Alpha-deoxyadenosine, a major anoxic radiolysis product of adenine in DNA, is a substrate for Escherichia coli endonuclease IV. Biochemistry 33 (1994) 7842–7847. [PMID: 7516707]
6.  Hosfield, D.J., Guan, Y., Haas, B.J., Cunningham, R.P. and Tainer, J.A. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell 98 (1999) 397–408. [PMID: 10458614]
[EC 3.1.21.2 created 1972 as EC 3.1.4.30, transferred 1978 to EC 3.1.21.2, modified 2014]
 
 
EC 3.1.21.3     
Accepted name: type I site-specific deoxyribonuclease
Reaction: Endonucleolytic cleavage of DNA to give random double-stranded fragments with terminal 5′-phosphates; ATP is simultaneously hydrolysed
Other name(s): type I restriction enzyme; deoxyribonuclease (ATP- and S-adenosyl-L-methionine-dependent); restriction-modification system; deoxyribonuclease (adenosine triphosphate-hydrolyzing); adenosine triphosphate-dependent deoxyribonuclease; ATP-dependent DNase; type 1 site-specific deoxyribonuclease
Comments: This is a large group of enzymes which, together with those now listed as EC 3.1.21.4 (type II site-specific deoxyribonuclease) and EC 3.1.21.5 (type III site-specific deoxyribonuclease), were previously listed separately in sub-subclasses EC 3.1.23 and EC 3.1.24. They have an absolute requirement for ATP (or dATP) and S-adenosyl-L-methionine. They recognize specific short DNA sequences and cleave at sites remote from the recognition sequence. They are multifunctional proteins that also catalyse the reactions of EC 2.1.1.72 [site-specific DNA-methyltransferase (adenine-specific)] and EC 2.1.1.37
References:
1.  Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331–2365. [PMID: 2159140]
[EC 3.1.21.3 created 1984 from EC 3.1.23 and EC 3.1.24]
 
 
EC 3.1.21.4     
Accepted name: type II site-specific deoxyribonuclease
Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5′-phosphates
Other name(s): type II restriction enzyme
Comments: This is a large group of enzymes which, together with those now listed as EC 3.1.21.3 (type 1 site-specific deoxyribonuclease) and EC 3.1.21.5.
References:
1.  Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331–2365. [PMID: 2159140]
[EC 3.1.21.4 created 1984 from EC 3.1.23 and EC 3.1.24]
 
 
EC 3.1.21.5     
Accepted name: type III site-specific deoxyribonuclease
Reaction: Endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5′-phosphates
Other name(s): type III restriction enzyme; restriction-modification system
Comments: This is a large group of enzymes which, together with those now listed as EC 3.1.21.3 (type 1 site-specific deoxyribonuclease) and EC 3.1.21.4 (type II site-specific deoxyribonuclease), were previously listed separately in sub-subclasses EC 3.1.23 and EC 3.1.24. They have an absolute requirement for ATP but do not hydrolyse it; S-adenosy-L-methionine stimulates the reaction, but is not absolutely required. They recognize specific, short DNA sequences and cleave a short distance away from the recognition sequence. These enzymes exist as complexes with enzymes of similar specificity listed under EC 2.1.1.72 [site-specific DNA-methyltransferase (adenine-specific)] or EC 2.1.1.73
References:
1.  Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331–2365. [PMID: 2159140]
[EC 3.1.21.5 created 1984 from EC 3.1.23 and EC 3.1.24]
 
 
EC 3.1.21.6     
Accepted name: CC-preferring endodeoxyribonuclease
Reaction: endonucleolytic cleavage to give 5′-phosphooligonucleotide end-products, with a preference for cleavage within the sequence CC
Other name(s): Streptomyces glaucescens exocytoplasmic dodeoxyribonuclease
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[1] may be the same enzyme.
References:
1.  Xia, Y.N., 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 (1988) 9477–9487. [PMID: 3186439]
2.  Aparicio, J.F., Lopez-Otin, C., Cal, S., Sanchez, J. A Streptomyces glaucescens endodeoxyribonuclease which shows a strong preference for CC dinucleotide. Eur. J. Biochem. 205 (1992) 695–699. [PMID: 1533367]
[EC 3.1.21.6 created 1999]
 
 
EC 3.1.21.7     
Accepted name: deoxyribonuclease V
Reaction: Endonucleolytic cleavage at apurinic or apyrimidinic sites to products with a 5′-phosphate
Other name(s): endodeoxyribonuclease V; DNase V; Escherichia coli endodeoxyribonuclease V
Comments: Previously classified erroneously as EC 3.1.22.3.
References:
1.  Gates, F.T. and Linn, S. Endonuclease V of Escherichia coli. J. Biol. Chem. 252 (1977) 1647–1653. [PMID: 14159]
[EC 3.1.21.7 created 1978 as EC 3.1.22.3, transferred 2001 to EC 3.1.21.7]
 
