Endonuclease - Revision history

Alexander Berchansky at 09:36, 5 December 2019

Alexander Berchansky — Thu, 05 Dec 2019 09:36:37 GMT

←Older revision		Revision as of 09:36, 5 December 2019
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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<ref>PMID:12483517</ref>.<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. Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN<ref>PMID:12483517</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 />		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]]
	*CRISPR type I-A (Cascade) - see [[CRISPR subtype I-A]]		*CRISPR type I-A (Cascade) - see [[CRISPR subtype I-A]]
	*CRISPR type I-B (Cascade) - see [[CRISPR subtype I-B]]		*CRISPR type I-B (Cascade) - see [[CRISPR subtype I-B]]

Alexander Berchansky at 09:35, 5 December 2019

Alexander Berchansky — Thu, 05 Dec 2019 09:35:42 GMT

←Older revision		Revision as of 09:35, 5 December 2019
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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<ref>PMID:12483517</ref>.<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. Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN<ref>PMID:12483517</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 />		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~~]]~~<br />~~	+	*CRISPR type I-A (Cascade) - see [[CRISPR subtype I-A]]
-	* [[CRISPR-~~Cas Part II~~]]~~<br />~~	+	*CRISPR type I-B (Cascade) - see [[CRISPR subtype I-B]]
-	* [[Cas9]]<br />	+	*CRISPR type I-C (Cascade) - see [[CRISPR subtype I-C]]
-	* [[CRISPR-~~Cas9~~]]~~<br />~~	+	*CRISPR type I-E (Cascade) - see [[CRISPR type I-E (Cascade)\|CRISPR subtype I-E]]
-	* [[CRISPR type I-E (Cascade)~~]]<br />~~	+	*(CRISPR type I-F (Csy1, Csy2, Csy3) - see [[CRISPR subtype I-F]]
-	* [[CRISPR type ~~V]]<br />~~	+	*CRISPR type III-A (Csm complex) - see [[CRISPR subtype III-A (Csm complex)]]
-	* [[CRISPR subtype I-~~A]]<br />~~	+	*CRISPR type II-A - see [[CRISPR-Cas9]]
-	* [[CRISPR subtype I-B]]~~<br />~~	+	*CRISPR type V (Cpf1, C2c1, C2c3) - see [[CRISPR type V]]
-	* [[CRISPR ~~subtype~~ I-~~C]]<br />~~	+	*CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
-	* [[CRISPR subtype I-F]]~~<br />~~	+
-	* [[CRISPR ~~subtype~~ III-A (Csm complex)~~]]<br />~~	+
-	* [[CRISPR subtype III-B (~~Cmr~~ complex)]]~~<br />~~	+
-	* [[CRISPR ~~subtype~~ V (Cpf1)]]~~<br />~~	+
-	* [[CRISPR type VI]]~~<br />~~	+
-		+

	'''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 />		'''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 />

Alexander Berchansky at 16:12, 4 December 2019

Alexander Berchansky — Wed, 04 Dec 2019 16:12:30 GMT

←Older revision		Revision as of 16:12, 4 December 2019
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	[[Category:Topic Page]]		[[Category:Topic Page]]
		+	[[Category:Endonuclease]]

Alexander Berchansky at 16:10, 4 December 2019

Alexander Berchansky — Wed, 04 Dec 2019 16:10:27 GMT

←Older revision		Revision as of 16:10, 4 December 2019
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	* [[CRISPR subtype V (Cpf1)]]<br />		* [[CRISPR subtype V (Cpf1)]]<br />
	* [[CRISPR type VI]]<br />		* [[CRISPR type VI]]<br />
-	* [[CRISPR type V (Cpf1)]]<br />

Michal Harel at 07:25, 20 June 2019

Michal Harel — Thu, 20 Jun 2019 07:25:51 GMT

(Difference between revisions)

Michal Harel at 11:08, 19 June 2019

Michal Harel — Wed, 19 Jun 2019 11:08:19 GMT

(Difference between revisions)

Michal Harel at 11:39, 8 January 2019

Michal Harel — Tue, 08 Jan 2019 11:39:53 GMT

←Older revision		Revision as of 11:39, 8 January 2019
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	* [[CRISPR subtype III-B (Cmr complex)]]<br />		* [[CRISPR subtype III-B (Cmr complex)]]<br />
	* [[CRISPR subtype V (Cpf1)]]<br />		* [[CRISPR subtype V (Cpf1)]]<br />
-	* [[CRISPR ~~subtype~~ VI]]<br />	+	* [[CRISPR type VI]]<br />
	* [[CRISPR type V (Cpf1)]]<br />		* [[CRISPR type V (Cpf1)]]<br />

