Endonuclease

Template:STRUCTURE 1rva Endonuclease (ENN) cleaves phosphodiester bond within polynucleotide chain. ENN cleaves DNA at a restriction site which is usually a 6-nucleotide palindrome. ENN is restriction site–specific. Various types of ENN differ by their mechanism of action. ENN is used in genetic engineering to make recombinant DNA. ENN requires a restriction site and a cleavage pattern. ENN-I operates on DNA with separate restriction site and cleavage pattern, while ENN-II operates on overlapping restriction site and cleavage pattern. The Cas1-Cas2 ENN are involved in the CRISPR immune system which provides immunity against mobile genetic elements like viruses. Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN.
The Cas ENN proteins are part of CRISPR/Cas prokaryotic immune system which confers protection from foreign genetic elements. The CRISPR (Custered Regularly Interspersed Short Palindromic Repeats) are DNA loci which are found in ca. 40% of the bacteria. The CRISPR/Cas system is being used lately as gene editing tool. For more details see Cas9.
See also

• Apurinic-Apyrimidinic Endonuclease-1
  
• DNA repair protein human endonuclease VIII-like 1 (NEIL1) .

3D structures of endonuclease3D structures of endonuclease

Updated on 29-March-2015

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• ENN-I
  • 1bix - hENN – human
    
  • 1cfr – ENN – Citrobacter freundii
    
  • 1af5 - CrENN – Chlamydomonas reinhardtii
    
  • 1fzr, 1m0d, 1m0i, 3cae – T7ENN - Enterobacteria phage T7
    
  • 2g7e, 2g7f – VcENN – Vibrio cholera
    
  • 2vnd - VcENN (mutant)
    
  • 2pu3 - VsENN – Vibrio salmonicida
• ENN-II
  • 1pvi, 1pvu - ENN – Proteus vulgaris
    
  • 2wsh - T4ENN (mutant) - Enterobacteria phage T4
    
  • 3w52, 4cwm, 4cxo, 4cxp, 4cxv – ENN – Arabidopsis thaliana
    
• ENN-III
  • 2abk, 1ako - EcENN – Escherichia coli
    
  • 1orn, 1orp, 1p59 - GsENN + DNA – Geobacillus stearothermophilus
• ENN-IV
  • 1qtw - EcENN
    
  • 2nqh - EcENN (mutant)
    
  • 1qum – EcENN + DNA
    
  • 2nqj, 2nq9, 4k1g - EcENN (mutant) + DNA
    
  • 1xp3 - ENN – Bacillus anthracis
    
  • 3aal - GkENN – Geobacillus kaustophilus
    
  • 3aam - TtENN – Thermus thermophilus
• ENN-V
  • 1eni, 1enj, 1enk, 2end - T4ENN
    
  • 1vas - T4ENN + DNA
    
  • 2w35, 2w36, 4b20 - TmENN + DNA – Thermotoga maritima
    
  • 3hd0 - TmENN
    
  • 3ga2 - BsENN (mutant) – Bacillus subtilis
    
  • 3goc - ENN – Streptomyces avermitilis
    
  • 2fcc – T4ENN + DNA
    
  • 4nsp – hENN catalytic domain
    
• ENN-VII
  • 1en7, 1e7d - T4ENN
    
  • 1e7l - T4ENN (mutant)
    
  • 2qnc, 2qnf - T4ENN (mutant) + DNA
• ENN-VIII
  • 1q39, 1q39 - EcENN
    
  • 1q3b, 1q3c - EcENN (mutant)
    
  • 1tdh – hENN
    
  • 1bix – hENN + DNA
    
  • 1k3x, 2ea0, 1k3w, 1k3x, 2ea0, 2opf, 2oq4 - EcENN + DNA
    
  • 2opf, 2oq4 - EcENN (mutant) + DNA
• AP ENN
  • 3ngf - ENN - Brucella melitensis
    
