Continued from EC 3.1.5 to 3.1.16
EC 3.1.21 Endodeoxyribonucleases Producing 5'-Phosphomonoesters
EC 3.1.22 Endodeoxyribonucleases Producing 3'-Phosphomonoesters
EC 3.1.25 Site-Specific Endodeoxyribonucleases Specific for Altered Bases
EC 3.1.26 Endoribonucleases Producing 5'-Phosphomonoesters
EC 3.1.27 Endoribonucleases Producing 3'-Phosphomonoesters
EC 3.1.30 Endoribonucleases Active with either Ribo- or Deoxyribonucleic Acids and Producing 5'-Phosphomonoesters
EC 3.1.31 Endoribonucleases Active with either Ribo- or Deoxyribonucleic Acids and Producing 3'-Phosphomonoesters
EC 3.1.21.8 T4 deoxyribonuclease II
EC 3.1.21.9 T4 deoxyribonuclease IV
EC 3.1.21.10 crossover junction endodeoxyribonuclease
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. Formerly EC 3.1.4.5.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9003-98-9
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.
2. Kunitz, M. Isolation of crystalline deoxyribonuclease from beef pancreas. Science 108 (1948) 19-20.
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.
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number: 63363-78-0
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]
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 [DNA (cytosine-5-)-methyltransferase], with similar site specificity. A complete listing of all of these enzymes has been produced by R.J. Roberts and is available at http://rebase.neb.com/rebase/rebase.html
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37263-09-5
References:
1. Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331-2365. [PMID: 2159140]
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 (type III site-specific deoxyribonuclease), were previously listed separately in sub-subclasses 3.1.23 and 3.1.24. They require only Mg2+. They recognize specific short DNA sequences and cleave either within, or at a short specific distance from, the recognition site. A complete listing of all of these enzymes has been produced by R.J. Roberts and is available at http://rebase.neb.com/rebase/rebase.html.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9075-08-5 (not distinguished from EC 3.1.21.5)
References:
1. Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331-2365. [PMID: 2159140]
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 [site-specific DNA-methyltransferase (cytosine-specific)]. A complete listing of all of these enzymes has been produced by R.J. Roberts and is available at http://rebase.neb.com/rebase/rebase.html
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9075-08-5 (not distinguished from EC 3.1.21.4)
References:
1. Roberts, R.J. Restriction enzymes and their isoschizomers. Nucleic Acids Res. 18 (1990) 2331-2365. [PMID: 2159140]
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.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 37211-67-9
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]
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.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 61970-03-4
References:
1. Gates, F.T. and Linn, S. Endonuclease V of Escherichia coli. J. Biol. Chem. 252 (1977) 1647-1653. [PMID: 14159]
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, PDB, CAS registry number:
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]
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
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]
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.
Links to other databases: BRENDA, EXPASY, KEGG, MetaCyc, CAS registry number:
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]
Accepted name: deoxyribonuclease II
Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
Other name(s): DNase II; pancreatic DNase II; deoxyribonucleate 3'-nucleotidohydrolase; DNase II; pancreatic DNase II; acid deoxyribonuclease; acid DNase
Comments: Preference for double-stranded DNA. Formerly EC 3.1.4.6.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9025-64-3
References:
1. Bernardi, G. Spleen acid deoxyribonuclease, in Cantoni, G.L. and Davies, D.R. (Eds.), Procedures in Nucleic Acid Research, Harper and Row, New York, 1966, pp. 102-121.
Accepted name: Aspergillus deoxyribonuclease K1
Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
Other name(s): Aspergillus DNase K1
Comments: Preference for single-stranded DNA.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 264922-12-5
References:
1. Kato, M. and Ikeda, Y. On the deoxyribonucleases, K1 and K2, isolated from mycelia of Aspergillus oryzae. I. Isolation and purification of DNases K1 and K2. J. Biochem. (Tokyo) 64 (1968) 321-328. [PMID: 4303413]
2. Shishido, K., Kato, M. and Ikeda, Y. Isolation of thymidylic acid-rich fragments from double-stranded deoxyribonucleic acids. J. Biochem. (Tokyo) 65 (1968) 479-481.