Michal Harel at 11:39, 8 January 2019

Michal Harel — Tue, 08 Jan 2019 11:39:23 GMT

←Older revision		Revision as of 11:39, 8 January 2019
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	* [[CRISPR subtype III-A (Csm complex)]]<br />		* [[CRISPR subtype III-A (Csm complex)]]<br />
	* [[CRISPR subtype III-B (Cmr complex)]]<br />		* [[CRISPR subtype III-B (Cmr complex)]]<br />
		+	* [[CRISPR subtype V (Cpf1)]]<br />
		+	* [[CRISPR subtype VI]]<br />
		+	* [[CRISPR type V (Cpf1)]]<br />
		+

	'''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 />		'''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 />

Michal Harel at 08:09, 16 May 2018

Michal Harel — Wed, 16 May 2018 08:09:48 GMT

←Older revision		Revision as of 08:09, 16 May 2018
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	**[[1bix]] - hENN – human<br />		**[[1bix]] - hENN – human<br />
		+	**[[5um9]], [[5kse]], [[5k97]] – hENN (mutant) + DNA <br />
	**[[1cfr]] – ENN – ''Citrobacter freundii''<br />		**[[1cfr]] – ENN – ''Citrobacter freundii''<br />
	**[[1af5]] - CrENN – ''Chlamydomonas reinhardtii''<br />		**[[1af5]] - CrENN – ''Chlamydomonas reinhardtii''<br />
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	**[[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 />
	**[[4ilr]], [[3zfv]] – SsCas6 <br />		**[[4ilr]], [[3zfv]] – SsCas6 <br />
	**[[3i4h]] – PfCas6 - ''Pyrococcus furiosus''<br />		**[[3i4h]] – PfCas6 - ''Pyrococcus furiosus''<br />
	**[[4dzd]] – EcCas6e<br />		**[[4dzd]] – EcCas6e<br />
		+	**[[4qr0]], [[4qr1]] - SpCas9 (Csn1) – ''Streptococcus pyogenes''<br />
	**[[4qr0]], [[4qr1]], [[4cmp]], [[4cmq]] - SpCas9 <br />		**[[4qr0]], [[4qr1]], [[4cmp]], [[4cmq]] - SpCas9 <br />
	**[[4ogc]], [[4oge]] – Cas9 II-C – ''Actinomyces naeslundii''<br />		**[[4ogc]], [[4oge]] – Cas9 II-C – ''Actinomyces naeslundii''<br />
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	*Cas ENN complex with RNA and DNA		*Cas ENN complex with RNA and DNA