  • 2j63 – ENN – Leishmania major
    
• Cas ENN
  • 1wj9, 4ej3 – TtCas
    
  • 4n06 – AfCas1 - Archaeoglobus fulgidus
    
  • 3god – PaCas1 – Pseudomonas aeruginosa
    
  • 3nkd – EcCas1
    
  • 4wj0 – PhCas1 - Pyrococcus horikoshii
    
  • 4xtk – TmCas1
    
  • 3oq2 – Cas2 – Desulfovibrio vulgaris
    
  • 4mak – EcCas2
    
  • 4p6i, 4qdl – EcCas1 + EcCas2
    
  • 3s4l – MjCas3 – Methanocaldococcus jannaschii
    
  • 4qqw – TfCas3 – Thermobifida fusca
    
  • 4qqx – TfCas3 + ATP
    
  • 4qqy – TfCas3 + ADP
    
  • 4qqz – TfCas3 + AMPPNP
    
  • 4q2c - TteCas3 – Thermobaclum terrenum
    
  • 4q2d - TteCas3 + ATP
    
  • 3i4h – Cas4 - Pyrobaculum calidifontis
    
  • 4qr0, 4qr1 - SpCas9 (Csn1) – Streptococcus pyogenes
    
  • 4ill, 4ilm – SsCas6 + RNA - Sulfolobus solfataricus
    
  • 4ilr, 3zfv – SsCas6
    
  • 3i4h – PfCas6 - Pyrococcus furiosus
    
  • 3pkm – PfCas6 + RNA
    
  • 4dzd – EcCas6e
    
  • 2y8w, 2y8y, 3qrp, 3qrq, 2qrr – TtCas6e (Cse3) + RNA
    
  • 2xli, 2xlj, 2xlk, 4al7 – PaCas6f (Csy4) + RNA
    
  • 4al5, 4al6 - PaCas6f (Csy4) (mutant) + RNA
    
  • 4cmp, 4cmq – SpCas9 (Csn1)
    
  • 4oo8, 4un3, 4un4, 4un5 - SpCas9 (Csn1) (mutant) + RNA + DNA
    
  • 4ogc, 4oge – Cas9 II-C – Actinomyces naeslundii
    
  • 3ung, 3ur3, 4doz, 4w8y – PfCas10 CMR2 subunit
    
  • 4h4k – PfCas10 CMR2+CMR3 subunits
    
  • 3w2v – PfCas10 CMR2+CMR3 subunits + AMP
    
  • 3w2w – PfCas10 CMR2+CMR3 subunits + ATP
    
  • 4gkf – PfCas10 CMR5 subunit
    
  • 4an8, 4f3e – TtCasA (Cse1)
    
  • 4h3t - CasA (Cse1) – Acidimicrobium ferrooxidans
    
  • 4h79 - TfCasB (Cse2)
    
  • 3wa8 - CasB (Cse2) – Meiothermus ruber
    
  • 4h7a - TtCasB (Cse2)
    
  • 4tvx – EcCasA (Cse1) + CasE
    
  • 4u7u – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA
    
  • 4qyz – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA
    
  • 3qhq - Csn2 – Streptococcus agalactiae
    
  • 3toc, 3v7f – SpCsn2
    
  • 3ps0 – SsCsa2
    
• EcoKI ENN
  • 2ar0 – EcENN (mutant)
    
• Ecoo109I ENN
  • 1wtd - EcENN
    
  • 1wte – EcENN + DNA
    
• EcoRI ENN
  • 1qc9 - EcENN
    
  • 1eri, 1ckq, 1cl8, 1qps – EcENN + DNA
    
  • 1qrh, 1qri, 2oxv - EcENN (mutant) + DNA
• EcoRII ENN
  • 1na6 – EcENN
    
  • 3hqf, 3hqg - EnENN + DNA
• EcoRV ENN
  • 1rve, 1az3 – EcENN
    
  • 1az4 - EcENN (mutant)
    
  • 2rve, 4rve, 1rva, 1rvb, 1rvc, 1az0, 1bsu, 1bua, 1bgb, 1rv5, 1b94, 1b95, 1eo3, 1eo4, 1eon, 1eoo, 1eop, 2b0d, 2b0e - EcENN + DNA
    
  • 1bss, 1b96, 1b97, 1stx, 1suz, 1sx5, 1sx8, 2ge5 - EcENN (mutant) + DNA
• BamHI ENN
  • 1bam – BaENN – Bacillus amyloliquefaciens
    
  • 1bhm, 3bam, 2bam, 1esg - BaENN + DNA
• FokI ENN
  • 1fok – PoENN + DNA – Planomicrobium okeanokoites
    
  • 2fok – PoENN
• PvuII ENN
  • 3pvi - PvENN (mutant) + DNA – Proteus vulgaris
    
  • 1k0z, 1h56, 3ksk - PvENN
    
  • 1ni0 - PvENN (mutant)
    