 
EC 3.1.21.8     
Accepted name: T4 deoxyribonuclease II
Reaction: Endonucleolytic nicking and cleavage of cytosine-containing double-stranded DNA.
Other name(s): T4 endonuclease II; EndoII (ambiguous); denA (gene name)
Comments: Requires Mg2+. This phage T4 enzyme is involved in degradation of host DNA. The enzyme primarily catalyses nicking of the bottom strand of double stranded DNA between the first and second base pair to the right of a top-strand CCGC motif. Double-stranded breaks are produced 5- to 10-fold less frequently [3]. It does not cleave the T4 native DNA, which contains 5-hydroxymethylcytosine instead of cytosine.
References:
1.  Carlson, K., Krabbe, M., Nystrom, A.C. and Kosturko, L.D. DNA determinants of restriction. Bacteriophage T4 endonuclease II-dependent cleavage of plasmid DNA in vivo. J. Biol. Chem. 268 (1993) 8908–8918. [PMID: 8386173]
2.  Carlson, K. and Kosturko, L.D. Endonuclease II of coliphage T4: a recombinase disguised as a restriction endonuclease. Mol. Microbiol. 27 (1998) 671–676. [PMID: 9515694]
3.  Carlson, K., Kosturko, L.D. and Nystrom, A.C. Sequence-specific cleavage by bacteriophage T4 endonuclease II in vitro. Mol. Microbiol. 31 (1999) 1395–1405. [PMID: 10200960]
4.  Andersson, C.E., Lagerback, P. and Carlson, K. Structure of bacteriophage T4 endonuclease II mutant E118A, a tetrameric GIY-YIG enzyme. J. Mol. Biol. 397 (2010) 1003–1016. [PMID: 20156453]
[EC 3.1.21.8 created 2014]
 
 
EC 3.1.21.9     
Accepted name: T4 deoxyribonuclease IV
Reaction: Endonucleolytic cleavage of the 5′ phosphodiester bond of deoxycytidine in single-stranded DNA.
Other name(s): T4 endonuclease IV; EndoIV (ambiguous); denB (gene name)
Comments: This phage T4 enzyme is involved in degradation of host DNA. The enzyme does not cleave double-stranded DNA or native T4 DNA, which contains 5-hydroxymethylcytosine instead of cytosine.
References:
1.  Sadowski, P.D. and Hurwitz, J. Enzymatic breakage of deoxyribonucleic acid. II. Purification and properties of endonuclease IV from T4 phage-infected Escherichia coli. J. Biol. Chem. 244 (1969) 6192–6198. [PMID: 4900512]
2.  Ling, V. Partial digestion of 32P-fd DNA with T4 endonuclease IV. FEBS Lett. 19 (1971) 50–54. [PMID: 11946172]
3.  Sadowski, P.D. and Bakyta, I. T4 endonuclease IV. Improved purification procedure and resolution from T4 endonuclease 3. J. Biol. Chem. 247 (1972) 405–412. [PMID: 4550601]
4.  Bernardi, A., Maat, J., de Waard, A. and Bernardi, G. Preparation and specificity of endonuclease IV induced by bacteriophage T4. Eur. J. Biochem. 66 (1976) 175–179. [PMID: 782881]
5.  Hirano, N., Ohshima, H. and Takahashi, H. Biochemical analysis of the substrate specificity and sequence preference of endonuclease IV from bacteriophage T4, a dC-specific endonuclease implicated in restriction of dC-substituted T4 DNA synthesis. Nucleic Acids Res. 34 (2006) 4743–4751. [PMID: 16971463]
6.  Ohshima, H., Hirano, N. and Takahashi, H. A hexanucleotide sequence (dC1-dC6 tract) restricts the dC-specific cleavage of single-stranded DNA by endonuclease IV of bacteriophage T4. Nucleic Acids Res. 35 (2007) 6681–6689. [PMID: 17940096]
[EC 3.1.21.9 created 2014]
 
 
EC 3.1.21.10     
Accepted name: crossover junction endodeoxyribonuclease
Reaction: Endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction)
Other name(s): Hje endonuclease; Holliday junction endonuclease CCE1; Holliday junction resolvase; Holliday junction-cleaving endonuclease; Holliday junction-resolving endoribonuclease; RusA Holliday junction resolvase; RusA endonuclease; RuvC endonuclease; SpCCe1 Holliday junction resolvase; crossover junction endoribonuclease; cruciform-cutting endonuclease; endo X3; endonuclease RuvC; endonuclease VII; endonuclease X3; resolving enzyme CCE1
Comments: The enzyme from Saccharomyces cerevisiae has no endonuclease or exonuclease activity on single-stranded or double-stranded DNA molecules that do not contain Holliday junctions.
References:
1.  Symington, L.S. and Kolodner, R. Partial purification of an enzyme from Saccharomyces cerevisiae that cleaves Holliday junctions. Proc. Natl. Acad. Sci. USA 82 (1985) 7247–7251. [PMID: 3903750]
2.  Shida, T., Iwasaki, H., Saito, A., Kyogoku, Y. and Shinagawa, H. Analysis of substrate specificity of the RuvC holliday junction resolvase with synthetic Holliday junctions. J. Biol. Chem. 271 (1996) 26105–26109. [PMID: 8824253]
3.  Shah, R., Cosstick, R. and West, S.C. The RuvC protein dimer resolves Holliday junctions by a dual incision mechanism that involves base-specific contacts. EMBO J. 16 (1997) 1464–1472. [PMID: 9135161]
4.  Fogg, J.M., Schofield, M.J., White, M.F. and Lilley, D.M. Sequence and functional-group specificity for cleavage of DNA junctions by RuvC of Escherichia coli. Biochemistry 38 (1999) 11349–11358. [PMID: 10471285]
5.  Lilley, D.M. and White, M.F. The junction-resolving enzymes. Nat. Rev. Mol. Cell. Biol. 2 (2001) 433–443. [PMID: 11389467]
6.  Middleton, C.L., Parker, J.L., Richard, D.J., White, M.F. and Bond, C.S. Crystallization and preliminary X-ray diffraction studies of Hje, a Holliday junction resolving enzyme from Sulfolobus solfataricus. Acta Crystallogr. D Biol. Crystallogr. 59 (2003) 171–173. [PMID: 12499561]
[EC 3.1.21.10 created 1989 as EC 3.1.22.4, modified 2003, transferred 2021 to EC 3.1.21.10]
 
 


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