-	**[[5dlj]], [[5dqt]], [[5dqu]], [[5dqz]], [[5ds4]], [[5ds5]], [[5ds6]] – EcCas1 + EcCas2 + DNA<br />	+	**[[5dlj]], [[5dqt]], [[5dqu]], [[5dqz]], [[5ds4]], [[5ds5]], [[5ds6]], [[5vvl]], [[5vvk]], [[5vvj]] – EcCas1 + EcCas2 + DNA<br />
		+	**[[5wfe]] – EcCas1 + EcCas2 + IHF-a + IHF-b + DNA<br />
		+	**[[5xvp]], [[5xvo]], [[5xvn]] – Cas1 + Cas2 + DNA – ''Enterococcus faecalis''<br />
	**[[4ill]], [[4ilm]] – SsCas6 + RNA - ''Sulfolobus solfataricus''<br />		**[[4ill]], [[4ilm]] – SsCas6 + RNA - ''Sulfolobus solfataricus''<br />
	**[[5uz9]] – PaCsa5f + Cas7f + Cas8f + anti-crispr protein + RNA<br />		**[[5uz9]] – PaCsa5f + Cas7f + Cas8f + anti-crispr protein + RNA<br />
		+	**[[6b48]], [[6b47]], [[6b46]], [[6b45]] – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + RNA<br />
		+	**[[6b44]] – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + DNA<br />
	**[[3pkm]] – PfCas6 + RNA<br />		**[[3pkm]] – PfCas6 + RNA<br />
	**[[2y8w]], [[2y8y]], [[3qrp]], [[3qrq]], [[2qrr]] – TtCas6e (Cse3) + RNA<br />		**[[2y8w]], [[2y8y]], [[3qrp]], [[3qrq]], [[2qrr]] – TtCas6e (Cse3) + RNA<br />
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	**[[4zt9]] - SpCas9 (mutant) + RNA <br />		**[[4zt9]] - SpCas9 (mutant) + RNA <br />
	**[[5f9r]] - SpCas9 + RNA + DNA<br />		**[[5f9r]] - SpCas9 + RNA + DNA<br />
-	**[[4oo8]], [[4un3]], [[4un4]], [[4un5]], [[5fw1]], [[5fw2]], [[5fw3]], [[5fq5]], [[5b2r]], [[5b2s]], [[5b2t]] - SpCas9 (Csn1) (mutant) + RNA + DNA<br />	+	**[[4oo8]], [[4un3]], [[4un4]], [[4un5]], [[5fw1]], [[5fw2]], [[5fw3]], [[5fq5]], [[5b2r]], [[5b2s]], [[5b2t]], [[5y36]] - SpCas9 (Csn1) (mutant) + RNA + DNA<br />
	**[[5x2h]], [[5x2g]] – Cas9 + RNA + DNA – ''Campylobacter jejuni''<br />		**[[5x2h]], [[5x2g]] – Cas9 + RNA + DNA – ''Campylobacter jejuni''<br />
	**[[5czz]] - SaCas9 (Csn1) + RNA + DNA - ''Staphylococcus aureus''<br />		**[[5czz]] - SaCas9 (Csn1) + RNA + DNA - ''Staphylococcus aureus''<br />
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	**[[5b2o]], [[5b2p]], [[5b2q]] - FtCas9 (mutant) + RNA + DNA – ''Francisella tularensis''<br />		**[[5b2o]], [[5b2p]], [[5b2q]] - FtCas9 (mutant) + RNA + DNA – ''Francisella tularensis''<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]], [[5h9f]], [[5h9e]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA<br />
	**[[5wqe]] – AaCas C2C1 + RNA – ''Alicyclobacillus acidoterrestris''<br />		**[[5wqe]] – AaCas C2C1 + RNA – ''Alicyclobacillus acidoterrestris''<br />
	**[[5u34]] – AaCas C2C1 (mutant) + RNA <br />		**[[5u34]] – AaCas C2C1 (mutant) + RNA <br />
	**[[5u30]], [[5u31]], [[5u33]] – AaCas C2C1 + RNA + DNA<br />		**[[5u30]], [[5u31]], [[5u33]] – AaCas C2C1 + RNA + DNA<br />
-	**[[5kk5]], [[5b43]] – ~~Cas~~ Cpf1 + RNA + DNA – ''Acidaminococcus''<br />	+	**[[5kk5]], [[5b43]] – AcCas Cpf1 + RNA + DNA – ''Acidaminococcus''<br />
		+	**[[5xh7]], [[5xh6]] – AcCas Cpf1 (mutant) + RNA + DNA <br />
		+	**[[5ng6]] – FtCas Cpf1 + RNA <br />
		+	**[[5nfv]], [[5mga]] – FtCas Cpf1 + RNA + DNA <br />

	*EcoKI ENN		*EcoKI ENN
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	**[[1fok]] – PoENN + DNA – ''Planomicrobium okeanokoites''<br />		**[[1fok]] – PoENN + DNA – ''Planomicrobium okeanokoites''<br />
	**[[2fok]] – PoENN		**[[2fok]] – PoENN
		+
		+	*LAGLIDAD ENN
		+
		+	**[[4z1x]] – fyENN + DNA – fission yeast<br />
		+	**[[5e5o]] – ENN + DNA – ''Sordaria macropora''<br />

	*PvuII ENN		*PvuII ENN
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	**[[1odg]] - EcENN + DNA<br />		**[[1odg]] - EcENN + DNA<br />
	**[[1h7u]] – hENN<br />		**[[1h7u]] – hENN<br />
		+	**[[5u5r]] – hENN + importin<br />

	*Vvn ENN		*Vvn ENN
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	**[[1ouo]] – VvENN – ''Vibrio vulnificus''<br />		**[[1ouo]] – VvENN – ''Vibrio vulnificus''<br />
	**[[1oup]], [[2ivk]] - VvENN + DNA		**[[1oup]], [[2ivk]] - VvENN + DNA
		+
		+	*Structure-specific ENN
		+
		+	**[[4xm5]] – CgENN SLX1 subunit – ''Candida glabrata''<br />
		+	**[[4xlg]] – CgENN SLX1 (mutant)+SLX4 subunits<br />
		+	**[[4zdt]] – fyENN SLX1+SLX4 subunits<br />
		+	**[[4zou]] – hENN SLX4 subunit BTB domain<br />
		+	**[[4uyi]] – hENN SLX4 subunit BTB domain (mutant)<br />