  • 2pvi, 1eyu, 1f0o - PvENN + DNA
• tRNA-splicing ENN
  • 1a79, 1a76, 1a77 - MjENN – Methanocaldococcus jannaschii
    
  • 2cv8 - ENN – Sulfolobus tokodaii
    
  • 2gw6 – hENN subunit sen15 – NMR
    
  • 2gjw - AfENN + RNA – Archaeoglobus fulgidus
    
  • 1r0v, 1r11 – AfENN
  • 2ohc, 2ohe - TaENN – Thermoplasma acidophilum
    
  • 2zyz – ENN – Pyrobaculum aerophilum
    
  • 3iey - ENN + NEQ261 – Nanoarchaeum equitans
    
  • 3ajv - ApENN (mutant) – Aeropyrum pernix
    
  • 3p1y - ApENN /AfENN
    
  • 3p1z - ApENN + protein
• VSR ENN
  • 1vsr – EcENN
    
  • 1cw0 - EcENN + DNA
• BglI ENN
  • 1dmu, 1d2i – BsENN + DNA
    
  • 1dfm - BsENN (mutant) + DNA
• BglII ENN
  • 1es8 - BsENN
• MunI ENN
  • 1d02 - ENN (mutant) + DNA - Mycoplasma
• Sm ENN
  • 1smn, 1qae, 1ql0, 1g8t – ENN – Serratia marcescens
• NaeI ENN
  • 1ev7 - LaENN – Lechevalieria aerocolonigenes
    
  • 1iaw - LaENN + DNA
• NgoMIV ENN
  • 1fiu, 4abt - ENN + DNA – Neisseria gonorrheae
• NEI ENN
  • 1tdh - hENN
• BsoBI ENN
  • 1dc1 - GsENN + DNA
• Bse634I ENN
  • 1knv – GsENN
    
  • 3v1z – GsENN + DNA
    
  • 3v20, 3v21 - GsENN (mutant) + DNA
• HincII ENN
  • 1kc6, 1tw8, 1xhu, 1xhv, 1tx3, 2gie - HiENN + DNA – Haemophilus influenza
    
  • 2gig, 2gih, 2gii, 2gij, 3e3y, 3e40, 3e41, 3e42, 3e43, 3e44, 3e45, 3ebc - HiENN (mutant) + DNA
    
  • 2aud – HiENN
• HinDIII ENN
  • 2e52, 3a4k - HiENN + DNA
• HinP1I ENN
  • 1ynm – HiENN
    
  • 2fkc, 2fkh, 2fl3, 2flc - HiENN + DNA
• Flap ENN
  • 1mc8 - PhENN (mutant)
    
  • 3ory– ENN – Desulfurococcus amylolyticus
    
  • 3q8k, 3q8l, 3q8m - hENN + DNA
    
  • 1rxv, 1rxw - AfENN + DNA
    
  • 1ul1 - hENN + PCNA
    
  • 2izo - SsENN + PCNA – Sulfolobus solfataricus
    
  • 1a76, 1a77 - MjENN
    
  • 1b43 – PfENN – Pyrococcus furiosus
    
  • 1rxz - AfENN + PCNA
    
  • 4wa8 – ENN – Methanopyrus kandleri
    
• DNA mismatch ENN
  • 1odg - EcENN + DNA
    
  • 1h7u – hENN
    
• Vvn ENN
  • 1ouo – VvENN – Vibrio vulnificus
    
  • 1oup, 2ivk - VvENN + DNA
• BfiI ENN
  • 2c1l – ENN – Bacillus firmus
• SfiI ENN
  • 2ezv, 2f03 – ENN + DNA – synthetic
• Ecl18kI ENN
  • 2fqz, 2gb7 – ENN + DNA – Enterobacter cloacae
• SdaI ENN
  • 2ixs – ENN – Streptomyces diastaticus
• PabI ENN
  • 2dvy – ENN – Pyrococcus abyssi
• PspGI ENN
  • 3bm3 – ENN – Pyrococcus
• NHN ENN
  • 2qgp, 4h6d – ENN – Geobacter metallireducens
• UV damage ENN
  • 2j6v, 3bzg, 3c0s – TtENN
    
  • 3bzj, 3c0l, 3c0q - TtENN (mutant)
    
