Endonuclease: Difference between revisions
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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.<br /> | '''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.<br /> | ||
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]].<br /> See also<br /> | 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]].<br /> See also<br /> | ||
* [[Apurinic-Apyrimidinic Endonuclease-1]]<br /> | * [[Apurinic-Apyrimidinic Endonuclease-1]]<br /> | ||
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**[[1pvi]], [[1pvu]] - ENN – ''Proteus vulgaris''<br /> | **[[1pvi]], [[1pvu]] - ENN – ''Proteus vulgaris''<br /> | ||
**[[2wsh]] - T4ENN (mutant) - Enterobacteria phage T4<br /> | **[[2wsh]] - T4ENN (mutant) - Enterobacteria phage T4<br /> | ||
**[[3w52]] – ENN – ''Arabidopsis thaliana''<br /> | **[[3w52]], [[4cwm]], [[4cxo]], [[4cxp]], [[4cxv]] – ENN – ''Arabidopsis thaliana''<br /> | ||
*ENN-III | *ENN-III | ||
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**[[3goc]] - ENN – ''Streptomyces avermitilis''<br /> | **[[3goc]] - ENN – ''Streptomyces avermitilis''<br /> | ||
**[[2fcc]] – T4ENN + DNA<br /> | **[[2fcc]] – T4ENN + DNA<br /> | ||
**[[4nsp]] – hENN catalytic domain<br /> | |||
*ENN-VII | *ENN-VII | ||
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**[[1k3x]], [[2ea0]], [[1k3w]], [[1k3x]], [[2ea0]], [[2opf]], [[2oq4]] - EcENN + DNA <br /> | **[[1k3x]], [[2ea0]], [[1k3w]], [[1k3x]], [[2ea0]], [[2opf]], [[2oq4]] - EcENN + DNA <br /> | ||
**[[2opf]], [[2oq4]] - EcENN (mutant) + DNA | **[[2opf]], [[2oq4]] - EcENN (mutant) + DNA | ||
*AP ENN | |||
**[[3ngf]] - ENN - ''Brucella melitensis''<br /> | |||
**[[2j63]] – ENN – ''Leishmania major''<br /> | |||
*Cas ENN | *Cas ENN | ||
**[[1wj9]], [[4ej3]] – TtCas<br /> | **[[1wj9]], [[4ej3]] – TtCas<br /> | ||
**[[4n06]] – AfCas1 - Archaeoglobus fulgidus <br /> | **[[4n06]] – AfCas1 - ''Archaeoglobus fulgidus'' <br /> | ||
**[[3oq2]] – Cas2 – Desulfovibrio vulgaris<br /> | **[[3god]] – PaCas1 – ''Pseudomonas aeruginosa''<br /> | ||
**[[3nkd]] – EcCas1<br /> | |||
**[[4wj0]] – PhCas1 - ''Pyrococcus horikoshii''<br /> | |||
**[[4xtk]] – TmCas1<br /> | |||
**[[3oq2]] – Cas2 – ''Desulfovibrio vulgaris''<br /> | |||
**[[4mak]] – EcCas2<br /> | **[[4mak]] – EcCas2<br /> | ||
**[[4p6i]], [[4qdl]] – EcCas1 + EcCas2<br /> | **[[4p6i]], [[4qdl]] – EcCas1 + EcCas2<br /> | ||
**[[3s4l]] – MjCas3 – Methanocaldococcus jannaschii<br /> | **[[3s4l]] – MjCas3 – ''Methanocaldococcus jannaschii''<br /> | ||
**[[4qqw]] – TfCas3 – Thermobifida fusca<br /> | **[[4qqw]] – TfCas3 – ''Thermobifida fusca''<br /> | ||
**[[4qqx]] – TfCas3 + ATP <br /> | **[[4qqx]] – TfCas3 + ATP <br /> | ||
**[[4qqy]] – TfCas3 + ADP <br /> | **[[4qqy]] – TfCas3 + ADP <br /> | ||
**[[4qqz]] – TfCas3 + AMPPNP <br /> | **[[4qqz]] – TfCas3 + AMPPNP <br /> | ||
**[[4q2c]] - TteCas3 – Thermobaclum terrenum<br /> | **[[4q2c]] - TteCas3 – ''Thermobaclum terrenum''<br /> | ||
**[[4q2d]] - TteCas3 + ATP<br /> | **[[4q2d]] - TteCas3 + ATP<br /> | ||
**[[3i4h]] – Cas4 - Pyrobaculum calidifontis<br /> | **[[3i4h]] – Cas4 - ''Pyrobaculum calidifontis''<br /> | ||
**[[4qr0]], [[4qr1]] - SpCas9 (Csn1) – Streptococcus pyogenes<br /> | **[[4qr0]], [[4qr1]] - SpCas9 (Csn1) – ''Streptococcus pyogenes''<br /> | ||
**[[4ill]], [[4ilm]] – SsCas6 + RNA - Sulfolobus solfataricus<br /> | **[[4ill]], [[4ilm]] – SsCas6 + RNA - ''Sulfolobus solfataricus''<br /> | ||
**[[4ilr]], [[3zfv]] – SsCas6 <br /> | **[[4ilr]], [[3zfv]] – SsCas6 <br /> | ||
**[[3i4h]] – PfCas6 - Pyrococcus furiosus<br /> | **[[3i4h]] – PfCas6 - ''Pyrococcus furiosus''<br /> | ||
**[[3pkm]] – PfCas6 + RNA<br /> | **[[3pkm]] – PfCas6 + RNA<br /> | ||
**[[4dzd]] – EcCas6e<br /> | **[[4dzd]] – EcCas6e<br /> | ||
**[[2y8w]], [[2y8y]], [[3qrp]], [[3qrq]], [[2qrr]] – TtCas6e (Cse3) + RNA<br /> | **[[2y8w]], [[2y8y]], [[3qrp]], [[3qrq]], [[2qrr]] – TtCas6e (Cse3) + RNA<br /> | ||
**[[2xli]], [[2xlj]], [[2xlk]], [[4al7]] – PaCas6f (Csy4) + RNA | **[[2xli]], [[2xlj]], [[2xlk]], [[4al7]] – PaCas6f (Csy4) + RNA <br /> | ||
**[[4al5]], [[4al6]] - PaCas6f (Csy4) (mutant) + RNA <br /> | **[[4al5]], [[4al6]] - PaCas6f (Csy4) (mutant) + RNA <br /> | ||
**[[4cmp]], [[4cmq]] – SpCas9 (Csn1)<br /> | **[[4cmp]], [[4cmq]] – SpCas9 (Csn1)<br /> | ||
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**[[4gkf]] – PfCas10 CMR5 subunit<br /> | **[[4gkf]] – PfCas10 CMR5 subunit<br /> | ||
**[[4an8]], [[4f3e]] – TtCasA (Cse1)<br /> | **[[4an8]], [[4f3e]] – TtCasA (Cse1)<br /> | ||
**[[4h3t]] - CasA (Cse1) – Acidimicrobium ferrooxidans<br /> | **[[4h3t]] - CasA (Cse1) – ''Acidimicrobium ferrooxidans''<br /> | ||
**[[4h79]] - TfCasB (Cse2)<br /> | **[[4h79]] - TfCasB (Cse2)<br /> | ||
**[[3wa8]] - CasB (Cse2) – Meiothermus ruber<br /> | **[[3wa8]] - CasB (Cse2) – ''Meiothermus ruber''<br /> | ||
**[[4h7a]] - TtCasB (Cse2)<br /> | **[[4h7a]] - TtCasB (Cse2)<br /> | ||
**[[4tvx]] – EcCasA (Cse1) + CasE<br /> | **[[4tvx]] – EcCasA (Cse1) + CasE<br /> | ||
**[[4u7u]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA<br /> | **[[4u7u]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA<br /> | ||
**[[4qyz]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA<br /> | **[[4qyz]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA<br /> | ||
**[[3qhq]] - Csn2 – Streptococcus agalactiae<br /> | **[[3qhq]] - Csn2 – ''Streptococcus agalactiae''<br /> | ||
**[[3toc]], [[3v7f]] – SpCsn2<br /> | **[[3toc]], [[3v7f]] – SpCsn2<br /> | ||
**[[3ps0]] – SsCsa2<br /> | **[[3ps0]] – SsCsa2<br /> | ||
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*Flap ENN | *Flap ENN | ||