[EC 3.1.22.3 Transferred entry: now EC 3.1.21.7, deoxyribonuclease V (EC 3.1.22.3 created 1978, deleted 2001)]
Transferred entry: crossover junction endodeoxyribonuclease. Now EC 3.1.21.10, crossover junction endodeoxyribonuclease
Accepted name: deoxyribonuclease X
Reaction: Endonucleolytic cleavage of supercoiled plasma DNA to linear DNA duplexes
Other name(s): Escherichia coli endodeoxyribonuclease; Escherichia coli endodeoxyribonuclease X
Comments: Preference for supercoiled DNA; little activity on linear double-stranded DNA. Inhibited by single-stranded DNA, ATP and AMP.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 97002-82-9
References:
1. Ghosh, S. and DasGupta, U. Studies with endonuclease X: a new deoxyendonuclease of E. coli that preferentially cleaves supercoiled plasmid DNA. Curr. Trends Life Sci. 12 (1984) 79-88.
In a previous edition, site specific endodeoxyribonucleases were set out individually here as subclasses EC 3.1.23 and EC 3.1.24, with 113 separate entries. These are now included in three entries EC 3.1.21.3, EC 3.1.21.4 and EC 3.1.21.5. A complete listing of all of these enzymes has been produced by R.J. Roberts and is available at http://rebase.neb.com/rebase/rebase.html.
Accepted name: deoxyribonuclease (pyrimidine dimer)
Reaction: Endonucleolytic cleavage near pyrimidine dimers to products with 5'-phosphate
Other name(s): endodeoxyribonuclease (pyrimidine dimer); endodeoxyribonuclease (pyrimidine dimer); bacteriophage T4 endodeoxyribonuclease V; T4 endonuclease V
Comments: Acts on a damaged strand, 5' from the damaged site.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 66143-22-4
References:
1. Braun, A.G., Radman, M. and Grossman, L. Enzymic repair of DNA: sites of hydrolysis by the Escherichia coli endonuclease specific for pyrimidine dimers (corendonuclease II) Biochemistry 15 (1976) 4116-4120.
2. Riazuddin, S. and Grossman, L. Micrococcus luteus correndonucleases. II. Mechanism of action of two endonucleases specific for DNA containing pyrimidine dimers. J. Biol. Chem. 252 (1977) 6287-6293. [PMID: 330526]
[EC 3.1.25.2 Transferred entry: now EC 4.2.99.18 DNA-(apurinic or apyrimidinic site) lyase (EC 3.1.25.2 created 1978, deleted 1992)]
Accepted name: Physarum polycephalum ribonuclease
Reaction: Endonucleolytic cleavage to 5'-phosphomonoester
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9001-99-4
References:
1. Hiramaru, M., Uchida, T. and Egami, F. Studies on two nucleases and a ribonuclease from Physarum polycephalum. Purification and mode of action. J. Biochem. (Tokyo) 65 (1969) 701-708. [PMID: 5817397]
Accepted name: ribonuclease alpha
Reaction: Endonucleolytic cleavage to 5'-phosphomonoester
Other name(s): 2'-O-methyl RNase
Comments: Specific for O-methylated RNA.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number:
References:
1. Norton, J. and Roth, J.S. A ribonuclease specific for 2'-O-methylated ribonucleic acid. J. Biol. Chem. 242 (1967) 2029-2034. [PMID: 6022850]
Accepted name: ribonuclease III
Reaction: Endonucleolytic cleavage to a 5'-phosphomonoester
Other name(s): RNase III; ribonuclease 3
Comments: This is an endoribonuclease that cleaves double-stranded RNA molecules [4]. The cleavage can be either a single-stranded nick or double-stranded break in the RNA, depending in part upon the degree of base-pairing in the region of the cleavage site [5]. Specificity is conferred by negative determinants, i.e., the presence of certain Watson-Crick base-pairs at specific positions that strongly inhibit cleavage [6]. RNase III is involved in both rRNA processing and mRNA processing and decay.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9073-62-5
References:
1. Crouch, R.J. Ribonuclease 3 does not degrade deoxyribonucleic acid-ribonucleic acid hybrids. J. Biol. Chem. 249 (1974) 1314-1316. [PMID: 4592261]
2. Rech, J., Cathala, G. and Jeanteur, P. Isolation and characterization of a ribonuclease activity specific for double-stranded RNA (RNase D) from Krebs II ascites cells. J. Biol. Chem. 255 (1980) 6700-6706. [PMID: 6248530]
3. Robertson, H.D., Webster, R.E. and Zinder, N.D. Purification and properties of ribonuclease III from Escherichia coli. J. Biol. Chem. 243 (1968) 82-91. [PMID: 4865702]
4. Grunberg-Manago, M. Messenger RNA stability and its role in control of gene expression in bacteria and phages. Annu. Rev. Genet. 33 (1999) 193-227. [PMID: 10690408]
5. Court, D. RNA processing and degradation by RNase III in control of mRNA stability. In: Belasco, J.G. and Brawerman, G. (Ed.), Control of Messenger RNA Stability, vol. , Academic Press, New York, 1993, pp. 71-116.