	*BfiI ENN		*BfiI ENN
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	**[[4h6d]] – ENN – ''Geobacter metallireducens''<br />		**[[4h6d]] – ENN – ''Geobacter metallireducens''<br />
	**[[5h0o]], [[5h0m]] – ENN – Geobacillus virus E2<br />		**[[5h0o]], [[5h0m]] – ENN – Geobacillus virus E2<br />
		+	**[[5cxr]] – ENN + pyrazole derivative – Influenza virus <br />

	*UV damage ENN		*UV damage ENN
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	**[[5uct]], [[5cca]] - MtENN – ''Mycobacterium tuberculosis''<br />		**[[5uct]], [[5cca]] - MtENN – ''Mycobacterium tuberculosis''<br />
		+
		+	*Vapc ENN
		+
		+	**[[5wzf]], [[5wz4]] – MtENN-20 <br />
		+	**[[5ed0]], [[5ecy]] – SfENN – ''Shigella flexneri''<br />
		+	**[[5ecy]], [[5ecw]], [[5ecd]] – SfENN (mutant)<br />

	*Muts2 ENN		*Muts2 ENN
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	**[[5gkc]], [[4qn0]] – CeENN (mutant) – ''Caenorhabdfitis elegans''<br />		**[[5gkc]], [[4qn0]] – CeENN (mutant) – ''Caenorhabdfitis elegans''<br />
	**[[5gkp]] – CeENN (mutant) + DNA <br />		**[[5gkp]] – CeENN (mutant) + DNA <br />
		+
		+	*ENN S
		+
		+	**[[5ybb]] – ENN + R-M system + DNA – ''Caldanaerobacter subterraneus'' <br />

	*ENN V		*ENN V
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	**[[5aoy]] – mENN (mutant) <br />		**[[5aoy]] – mENN (mutant) <br />
	**[[4xpu]] – EcENN <br />		**[[4xpu]] – EcENN <br />
		+
		+	*Apurinic-apyrimidinic ENN
		+
		+	**[[5cfg]] – hENN <br />
		+	**[[5dff]], [[5dfh]], [[5dfi]], [[5dfj]], [[5dg0]], [[5wn5]], [[5wn4]], [[5wn3]], [[5wn2]], [[5wn1]], [[5wn0]] – hENN + DNA<br />

	*'''Intron-encoded endonuclease'''		*'''Intron-encoded endonuclease'''
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	*I-DmoI ENN		*I-DmoI ENN

-	**[[1b24]], [[2vs7]], [[2vs8]], [[4un7]], [[4un8]], [[4un9]], [[4una]], [[4unb]], [[4unc]], [[4ut0]], [[4d6n]], [[4d6o]], [[5ak9]], [[5a0w]] - DmENN + DNA – ''Desulfurococcus mobilis''<br />	+	**[[1b24]], [[2vs7]], [[2vs8]], [[4un7]], [[4un8]], [[4un9]], [[4una]], [[4unb]], [[4unc]], [[4ut0]], [[4d6n]], [[4d6o]], [[5ak9]], [[5a0w]], [[5o6g]], [[5o6i]] - DmENN + DNA – ''Desulfurococcus mobilis''<br />
	**[[5akf]], [[5akm]], [[5akn]] - DmENN (mutant) + DNA <br />		**[[5akf]], [[5akm]], [[5akn]] - DmENN (mutant) + DNA <br />
	**[[1mow]] – DmENN/CrENN + DNA		**[[1mow]] – DmENN/CrENN + DNA

Michal Harel at 10:59, 2 January 2018

Michal Harel — Tue, 02 Jan 2018 10:59:30 GMT

←Older revision		Revision as of 10:59, 2 January 2018
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	* [[CRISPR type I-E (Cascade)]]<br />		* [[CRISPR type I-E (Cascade)]]<br />
	* [[CRISPR type V]]<br />		* [[CRISPR type V]]<br />
		+	* [[CRISPR subtype I-A]]<br />
	* [[CRISPR subtype I-B]]<br />		* [[CRISPR subtype I-B]]<br />
	* [[CRISPR subtype I-C]]<br />		* [[CRISPR subtype I-C]]<br />