Endonuclease

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{{STRUCTURE_1rva| PDB=1rva | SIZE=400| SCENE= |right|CAPTION=E. coli EcoRV endonuclease dimer complex with DNA, [[1rva]] }}
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<StructureSection load='' size='350' side='right' scene='49/496318/Cv/1' caption='E. coli EcoRV endonuclease dimer (magenta, green) complex with DNA, (PDB code [[1rva]])'>
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'''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. Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN. See also<br />
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* [[Apurinic-Apyrimidinic Endonuclease-1]]<br />
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* [[DNA repair protein human endonuclease VIII-like 1 (NEIL1)]] .
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==3D structures of endonuclease==
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== Function ==
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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'''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.
 +
*'''ENN-II''' operates on overlapping restriction site and cleavage pattern.
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*'''ENN-III''' is a bifunctional DNA glycosylase that removes oxidized pyrimidines from DNA<ref>PMID:30959406</ref>.
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*'''ENN-IV''' cleaves the DNA backbone 5' of AP sites<ref>PMID:10458614</ref>.
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*'''ENN-V''' removes deaminated bases from DNA<ref>PMID:23263163</ref>.
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*'''ENN-VII''' recognizes mixmatches in DNA recombinational heteroduplexes and performs their incision<ref>PMID:21237725</ref>.
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*'''ENN-VIII''' removes radiolysis thymine products from phage DNA and cleaves the DNA at AP sites<ref>PMID:9405426</ref>.
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*'''Structure-specific ENN''' specific for DNA secondary structure rather than for its sequence<ref>PMID:28327556</ref>.
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*'''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<ref>PMID:9665136</ref>. <br />
 +
The '''Cas ENN''' proteins are part of '''CRISPR/Cas''' prokaryotic immune system which confers protection from foreign genetic elements like viruses. The '''CRISPR''' ('''C'''lustered '''R'''egularly '''I'''nterspersed '''S'''hort '''P'''alindromic '''R'''epeats) are DNA loci which are found in ca. 40% of the bacteria. The CRISPR/Cas system is being used lately as gene editing tool<ref>PMID:20056882</ref>. For more details see<br />
 +
*[[CRISPR-Cas]]
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*CRISPR type I-A (Cascade) - see [[CRISPR subtype I-A]]
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*CRISPR type I-B (Cascade) - see [[CRISPR subtype I-B]]
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*CRISPR type I-C (Cascade) - see [[CRISPR subtype I-C]]
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*CRISPR type I-E (Cascade) - see [[CRISPR type I-E (Cascade)|CRISPR subtype I-E]]
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*(CRISPR type I-F (Csy1, Csy2, Csy3) - see [[CRISPR subtype I-F]]
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*CRISPR type III-A (Csm complex) - see [[CRISPR subtype III-A (Csm complex)]]
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*CRISPR type II-A - see [[CRISPR-Cas9]]
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*CRISPR type V (Cpf1, C2c1, C2c3) - see [[CRISPR type V]]
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*CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
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See also<br />
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* [[Apurinic-Apyrimidinic Endonuclease-1]]<br />
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* For EcoRV ENN see [[Student Projects for UMass Chemistry 423 Spring 2012-3]]<br />
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* For NEI ENN see [[DNA repair protein human endonuclease VIII-like 1 (NEIL1)]].
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===ENN-I===
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== Relevance ==
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[[1bix]] - hENN – human<br />
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Sickle cell anemia is caused by mutation in the recognition site of MstII ENN.
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[[1cfr]] – ENN – ''Citrobacter freundii''<br />
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[[1af5]] - CrENN – ''Chlamydomonas reinhardtii''<br />
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[[1fzr]], [[1m0d]], [[1m0i]], [[3cae]] – T7ENN - Enterobacteria phage T7<br />
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[[2g7e]], [[2g7f]] – VcENN – ''Vibrio cholera''<br />
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[[2vnd]] - VcENN (mutant) <br />
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[[2pu3]] - VsENN – ''Vibrio salmonicida''
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===ENN-II===
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== Disease ==
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[[1pvi]], [[1pvu]] - ENN – ''Proteus vulgaris''<br />
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Mutation in UV-specific ENN causes Xeroderma pigmentosa. Mutations in tRNA-splicing ENN cause pontocerebellar hypoplasia.
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[[2wsh]] - T4ENN (mutant) - Enterobacteria phage T4<br />
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[[3w52]] – ENN – ''Arabidopsis thaliana''<br />
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===ENN-III===
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== Structural highlights ==
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<scene name='49/496318/Cv/1'>E. coli EcoRV endonuclease dimer with DNA</scene>
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[[2abk]], [[1ako]] - EcENN – ''Escherichia coli''<br />
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<scene name='49/496318/Cv/2'>DNA-protein binding</scene> (PDB code [[1rva]]).
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[[1orn]], [[1orp]], [[1p59]] - GsENN + DNA – ''Geobacillus stearothermophilus''
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===ENN-IV===
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==3D structures of endonuclease==
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[[Endonuclease 3D structures]]
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[[1qtw]] - EcENN <br />
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[[2nqh]] - EcENN (mutant) <br />
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[[1qum]] – EcENN + DNA<br />
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[[2nqj]], [[2nq9]], [[4k1g]] - EcENN (mutant) + DNA<br />
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[[1xp3]] - ENN – ''Bacillus anthracis''<br />
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[[3aal]] - GkENN – ''Geobacillus kaustophilus''<br />
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[[3aam]] - TtENN – ''Thermus thermophilus''
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===ENN-V===
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[[1eni]], [[1enj]], [[1enk]], [[2end]] - T4ENN <br />
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[[1vas]] - T4ENN + DNA<br />
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[[2w35]], [[2w36]], [[4b20]] - TmENN + DNA – ''Thermotoga maritima''<br />
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[[3hd0]] - TmENN <br />
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[[3ga2]] - BsENN (mutant) – ''Bacillus subtilis''<br />
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[[3goc]] - ENN – ''Streptomyces avermitilis''<br />
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[[2fcc]] – T4ENN + DNA<br />
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===ENN-VII===
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[[1en7]], [[1e7d]] - T4ENN <br />
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[[1e7l]] - T4ENN (mutant) <br />
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[[2qnc]], [[2qnf]] - T4ENN (mutant) + DNA
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===ENN-VIII===
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[[1q39]], [[1q39]] - EcENN <br />
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[[1q3b]], [[1q3c]] - EcENN (mutant) <br />
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[[1tdh]] – hENN <br />
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[[1bix]] – hENN + DNA<br />
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[[1k3x]], [[2ea0]], [[1k3w]], [[1k3x]], [[2ea0]], [[2opf]], [[2oq4]] - EcENN + DNA <br />
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[[2opf]], [[2oq4]] - EcENN (mutant) + DNA
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===EcoKI ENN===
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[[2ar0]] – EcENN (mutant)<br />
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-
 