6. Zhang, K. and Nicholson, A.W. Regulation of ribonuclease III processing by double-helical sequence antideterminants. Proc. Natl. Acad. Sci. USA 94 (1997) 13437-13441. [PMID: 9391043]
Accepted name: ribonuclease H
Reaction: Endonucleolytic cleavage to 5'-phosphomonoester
Other name(s): endoribonuclease H (calf thymus); RNase H; RNA*DNA hybrid ribonucleotidohydrolase; hybrid ribonuclease; hybridase; hybridase (ribonuclease H); ribonuclease H; hybrid nuclease; calf thymus ribonuclease H
Comments: Acts on RNA-DNA hybrids.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9050-76-4
References:
1. Haberkern, R.C. and Cantoni, G.L. Studies on a calf thymus ribonuclease specific for ribonucleic acid-deoxyribonucleic acid hybrids. Biochemistry 12 (1973) 2389-2395. [PMID: 4709937]
2. Stavrianopoulos, J.G. and Chargaff, E. Purification and properties of ribonuclease H of calf thymus. Proc. Natl. Acad. Sci. USA 70 (1973) 1959-1963. [PMID: 4516197]
Accepted name: ribonuclease P
Reaction: Endonucleolytic cleavage of RNA, removing 5'-extranucleotides from tRNA precursor
Other name(s): RNase P
Comments: An RNA-containing enzyme, essential for tRNA processing; generates 5'-termini or mature tRNA molecules.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 71427-00-4 (not distinguished from EC 3.1.26.7)
References:
1. Bikoff, E.K. and Gefter, M.L. In vitro synthesis of transfer RNA. I. Purification of required components. J. Biol. Chem. 250 (1975) 6240-6247. [PMID: 1099089]
2. Bikoff, E.K., La Rue, B.F. and Gefter, M.L. In vitro synthesis of transfer RNA. II. Identification of required enzymatic activities. J. Biol. Chem. 250 (1975) 6248-6255. [PMID: 1099090]
3. Robertson, H.D., Altman, S. and Smith, J.D. Purification and properties of a specific Escherichia coli ribonuclease which cleaves a tyrosine transfer ribonucleic acid presursor. J. Biol. Chem. 247 (1972) 5243-5251. [PMID: 4560501]
Accepted name: ribonuclease IV
Reaction: Endonucleolytic cleavage of poly(A) to fragments terminated by 3'-hydroxy and 5'-phosphate groups
Other name(s): endoribonuclease IV; poly(A)-specific ribonuclease
Comments: Forms oligonucleotides with an average chain length of 10.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 61536-76-3
References:
1. Müller, E.G. Endoribonuclease IV. A poly(A)-specific ribonuclease from chick oviduct. 1. Purification of the enzyme. Eur. J. Biochem. 70 (1976) 241-248. [PMID: 1009928]
2. Müller, E.G., Seibert, G., Steffen, R. and Zahn, R.K. Endoribonuclease IV. 2. Further investigation on the specificity. Eur. J. Biochem. 70 (1976) 249-258. [PMID: 1009929]
Accepted name: ribonuclease P4
Reaction: Endonucleolytic cleavage of RNA, removing 3'-extranucleotides from tRNA precursor
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 71427-00-4 (not distinguished from EC 3.1.26.5)
References:
1. Sekiya, T., Contreras, R., Takeya, T. and Khorana, H.G. Total synthesis of a tyrosine suppressor transfer RNA gene. XVII. Transcription, in vitro, of the synthetic gene and processing of the primary transcript to transfer RNA. J. Biol. Chem. 254 (1979) 5802-5816. [PMID: 109442]
Accepted name: ribonuclease M5