  • 3tc3 - SaENN
    
  • 4gle - SaENN + DNA
    
• NotI ENN
  • 3bvq - NoENN – Nocardia otitidiscaviarum
    
  • 3c25 - NoENN + DNA
• BpujI ENN
  • 2vla, 3s1s – ENN – Bacillus pumilus
• Sau3AI ENN
  • 2reu – ENN C terminal – Staphylococcus aureus
• HpyI ENN
  • 3fc3, 3gox – HpENN99 + DNA – Helicobacter pylori
    
  • 3or3 – HpENN88 + DNA
• PacI ENN
  • 3ldy, 3m7k - PaENN + DNA – Psdeudomonas alcaligenes
• Crossover junction ENN
  • 2kpf - ENN – mouse
    
  • 2ziw, 2zix, 2ziu – hENN EME1 + Mus81
    
  • 2ziv – hENN EME1 (mutant) + Mus81
    
  • 4p0p, 4p0q, 4p0r, 4p0s – hENN EME1 + Mus81 + DNA
    
• OkrAI ENN
  • 3odh - ENN + DNA – Oceanobacter kriegii
• BspD6I ENN
  • 2ewf - ENN – Bacillus
• ThaI ENN
  • 3ndh - TaENN + DNA
• Xpf ENN
  • 1z00, 2a1j - hENN C terminal + DNA excision repair protein
    
  • 2aq0 – hENN residues 823-905 – NMR
    
  • 2kn7 – hENN residues 823-905 + DNA – NMR
    
  • 2bgw - ApENN + DNA
    
  • 2bhn - ApENN
    
• Intron-encoded endonuclease
• I-PpoI ENN
  • 1a74, 1ipp, 1a73, 1cz0 - PpENN + DNA – Physarum polycephalum
    
  • 1cyq, 1evw, 2o6m - PpENN (mutant) + DNA
    
  • 1evx - PpENN
• I-CreI ENN
  • 1bp7, 1g9y, 1g9z, 1n3e, 1n3f, 2vbj, 2vbl, 2vbn, 2vbo, 4aqu, 4aqx - CrENN + DNA
    
  • 1u0c, 1u0d, 1t9i, 1t9j, 2i3p, 2i3q, 4aab, 4aad, 4aae, 4aaf, 4aag - CrENN (mutant) + DNA
    
  • 2o7m - CrENN
• I-CeuI ENN
  • 2ex5 - ENN (mutant) + DNA – Chlamydomonas eugametos
• I-DmoI ENN
  • 1b24, 2vs7, 2vs8, 4un7, 4un8, 4un9, 4una, 4unb, 4unc, 4ut0, 4d6n, 4d6o - DmENN + DNA – Desulfurococcus mobilis
    
  • 1mow – DmENN/CrENN + DNA
• I-AniI ENN
  • 1p8k, 2qoj, 3uvf - EnENN + DNA – Emericella nidulans
    
  • 3eh8 - EnENN (mutant) + DNA
• I-HmuI ENN
  • 1u3e - ENN + DNA – Bacillus phage spo1
• I-TevI ENN
  • 1i3j, 1t2t - T4ENN + DNA
    
  • 1ln0, 1mk0 – T4ENN (mutant)
• I-SceI ENN
  • 1dfa, 1ef0 – yENN – yeast
    
  • 1gpp – yENN (mutant)
    
  • 1lws, 1lwt, 1r7m, 3c0w, 3c0x, 3ool - yENN + DNA
    
  • 3oor - yENN (mutant) + DNA
• I-PkoII ENN
  • 2cw7, 2cw8 – ENN – Thermococcus kodakarensis
• I-MspI ENN
  • 1sa3, 1yfi, 2fld – ENN + DNA – Moraxella
• I-PfuI ENN
  • 1dq3 – PfENN
• I-Tsp061I ENN
  • 2dch – ENN – Thermoproteus
• I-Vdi141I ENN
  • 3e54 – ENN – Vulcanisaeta distribute
• I-MtuI ENN
  • 3ifj, 3igd - MtENN (mutant) – Mycobacterium tuberculosis
    
  • 2l8l - MtENN
• I-MsoI ENN
  • 1m5x, 3fd2 – MoENN + DNA – Monomastix
    
  • 3ko2 – MoENN (mutant) + DNA
• I-GzeMII ENN
  • 4efj – ENN + DNA – Gibberella zeae
• I-tRNA ENN
  • 4fz2 – MoENN – Candidatus micrarchaeum