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===Ecoo109I ENN===
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[[1wtd]] - EcENN<br />
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[[1wte]] – EcENN + DNA<br />
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===EcoRI ENN===
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[[1qc9]] - EcENN<br />
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[[1eri]], [[1ckq]], [[1cl8]], [[1qps]] – EcENN + DNA<br />
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[[1qrh]], [[1qri]], [[2oxv]] - EcENN (mutant) + DNA
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===EcoRII ENN===
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[[1na6]] – EcENN<br />
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[[3hqf]], [[3hqg]] - EnENN + DNA
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===EcoRV ENN===
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[[1rve]], [[1az3]] – EcENN<br />
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[[1az4]] - EcENN (mutant) <br />
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[[2rve]], [[4rve]], [[1rva]], [[1rvb]], [[1rvc]], [[1az0]], [[1bsu]], [[1bua]], [[1bgb]], [[1rv5]], [[1b94]], [[1b95]], [[1eo3]], [[1eo4]], [[1eon]], [[1eoo]], [[1eop]], [[2b0d]], [[2b0e]] - EcENN + DNA<br />
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[[1bss]], [[1b96]], [[1b97]], [[1stx]], [[1suz]], [[1sx5]], [[1sx8]], [[2ge5]] - EcENN (mutant) + DNA
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===BamHI ENN===
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[[1bam]] – BaENN – ''Bacillus amyloliquefaciens''<br />
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[[1bhm]], [[3bam]], [[2bam]], [[1esg]] - BaENN + DNA
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===FokI ENN===
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[[1fok]] – PoENN + DNA – ''Planomicrobium okeanokoites''<br />
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[[2fok]] – PoENN
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===PvuII ENN===
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[[3pvi]] - PvENN (mutant) + DNA – ''Proteus vulgaris''<br />
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[[1k0z]], [[1h56]], [[3ksk]] - PvENN<br />
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[[1ni0]] - PvENN (mutant) <br />
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[[2pvi]], [[1eyu]], [[1f0o]] - PvENN + DNA
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===tRNA-splicing ENN===
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[[1a79]], [[1a76]], [[1a77]] - MjENN – ''Methanocaldococcus jannaschii''<br />
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[[2cv8]] - ENN – ''Sulfolobus tokodaii''<br />
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[[2gw6]] – hENN subunit sen15 – NMR<br />
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[[2gjw]] - AfENN + RNA –'' Archaeoglobus fulgidus''<br />
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[[1r0v]], [[1r11]] – AfENN
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[[2ohc]], [[2ohe]] - TaENN – ''Thermoplasma acidophilum''<br />
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[[2zyz]] – ENN – ''Pyrobaculum aerophilum''<br />
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[[3iey]] - ENN + NEQ261 – ''Nanoarchaeum equitans''<br />
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[[3ajv]] - ApENN (mutant) – ''Aeropyrum pernix''<br />
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[[3p1y]] - ApENN /AfENN<br />
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[[3p1z]] - ApENN + protein
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+
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===VSR ENN===
+
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[[1vsr]] – EcENN<br />
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[[1cw0]] - EcENN + DNA
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===BglI ENN===
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[[1dmu]], [[1d2i]] – BsENN + DNA <br />
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[[1dfm]] - BsENN (mutant) + DNA
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===BglII ENN===
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[[1es8]] - BsENN
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===MunI ENN===
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[[1d02]] - ENN (mutant) + DNA - ''Mycoplasma''
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===Sm ENN===
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[[1smn]], [[1qae]], [[1ql0]], [[1g8t]] – ENN – ''Serratia marcescens''
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===NaeI ENN===
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+
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[[1ev7]] - LaENN – ''Lechevalieria aerocolonigenes''<br />
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[[1iaw]] - LaENN + DNA
+
-
 