Reaction: Endonucleolytic cleavage of RNA, removing 21 and 42 nucleotides, respectively, from the 5'- and 3'-termini of a 5S-rRNA precursor
Other name(s): RNase M5; 5S ribosomal maturation nuclease; 5S ribosomal RNA maturation endonuclease
Comments: Converts the 5S-rRNA precursor from Bacillus subtilis into 5S-rRNA, with 5'-phosphate and 3'-hydroxy groups.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 62253-00-3
References:
1. Sogin, M.L., Pace, B. and Pace, N.R. Partial purification and properties of a ribosomal RNA maturation endonuclease from Bacillus subtilis. J. Biol. Chem. 252 (1977) 1350-1357. [PMID: 402365]
Accepted name: ribonuclease [poly-(U)-specific]
Reaction: Endonucleolytic cleavage of poly(U) to fragments terminated by 3'-hydroxy and 5'-phosphate groups
Other name(s): ribonuclease (uracil-specific); uracil-specific endoribonuclease; uracil-specific RNase
Comments: Forms oligonucleotides with chain lengths of 6 to 12.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 54249-90-0 (not distinguished from EC 3.1.27.6)
References:
1. Bachmann, M., Trautmann, F., Messer, R., Zahn, R.K., Meyer zum Büschenfelde, K.H. and Müller, W.E.G. Association of a polyuridylate-specific endoribonuclease with small nuclear ribonucleo-proteins which had been isolated by affinity chromatography using antibodies from a patient with systemic lupus erythematosus. Eur. J. Biochem. 136 (1983) 447-451. [PMID: 6227485]
Accepted name: ribonuclease IX
Reaction: Endonucleolytic cleavage of poly(U) or poly(C) to fragments terminated by 3'-hydroxy and 5'-phosphate groups
Other name(s): poly(U)- and poly(C)-specific endoribonuclease
Comments: Acts on poly(U) and poly(C), with a higher affinity for poly(C), but does not act on poly(A) or poly(G).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 9001-99-4
References:
1. Sideris, D.C. and Fragoulis, E.G. Purification and characterization of a ribonuclease specific for poly(U) and poly(C) from the larvae of Ceratitis capitata. Eur. J. Biochem. 164 (1987) 309-315. [PMID: 3569265]
Accepted name: tRNase Z
Reaction: endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule
Other name(s): 3 tRNase; tRNA 3 endonuclease; RNase Z; 3' tRNase
Comments: No cofactor requirements. An homologous enzyme to that found in Arabidopsis thaliana has been found in Methanococcus janaschii.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 98148-84-6
References:
1. Schiffer, S., Rösch, S. and Marchfelder, A. Assigning a function to a conserved group of proteins: the tRNA 3'-processing enzymes. EMBO J. 21 (2002) 2769-2777. [PMID: 12032089]
2. Mayer, M., Schiffer, S. and Marchfelder, A. tRNA 3' processing in plants: nuclear and mitochondrial activities differ. Biochemistry 39 (2000) 2096-2105. [PMID: 10684660]
3. Schiffer, S., Helm, M., Theobald-Dietrich, A., Giege, R. and Marchfelder, A. The plant tRNA 3' processing enzyme has a broad substrate spectrum. Biochemistry 40 (2001) 8264-8272. [PMID: 11444972]
4. Kunzmann, A., Brennicke, A. and Marchfelder, A. 5' end maturation and RNA editing have to precede tRNA 3' processing in plant mitochondria. Proc. Natl. Acad. Sci. USA 95 (1998) 108-113. [PMID: 9419337]
5. Mörl, M. and Marchfelder, A. The final cut. The importance of tRNA 3'-processing. EMBO Rep. 2 (2001) 17-20. [PMID: 11252717]