**[[1mc8]] - | **[[1mc8]] - PhENN (mutant) <br /> | ||
**[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br /> | **[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br /> | ||
**[[3q8k]], [[3q8l]], [[3q8m]] - hENN + DNA<br /> | **[[3q8k]], [[3q8l]], [[3q8m]] - hENN + DNA<br /> | ||
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**[[1b43]] – PfENN – ''Pyrococcus furiosus''<br /> | **[[1b43]] – PfENN – ''Pyrococcus furiosus''<br /> | ||
**[[1rxz]] - AfENN + PCNA <br /> | **[[1rxz]] - AfENN + PCNA <br /> | ||
**[[4wa8]] – ENN – ''Methanopyrus kandleri''<br /> | |||
*DNA mismatch ENN | *DNA mismatch ENN | ||
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*NHN ENN | *NHN ENN | ||
**[[2qgp]] – ENN – ''Geobacter metallireducens'' | **[[2qgp]], [[4h6d]] – ENN – ''Geobacter metallireducens'' | ||
*UV damage ENN | *UV damage ENN | ||
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**[[2j6v]], [[3bzg]], [[3c0s]] – TtENN <br /> | **[[2j6v]], [[3bzg]], [[3c0s]] – TtENN <br /> | ||
**[[3bzj]], [[3c0l]], [[3c0q]] - TtENN (mutant)<br /> | **[[3bzj]], [[3c0l]], [[3c0q]] - TtENN (mutant)<br /> | ||
**[[3tc3]] - SaENN <br /> | |||
**[[4gle]] - SaENN + DNA<br /> | **[[4gle]] - SaENN + DNA<br /> | ||
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*Crossover junction ENN | *Crossover junction ENN | ||
**[[2kpf]] - ENN – mouse | **[[2kpf]] - ENN – mouse<br /> | ||
**[[2ziw]], [[2zix]], [[2ziu]] – hENN EME1 + Mus81<br /> | |||
**[[2ziv]] – hENN EME1 (mutant) + Mus81<br /> | |||
**[[4p0p]], [[4p0q]], [[4p0r]], [[4p0s]] – hENN EME1 + Mus81 + DNA<br /> | |||
*OkrAI ENN | *OkrAI ENN | ||
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**[[1z00]], [[2a1j]] - hENN C terminal + DNA excision repair protein<br /> | **[[1z00]], [[2a1j]] - hENN C terminal + DNA excision repair protein<br /> | ||
**[[2aq0]] – hENN residues 823-905 – NMR<br /> | |||
**[[2kn7]] – hENN residues 823-905 + DNA – NMR<br /> | |||
**[[2bgw]] - ApENN + DNA <br /> | **[[2bgw]] - ApENN + DNA <br /> | ||
**[[2bhn]] - ApENN <br /> | **[[2bhn]] - ApENN <br /> | ||
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*I-DmoI ENN | *I-DmoI ENN | ||
**[[1b24]], [[2vs7]], [[2vs8]] - DmENN + DNA – ''Desulfurococcus mobilis''<br /> | **[[1b24]], [[2vs7]], [[2vs8]], [[4un7]], [[4un8]], [[4un9]], [[4una]], [[4unb]], [[4unc]], [[4ut0]], [[4d6n]], [[4d6o]] - DmENN + DNA – ''Desulfurococcus mobilis''<br /> | ||
**[[1mow]] – DmENN/CrENN + DNA | **[[1mow]] – DmENN/CrENN + DNA | ||
Revision as of 13:59, 29 March 2015
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
3D structures of endonuclease3D structures of endonuclease
Updated on 29-March-2015