+
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===NgoMIV ENN===
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+
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[[1fiu]], [[4abt]] - ENN + DNA – ''Neisseria gonorrheae''
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===NEI ENN===
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[[1tdh]] - hENN
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===BsoBI ENN===
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[[1dc1]] - GsENN + DNA
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===Bse634I ENN===
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[[1knv]] – GsENN<br />
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[[3v1z]] – GsENN + DNA<br />
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[[3v20]], [[3v21]] - GsENN (mutant) + DNA
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===HincII ENN===
+
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+
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[[1kc6]], [[1tw8]], [[1xhu]], [[1xhv]], [[1tx3]], [[2gie]] - HiENN + DNA – ''Haemophilus influenza''<br />
+
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[[2gig]], [[2gih]], [[2gii]], [[2gij]], [[3e3y]], [[3e40]], [[3e41]], [[3e42]], [[3e43]], [[3e44]], [[3e45]], [[3ebc]] - HiENN (mutant) + DNA<br />
+
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[[2aud]] – HiENN
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===HinDIII ENN===
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[[2e52]], [[3a4k]] - HiENN + DNA
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===HinP1I ENN===
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[[1ynm]] – HiENN<br />
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[[2fkc]], [[2fkh]], [[2fl3]], [[2flc]] - HiENN + DNA
+
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+
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===Flap ENN===
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+
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[[1mc8]] - ENN (mutant) – ''Pyrococcus horikoshii''<br />
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[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br />
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[[3q8k]], [[3q8l]], [[3q8m]] - hENN + DNA<br />
+
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[[1rxv]], [[1rxw]] - AfENN + DNA<br />
+
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[[1ul1]] - hENN + PCNA <br />
+
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[[2izo]] - SsENN + PCNA – ''Sulfolobus solfataricus''<br />
+
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[[1a76]], [[1a77]] - MjENN <br />
+
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[[1b43]] – PfENN – ''Pyrococcus furiosus''<br />
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[[1rxz]] - AfENN + PCNA <br />
+
-
 