6. Minagawa, A., Takaku, H., Takagi, M. and Nashimoto, M. A novel endonucleolytic mechanism to generate the CCA 3' termini of tRNA molecules in Thermotoga maritima. J. Biol. Chem. 279 (2004) 15688-15697.[PMID: 14749326]
7. Takaku, H., Minagawa, A., Takagi, M. and Nashimoto, M. A candidate prostate cancer susceptibility gene encodes tRNA 3' processing endoribonuclease. Nucleic Acids Res. 31 (2003) 2272-2278. [PMID: 12711671]
Accepted name: ribonuclease E
Reaction: Endonucleolytic cleavage of single-stranded RNA in A- and U-rich regions
Other name(s): endoribonuclease E; RNase E; Rne protein
Comments: RNase E is a bacterial ribonuclease that plays a role in the processing of ribosomal RNA (9S to 5S rRNA), the chemical degradation of bulk cellular RNA, the decay of specific regulatory, messenger and structural RNAs and the control of plasmid DNA replication [1]. The enzyme binds to monophosphorylated 5' ends of substrates but exhibits sequential cleavages in the 3' to 5' direction [1]. 2'-O-Methyl nucleotide substitutions at RNase E binding sites do not prevent binding but do prevent cleavage of non-modified target sequences 5' to that locus [1]. In Escherichia coli, the enzyme is found in the RNA degradosome. The C-terminal half of the protein contains binding sites for the three other major degradosomal components, the DEAD-box RNA helicase Rh1B, enolase (EC 4.1.1.11) and polynucleotide phosphorylase (EC 2.7.7.8).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 76106-82-6
References:
1. Feng, Y., Vickers, T.A. and Cohen, S.N. The catalytic domain of RNase E shows inherent 3' to 5' directionality in cleavage site selection. Proc. Natl. Acad. Sci. USA 99 (2002) 14746-14751. [PMID: 12417756]
2. Ehretsmann, C.P., Carpousis, A.J. and Krisch, H.M. Specificity of Escherichia coli endoribonuclease RNase E: in vivo and in vitro analysis of mutants in a bacteriophage T4 mRNA processing site. Genes Dev. 6 (1992) 149-159. [PMID: 1730408]
3. Cormack, R.S., Genereaux, J.L. and Mackie, G.A. RNase E activity is conferred by a single polypeptide: overexpression, purification, and properties of the ams/rne/hmp1 gene product. Proc. Natl. Acad. Sci. USA 90 (1993) 9006-9010. [PMID: 8415644]
4. Vanzo, N.F., Li, Y.S., Py, B., Blum, E., Higgins, C.F., Raynal, L.C., Krisch, H.M. and Carpousis, A.J. Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome. Genes Dev. 12 (1998) 2770-2781. [PMID: 9732274]
5. Steege, D.A. Emerging features of mRNA decay in bacteria. RNA 6 (2000) 1079-1090. [PMID: 10943888]
6. Callaghan, A.J., Grossmann, J.G., Redko, Y.U., Ilag, L.L., Moncrieffe, M.C., Symmons, M.F., Robinson, C.V., McDowall, K.J. and Luisi, B.F. Quaternary structure and catalytic activity of the Escherichia coli ribonuclease E amino-terminal catalytic domain. Biochemistry 42 (2003) 13848-13855. [PMID: 14636052]
Accepted name: retroviral ribonuclease H
Reaction: Endohydrolysis of RNA in RNA/DNA hybrids. Three different cleavage modes:
1. sequence-specific internal cleavage of RNA [1-4]. Human immunodeficiency virus type 1 and Moloney murine leukemia virus enzymes prefer to cleave the RNA strand one nucleotide away from the RNA-DNA junction [5].
