Endonuclease
FunctionEndonuclease (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. Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN[1]. The Cas ENN proteins are part of CRISPR/Cas prokaryotic immune system which confers protection from foreign genetic elements like viruses. The CRISPR (Clustered 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[2]. For more details see
Intron-encoded ENN or homing ENN are encoded by genes with mobile, self-splicing introns. They promote the movement of DNA sequences from one chromosome location to another[3].
RelevanceSickle cell anemia is caused by mutation in the recognition site of MstII ENN. DiseaseMutation in UV-specific ENN causes Xeroderma pigmentosa. Mutations in tRNA-splicing ENN cause pontocerebellar hypoplasia. Structural highlights
(PDB code 1rva). 3D structures of endonuclease
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3D structures of endonuclease3D structures of endonuclease
Updated on 19-June-2019 {{#tree:id=OrganizedByTopic|openlevels=0|
- ENN-I
- ENN-II
- ENN-III
- ENN-IV
- ENN-V
- ENN-VII
- ENN-VIII
- AP ENN
- Cas ENN
- 1wj9, 4ej3 – TtCas
- 4n06 – AfCas1 - Archaeoglobus fulgidus
- 3god – PaCas1 – Pseudomonas aeruginosa
- 3nkd – EcCas1
- 4wj0 – PhCas1 - Pyrococcus horikoshii
- 4xtk – TmCas1
- 5fcl – Cas1 - Pectobacterium atrosepticum
- 4zkj - SpCas1 – Streptococcus pyogenes
- 3oq2 – Cas2 – Desulfovibrio vulgaris
- 4mak – EcCas2
- 4p6i, 4qdl – EcCas1 + EcCas2
- 6qy3 – GsCas1 + EcCas2 + Csn2 – Cryo EM
- 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<br /
- 4qr0, 4qr1 - SpCas9 (Csn1) – Streptococcus pyogenes
- 4ilr, 3zfv – SsCas6
- 3i4h – PfCas6 - Pyrococcus furiosus
- 4dzd – EcCas6e
- 4qr0, 4qr1 - SpCas9 (Csn1) – Streptococcus pyogenes
- 4qr0, 4qr1, 4cmp, 4cmq - SpCas9
- 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
- 3qhq - Csn2 – Streptococcus agalactiae
- 3toc, 3v7f – SpCsn2
- 3ps0 – SsCsa2
- 1wj9, 4ej3 – TtCas
- Cas ENN complex with RNA and DNA
- 5dlj, 5dqt, 5dqu, 5dqz, 5ds4, 5ds5, 5ds6, 5vvl, 5vvk, 5vvj – EcCas1 + EcCas2 + DNA
- 5wfe – EcCas1 + EcCas2 + IHF-a + IHF-b + DNA
- 5xvp, 5xvo, 5xvn – Cas1 + Cas2 + DNA – Enterococcus faecalis
- 6qxt, 6qxf – GsCas1 (mutant) + EcCas2 + Csn2 + DNA – Cryo EM
- 4ill, 4ilm – SsCas6 + RNA - Sulfolobus solfataricus
- 5uz9 – PaCsa5f + Cas7f + Cas8f + anti-crispr protein + RNA - Cryo EM
- 6b48, 6b47, 6b46, 6b45 – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + RNA - Cryo EM
- 6b44 – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + DNA - Cryo EM
- 6ne0 – PaCsa6/Csy4 + Csy1 + Csy2 + Csy3 + DNA + RNA – Cryo EM
- 3pkm – PfCas6 + RNA
- 2y8w, 2y8y, 3qrp, 3qrq, 2qrr – TtCas6e (Cse3) + RNA
- 2xli, 2xlj, 2xlk, 4al7 – PaCas6f (Csy4) + RNA
- 4al5, 4al6 - PaCas6f (Csy4) (mutant) + RNA
- 4zt0 - SpCas9 + RNA
- 4zt9 - SpCas9 (mutant) + RNA
- 5f9r - SpCas9 + RNA + DNA
- 4oo8, 4un3, 4un4, 4un5, 5fw1, 5fw2, 5fw3, 5fq5, 5b2r, 5b2s, 5b2t, 5y36, 6ia6 - SpCas9 (Csn1) (mutant) + RNA + DNA
- 5xbl - SpCas9 + associated protein + RNA
- 6ifo - SpCas9 + AcriiA2 + RNA
- 5vw1 - SpCas9 + AcriiA4 + RNA
- 6mcc, 5vzl, 6mcb - SpCas9 + AcriiA4 + RNA – Cryo EM
- 5vgb - NmCas9 + AcriiC1 – Neisseria meningitidis
- 6jdx, [[6jdj], 6j9m] - NmCas9 + AcriiC2
- 6j9n - NmCas9 + AcriiC3
- 5x2h, 5x2g – Cas9 + RNA + DNA – Campylobacter jejuni
- 5czz - SaCas9 (Csn1) + RNA + DNA - Staphylococcus aureus
- 5axw - SaCas9 (Csn1) (mutant) + RNA + DNA
- 6joo - Cas9 + RNA + DNA – Corynebacterium diphtheriae
- 5b2o, 5b2p, 5b2q - FtCas9 (mutant) + RNA + DNA – Francisella tularensis
- 6i1l, 6i1k, 6gtg, 6gtf, 6gte, 6gtd, 6gtc – FtCas12a (mutant) + RNA + DNA