+
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===DNA mismatch ENN===
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[[1odg]] - EcENN + DNA<br />
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[[1h7u]] – hENN<br />
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===Vvn ENN===
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+
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[[1ouo]] – VvENN – ''Vibrio vulnificus''<br />
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[[1oup]], [[2ivk]] - VvENN + DNA
+
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===BfiI ENN===
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[[2c1l]] – ENN – ''Bacillus firmus''
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===SfiI ENN===
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[[2ezv]], [[2f03]] – ENN + DNA – synthetic
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===Ecl18kI ENN===
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[[2fqz]], [[2gb7]] – ENN + DNA – ''Enterobacter cloacae''
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===SdaI ENN===
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[[2ixs]] – ENN – ''Streptomyces diastaticus''
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===PabI ENN===
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[[2dvy]] – ENN – ''Pyrococcus abyssi''
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===PspGI ENN===
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[[3bm3]] – ENN – ''Pyrococcus''
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===NHN ENN===
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[[2qgp]] – ENN – ''Geobacter metallireducens''
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===UV damage ENN===
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[[2j6v]], [[3bzg]], [[3c0s]] – TtENN <br />
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[[3bzj]], [[3c0l]], [[3c0q]] - TtENN (mutant)<br />
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[[4gle]] - SaENN + DNA<br />
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-
 
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===NotI ENN===
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[[3bvq]] - NoENN – ''Nocardia otitidiscaviarum''<br />
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[[3c25]] - NoENN + DNA
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-
 
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===BpujI ENN===
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[[2vla]], [[3s1s]] – ENN – ''Bacillus pumilus''
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===Sau3AI ENN===
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[[2reu]] – ENN C terminal – ''Staphylococcus aureus''
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===HpyI ENN===
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[[3fc3]], [[3gox – HpENN99 + DNA – ''Helicobacter pylori''<br />
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[[3or3]] – HpENN88 + DNA
+
-
 
+
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===PacI ENN===
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[[3ldy]], [[3m7k]] - PaENN + DNA – ''Psdeudomonas alcaligenes''
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-
 
+
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===Crossover junction ENN===
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-
 
+
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[[2kpf]] - ENN – mouse
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-
 
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===OkrAI ENN===
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[[3odh]] - ENN + DNA – ''Oceanobacter kriegii''
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-
 
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===BspD6I ENN===
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[[2ewf]] - ENN – ''Bacillus''
+
-
 
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===ThaI ENN===
+
-
 
+
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[[3ndh]] - TaENN + DNA
+
-
 
+
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===Xpf ENN===
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-
 
+
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[[1z00]], [[2a1j]] - hENN C terminal + DNA excision repair protein<br />
+
-
[[2bgw]] - ApENN + DNA <br />
+
-
[[2bhn]] - ApENN <br />
+
-
 
+
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===Intron-encoded endonuclease===
+
-
 
+
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===I-PpoI ENN===
+
-
 
+
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[[1a74]], [[1ipp]], [[1a73]], [[1cz0]] - PpENN + DNA – ''Physarum polycephalum''<br />
+
-
[[1cyq]], [[1evw]], [[2o6m]] - PpENN (mutant) + DNA<br />
+
-
[[1evx]] - PpENN
+
-
 
+
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===I-CreI ENN===
+
-
 
+
-
[[1bp7]], [[1g9y]], [[1g9z]], [[1n3e]], [[1n3f]], [[2vbj]], [[2vbl]], [[2vbn]], [[2vbo]], [[4aqu]], [[4aqx]] - CrENN + DNA <br />
+
-
[[1u0c]], [[1u0d]], [[1t9i]], [[1t9j]], [[2i3p]], [[2i3q]], [[4aab]], [[4aad]], [[4aae]], [[4aaf]], [[4aag]] - CrENN (mutant) + DNA<br />
+
-
[[2o7m]] - CrENN
+
-
 