2. RNA 5'-end directed cleavage 13-19 nucleotides from the RNA end [6,7].
3. DNA 3'-end directed cleavage 15-20 nucleotides away from the primer terminus [8-10].
Other name(s): RT/RNase H; retroviral reverse transcriptase RNaseH; HIV RNase H
Comments: Retroviral reverse transcriptase is a multifunctional enzyme responsible for viral replication. To perform this task the enzyme combines two distinct activities. The polymerase domain (EC 2.7.7.49, RNA-directed DNA polymerase) occupies the N-terminal two-thirds of the reverse transcriptase whereas the ribonuclease H domain comprises the C-terminal remaining one-third [13,14]. The RNase H domain of Moloney murine leukemia virus and Human immunodeficiency virus display two metal binding sites [15-17]
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number:
References:
1. Schultz, S.J., Zhang, M. and Champoux, J.J. Recognition of internal cleavage sites by retroviral RNases H. J. Mol. Biol. 344 (2004) 635-652. [PMID: 15533434]
2. Sarafianos, S.G., Das, K., Tantillo, C., Clark, A.D., Jr., Ding, J., Whitcomb, J.M., Boyer, P.L., Hughes, S.H. and Arnold, E. Crystal structure of HIV-1 reverse transcriptase in complex with a polypurine tract RNA:DNA. EMBO J. 20 (2001) 1449-1461. [PMID: 11250910]
3. Rausch, J.W., Lener, D., Miller, J.T., Julias, J.G., Hughes, S.H. and Le Grice, S.F. Altering the RNase H primer grip of human immunodeficiency virus reverse transcriptase modifies cleavage specificity. Biochemistry 41 (2002) 4856-4865. [PMID: 11939780]
4. Brehm, J.H., Mellors, J.W. and Sluis-Cremer, N. Mechanism by which a glutamine to leucine substitution at residue 509 in the ribonuclease H domain of HIV-1 reverse transcriptase confers zidovudine resistance. Biochemistry 47 (2008) 14020-14027. [PMID: 19067547]
5. Schultz, S.J., Zhang, M., Kelleher, C.D. and Champoux, J.J. Analysis of plus-strand primer selection, removal, and reutilization by retroviral reverse transcriptases. J. Biol. Chem. 275 (2000) 32299-32309. [PMID: 10913435]
6. DeStefano, J.J., Mallaber, L.M., Fay, P.J. and Bambara, R.A. Determinants of the RNase H cleavage specificity of human immunodeficiency virus reverse transcriptase. Nucleic Acids Res. 21 (1993) 4330-4338. [PMID: 7692401]
7. Kati, W.M., Johnson, K.A., Jerva, L.F. and Anderson, K.S. Mechanism and fidelity of HIV reverse transcriptase. J. Biol. Chem. 267 (1992) 25988-25997. [PMID: 1281479]
8. Palaniappan, C., Fuentes, G.M., Rodriguez-Rodriguez, L., Fay, P.J. and Bambara, R.A. Helix structure and ends of RNA/DNA hybrids direct the cleavage specificity of HIV-1 reverse transcriptase RNase H. J. Biol. Chem. 271 (1996) 2063-2070. [PMID: 8567660]
9. Fu, T.B. and Taylor, J. When retroviral reverse transcriptases reach the end of their RNA templates. J. Virol. 66 (1992) 4271-4278. [PMID: 1376369]
10. Beilhartz, G.L., Wendeler, M., Baichoo, N., Rausch, J., Le Grice, S. and Gotte, M. HIV-1 reverse transcriptase can simultaneously engage its DNA/RNA substrate at both DNA polymerase and RNase H active sites: implications for RNase H inhibition. J. Mol. Biol. 388 (2009) 462-474. [PMID: 19289131]
11. Huang, H., Chopra, R., Verdine, G.L. and Harrison, S.C. Structure of a covalently trapped catalytic complex of HIV-1 reverse transcriptase: implications for drug resistance. Science 282 (1998) 1669-1675. [PMID: 9831551]