- 4u7u – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA
- 4qyz, 5h9f, 5h9e – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA
- 5wqe – AaCas C2C1 + RNA – Alicyclobacillus acidoterrestris
- 5u34 – AaCas C2C1 (mutant) + RNA
- 5u30, 5u31, 5u33 – AaCas C2C1 + RNA + DNA
- 5kk5, 5b43 – AcCas Cpf1 + RNA + DNA – Acidaminococcus
- 5xh7, 5xh6 – AcCas Cpf1 (mutant) + RNA + DNA
- 5ng6 – FtCas Cpf1 + RNA
- 5nfv, 5mga – FtCas Cpf1 + RNA + DNA
- 5dlj, 5dqt, 5dqu, 5dqz, 5ds4, 5ds5, 5ds6, 5vvl, 5vvk, 5vvj – EcCas1 + EcCas2 + DNA
- EcoKI ENN
- 2ar0 – EcENN (mutant)
- 2ar0 – EcENN (mutant)
- Ecoo109I ENN
- EcoRI ENN
- EcoRII ENN
- EcoRV ENN
- BamHI ENN
- Bbvci ENN
- FokI ENN
- LAGLIDAD ENN
- PvuII ENN
- tRNA-splicing ENN
- 2gw6 – hENN subunit sen15 – NMR
- 1a79, 1a76, 1a77 - MjENN – Methanocaldococcus jannaschii
- 2cv8 - ENN – Sulfolobus tokodaii
- 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
- 2gw6 – hENN subunit sen15 – NMR
- VSR ENN
- BglI ENN
- BglII ENN
- 1es8 - BsENN
- MunI ENN
- 1d02 - ENN (mutant) + DNA - Mycoplasma
- Sm ENN
- NaeI ENN
- NgoMIV ENN
- NEI ENN
- 1tdh - hENN
- BsoBI ENN
- 1dc1 - GsENN + DNA
- Bse634I ENN
- HincII ENN
- HinDIII ENN
- HinP1I ENN
- Flap ENN
- 5zod - hENN
- 3q8k, 3q8l, 3q8m - hENN + DNA
- 5zog, 5zof, 5zoe - hENN (mutant) + DNA
- 5fv7 - hENN + inhibitor
- 1ul1 - hENN + PCNA
- 1mc8 - PhENN (mutant)
- 3ory– ENN – Desulfurococcus amylolyticus
- 1rxv, 1rxw - AfENN + DNA
- 2izo - SsENN + PCNA – Sulfolobus solfataricus
- 1a76, 1a77 - MjENN
- 1b43 – PfENN – Pyrococcus furiosus
- 1rxz - AfENN + PCNA
- 4wa8 – ENN – Methanopyrus kandleri
- 5zod - hENN
- DNA mismatch ENN
- Vvn ENN
- Structure-specific ENN
- BfiI ENN
- 2c1l – ENN – Bacillus firmus
- SfiI ENN
- Ecl18kI ENN
- SdaI ENN
- 2ixs – ENN – Streptomyces diastaticus
- PabI ENN
- 2dvy – ENN – Pyrococcus abyssi
- PspGI ENN
- 3bm3 – ENN – Pyrococcus
- HNH ENN
- UV damage ENN
- NotI ENN
- BpujI ENN
- Sau3AI ENN
- HpyI ENN
- PacI ENN
- Crossover junction ENN
- OkrAI ENN
- 3odh - ENN + DNA – Oceanobacter kriegii
- BspD6I ENN
- 2ewf - ENN – Bacillus
- ThaI ENN
- 3ndh - TaENN + DNA
- Xpf ENN
- Mazf3 ENN
- Vapc ENN
- Muts2 ENN
- Endoms ENN
- ENN G
- ENN S
- 5ybb – ENN + R-M system + DNA – Caldanaerobacter subterraneus
- 5ybb – ENN + R-M system + DNA – Caldanaerobacter subterraneus
- ENN V
- Apurinic-apyrimidinic ENN
- Intron-encoded endonuclease
- I-PpoI ENN
- I-CreI ENN
- I-CeuI ENN
- 2ex5 - ENN (mutant) + DNA – Chlamydomonas eugametos
- I-DmoI ENN
- I-AniI ENN
- I-HmuI ENN
- 1u3e - ENN + DNA – Bacillus phage spo1
- I-TevI ENN
- I-SceI ENN
- I-PkoII ENN
- I-MspI ENN
- I-PfuI ENN
- 1dq3 – PfENN
- I-Tsp061I ENN
- 2dch – ENN – Thermoproteus
- I-Vdi141I ENN
- 3e54 – ENN – Vulcanisaeta distribute
- I-MtuI ENN
- I-MsoI ENN
- I-GzeMII ENN
- 4efj – ENN + DNA – Gibberella zeae
- I-tRNA ENN
- 4fz2 – ENN – Candidatus micrarchaeum
- 4fz2 – ENN – Candidatus micrarchaeum
- I-Cvui ENN
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ReferencesReferences
- ↑ Nishino T, Morikawa K. Structure and function of nucleases in DNA repair: shape, grip and blade of the DNA scissors. Oncogene. 2002 Dec 16;21(58):9022-32. PMID:12483517 doi:http://dx.doi.org/10.1038/sj.onc.1206135
- ↑ Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science. 2010 Jan 8;327(5962):167-70. doi: 10.1126/science.1179555. PMID:20056882 doi:http://dx.doi.org/10.1126/science.1179555
- ↑ Flick KE, Jurica MS, Monnat RJ Jr, Stoddard BL. DNA binding and cleavage by the nuclear intron-encoded homing endonuclease I-PpoI. Nature. 1998 Jul 2;394(6688):96-101. PMID:9665136 doi:10.1038/27952