+
-
===I-CeuI ENN===
+
-
 
+
-
[[2ex5]] - ENN (mutant) + DNA – ''Chlamydomonas eugametos''
+
-
 
+
-
===I-DmoI ENN===
+
-
 
+
-
[[1b24]], [[2vs7]], [[2vs8]] - DmENN + DNA – ''Desulfurococcus mobilis''<br />
+
-
[[1mow]] – DmENN/CrENN + DNA
+
-
 
+
-
===I-AniI ENN===
+
-
 
+
-
[[1p8k]], [[2qoj]], [[3uvf]] - EnENN + DNA – ''Emericella nidulans''<br />
+
-
[[3eh8]] - EnENN (mutant) + DNA
+
-
 
+
-
===I-HmuI ENN===
+
-
 
+
-
[[1u3e]] - ENN + DNA – Bacillus phage spo1
+
-
 
+
-
===I-TevI ENN===
+
-
 
+
-
[[1i3j]], [[1t2t]] - T4ENN + DNA<br />
+
-
[[1ln0]], [[1mk0]] – T4ENN (mutant)
+
-
 
+
-
===I-SceI ENN===
+
-
 
+
-
[[1dfa]], [[1ef0]] – yENN – yeast<br />
+
-
[[1gpp]] – yENN (mutant) <br />
+
-
[[1lws]], [[1lwt]], [[1r7m]], [[3c0w]], [[3c0x]], [[3ool]] - yENN + DNA<br />
+
-
[[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''<br />
+
-
[[2l8l]] - MtENN
+
-
 
+
-
===I-MsoI ENN===
+
-
 
+
-
[[1m5x]], [[3fd2]] – MoENN + DNA – ''Monomastix''<br />
+
-
[[3ko2]] – MoENN (mutant) + DNA
+
-
 
+
-
===I-GzeMII ENN===
+
-
[[4efj]] – ENN + DNA – ''Gibberella zeae''
+
</StructureSection>
-
===I-tRNA ENN===
+
== References ==
 +
<references/>
-
[[4fz2]] – MoENN – ''Candidatus micrarchaeum''<br />
 
[[Category:Topic Page]]
[[Category:Topic Page]]
 +
[[Category:Endonuclease]]

Current revision

E. coli EcoRV endonuclease dimer (magenta, green) complex with DNA, (PDB code 1rva)

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References

  1. ↑ Sarre A, Stelter M, Rollo F, De Bonis S, Seck A, Hognon C, Ravanat JL, Monari A, Dehez F, Moe E, Timmins J. The three Endonuclease III variants of Deinococcus radiodurans possess distinct and complementary DNA repair activities. DNA Repair (Amst). 2019 Jun;78:45-59. PMID:30959406 doi:10.1016/j.dnarep.2019.03.014
  2. ↑ Hosfield DJ, Guan Y, Haas BJ, Cunningham RP, Tainer JA. Structure of the DNA repair enzyme endonuclease IV and its DNA complex: double-nucleotide flipping at abasic sites and three-metal-ion catalysis. Cell. 1999 Aug 6;98(3):397-408. PMID:10458614
  3. ↑ Cao W. Endonuclease V: an unusual enzyme for repair of DNA deamination. Cell Mol Life Sci. 2013 Sep;70(17):3145-56. PMID:23263163 doi:10.1007/s00018-012-1222-z
  4. ↑ Shcherbakov VP, Plugina L, Shcherbakova T. Endonuclease VII is a key component of the mismatch repair mechanism in bacteriophage T4. DNA Repair (Amst). 2011 Apr 3;10(4):356-62. PMID:21237725 doi:10.1016/j.dnarep.2010.12.006
  5. ↑ Jiang D, Hatahet Z, Melamede RJ, Kow YW, Wallace SS. Characterization of Escherichia coli endonuclease VIII. J Biol Chem. 1997 Dec 19;272(51):32230-9. PMID:9405426
  6. ↑ Dehé PM, Gaillard PHL. Control of structure-specific endonucleases to maintain genome stability. Nat Rev Mol Cell Biol. 2017 May;18(5):315-330. PMID:28327556 doi:10.1038/nrm.2016.177
  7. ↑ 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
  8. ↑ 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

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