12. Krug, M.S. and Berger, S.L. Ribonuclease H activities associated with viral reverse transcriptases are endonucleases. Proc. Natl. Acad. Sci. USA 86 (1989) 3539-3543. [PMID: 2471188]
13. Champoux, J.J. and Schultz, S.J. Ribonuclease H: properties, substrate specificity and roles in retroviral reverse transcription. FEBS J. 276 (2009) 1506-1516. [PMID: 19228195]
14. Schultz, S.J. and Champoux, J.J. RNase H activity: structure, specificity, and function in reverse transcription. Virus Res 134 (2008) 86-103. [PMID: 18261820]
15. Goedken, E.R. and Marqusee, S. Metal binding and activation of the ribonuclease H domain from moloney murine leukemia virus. Protein Eng. 12 (1999) 975-980. [PMID: 10585503]
16. Davies, J.F., 2nd, Hostomska, Z., Hostomsky, Z., Jordan, S.R. and Matthews, D.A. Crystal structure of the ribonuclease H domain of HIV-1 reverse transcriptase. Science 252 (1991) 88-95. [PMID: 1707186]
17. Pari, K., Mueller, G.A., DeRose, E.F., Kirby, T.W. and London, R.E. Solution structure of the RNase H domain of the HIV-1 reverse transcriptase in the presence of magnesium. Biochemistry 42 (2003) 639-650. [PMID: 12534276]
[EC 3.1.27.2 Transferred entry: Bacillus subtilis ribonuclease. Now EC 4.6.1.22, Bacillus subtilis ribonuclease, since the reaction catalysed is that of a lyase(EC 3.1.27.2 created 1978, deleted 2018)]
[EC 3.1.27.3 Transferred entry: ribonuclease T1. Now EC 4.6.1.24, ribonuclease T1, since the primary reaction is that of a lyase (EC 3.1.27.3 created 1961 as EC 3.1.4.8, transferred 1965 to EC 2.7.7.26, reinstated 1972 as EC 3.1.4.8, transferred 1978 to EC 3.1.27.3, deleted 2020)]
[EC 3.1.27.4 Transferred entry: ribonuclease U2. Now EC 4.6.1.20, ribonuclease U2, since the primary reaction is that of a lyase(EC 3.1.27.4 created 1978, modified 1981, deleted 2018)]
[EC 3.1.27.5 Transferred entry: pancreatic ribonuclease. Now EC 4.6.1.18, pancreatic ribonuclease. This reaction is now known to involve an internal-transfer (lyase) process to produce the cyclic derivative, followed by a reversal of that step with water in the "hydrolytic step"[EC 3.1.27.5 created 1972 as EC 3.1.4.22, transferred 1978 to EC 3.1.27.5, modified 1981, deleted 2018]]
[EC 3.1.27.6 Transferred entry: Enterobacter ribonuclease. Now EC 4.6.1.21, Enterobacter ribonuclease, since the primary reaction is that of a lyase(EC 3.1.27.6 created 1978, modified 1981, deleted 2018)]
Accepted name: ribonuclease F
Reaction: Endonucleolytic cleavage of RNA precursor into two, leaving 5'-hydroxy and 3'-phosphate groups
Other name(s): ribonuclease F (E. coli)
Comments: Cleavage takes place between a cytosine and an adenine moiety.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 80498-18-6
References:
1. Gurevitz, M., Watson, N. and Apirion, D. A cleavage site of ribonuclease F. A putative processing endoribonuclease from Escherichia coli. Eur. J. Biochem. 124 (1982) 553-559. [PMID: 6179777]
2. Watson, N. and Apirion, D. Ribonuclease F, a putative processing endoribonuclease from Escherichia coli. Biochem. Biophys. Res. Commun. 103 (1981) 543-551. [PMID: 6277308]
Accepted name: ribonuclease V
Reaction: Hydrolysis of poly(A), forming oligoribonucleotides and ultimately 3'-AMP
Other name(s): endoribonuclease V
Comments: Also hydrolyses poly(U).
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, CAS registry number: 74505-36-5
References:
1. Schröder, H.C., Dose, K., Zahn, R.K. and Müller, E.G. Isolation and characterization of the novel polyadenylate- and polyuridylate-degrading acid endoribonuclease V from calf thymus. J. Biol. Chem. 255 (1980) 5108-5112. [PMID: 6246098]
[EC 3.1.27.9 Transferred entry: tRNA-intron endonuclease. Now EC 4.6.1.16, tRNA-intron lyase (EC 3.1.27.9 created 1992, deleted 2013)]
[EC 3.1.27.10 Transferred entry: rRNA endonuclease. Now EC 4.6.1.23, ribotoxin, since the primary reaction is that of a lyase.(EC 3.1.27.10 created 1992, deleted 2019)]
Accepted name: Aspergillus nuclease S1
Reaction: Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Other name(s): endonuclease S1 (Aspergillus); single-stranded-nucleate endonuclease; deoxyribonuclease S1; deoxyribonuclease S1; nuclease S1; Neurospora crassa single-strand specific endonuclease; S1 nuclease; single-strand endodeoxyribonuclease; single-stranded DNA specific endonuclease; single-strand-specific endodeoxyribonuclease; single strand-specific DNase; Aspergillus oryzae S1 nuclease
Comments: Formerly EC 3.1.4.21.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 37288-25-8
References:
1. Ando, T. A nuclease specific for heat-denatured DNA isolated from a product of Aspergillus oryzae. Biochim. Biophys. Acta 114 (1966) 158-168. [PMID: 4287053]
2. Sutton, W.D. A crude nuclease preparation suitable for use in DNA reassociation experiments. Biochim. Biophys. Acta 240 (1971) 522-531. [PMID: 5123563]
3. Vogt, V.M. Purification and further properties of single-strand-specific nuclease from Aspergillus oryzae. Eur. J. Biochem. 33 (1973) 192-200. [PMID: 4691350]
Accepted name: Serratia marcescens nuclease
Reaction: Endonucleolytic cleavage to 5'-phosphomononucleotide and 5'-phosphooligonucleotide end-products
Other name(s): endonuclease (Serratia marcescens); barley nuclease; plant nuclease I; nucleate endonuclease
Comments: Hydrolyses double- or single-stranded substrate. Formerly EC 3.1.4.9.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9025-65-4
References:
1. Mikulski, A.J. and Laskowski, M., Sr. Mung bean nuclease I. 3. Purification procedure and (3') omega monophosphatase activity. J. Biol. Chem. 245 (1970) 5026-5031. [PMID: 4319109]
2. Stevens, A. and Hilmoe, R.J. Studies on a nuclease from Azotobacter agilis. I. Isolation and mode of action. J. Biol. Chem. 235 (1960) 3016-3022.
3. Stevens, A. and Hilmoe, R.J. Studies on a nuclease from Azotobacter agilis. II. Hydrolysis of ribonucleic and deoxyribonucleic acids. J. Biol. Chem. 235 (1960) 3023-3027.
4. Wechter, W.J., Mikulski, A.J. and Laskowski, M., Sr. Gradation of specificity with regard to sugar among nucleases. Biochem. Biophys. Res. Commun. 30 (1968) 318-322. [PMID: 4296679]
Accepted name: micrococcal nuclease
Reaction: Endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotide end-products
Other name(s): spleen endonuclease; thermonuclease; nuclease T; micrococcal endonuclease; nuclease T'; staphylococcal nuclease; spleen phosphodiesterase; Staphylococcus aureus nuclease; Staphylococcus aureus nuclease B; ribonucleate (deoxynucleate) 3'-nucleotidohydrolase
Comments: Hydrolyses double- or single-stranded substrate. Formerly EC 3.1.4.7. cf. EC 3.1.16.1 spleen exonuclease.
Links to other databases: BRENDA, EXPASY, KEGG, Metacyc, PDB, CAS registry number: 9013-53-0
References:
1. Alexander, M., Heppel, L.A. and Hurwitz, J. The purification and properties of micrococcal nuclease. J. Biol. Chem. 236 (1961) 3014-3019.
2. Anfinsen, C.B., Cuatrecasas, P. and Taniuchi, H. Staphylococcal nuclease, chemical properties and catalysis, in Boyer, P.D. (Ed.), The Enzymes, 3rd edn., vol. 4, Academic Press, New York, 1971, pp. 177-204.
3. Reddi, K.K. Micrococcal nuclease. Methods Enzymol. 12A (1967) 257-262.
4. Sulkowski, E. and Laskowski, M., Sr. Phosphatase-free crystalline micrococcal nuclease. J. Biol. Chem. 241 (1966) 4386-4388. [PMID: 5922962]