Endonuclease

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Revision as of 11:39, 8 January 2019 (edit) Michal Harel (Talk | contribs) ← Previous diff		Revision as of 11:08, 19 June 2019 (edit) (undo) Michal Harel (Talk | contribs) Next diff →
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	<scene name='49/496318/Cv/2'>DNA-protein binding</scene> (PDB code [[1rva]]).		<scene name='49/496318/Cv/2'>DNA-protein binding</scene> (PDB code [[1rva]]).
		+
		+	==3D structures of endonuclease==
		+	[[Endonuclease 3D structures]]
		+
	</StructureSection>		</StructureSection>
	==3D structures of endonuclease==		==3D structures of endonuclease==
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	*ENN-V		*ENN-V
		+	**[[4nsp]] – hENN catalytic domain<br />
	**[[1eni]], [[1enj]], [[1enk]], [[2end]] - T4ENN <br />		**[[1eni]], [[1enj]], [[1enk]], [[2end]] - T4ENN <br />
	**[[1vas]] - T4ENN + DNA<br />		**[[1vas]] - T4ENN + DNA<br />
Line 89:		Line 94:
	**[[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
Line 99:		Line 103:
	*ENN-VIII		*ENN-VIII
		+	**[[1tdh]] – hENN <br />
		+	**[[1bix]] – hENN + DNA<br />
	**[[1q39]], [[1q39]] - EcENN <br />		**[[1q39]], [[1q39]] - EcENN <br />
	**[[1q3b]], [[1q3c]] - EcENN (mutant) <br />		**[[1q3b]], [[1q3c]] - EcENN (mutant) <br />
-	**[[1tdh]] – hENN <br />
-	**[[1bix]] – hENN + DNA<br />
	**[[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]], [[6fbu]] - EcENN (mutant) + DNA
	*AP ENN		*AP ENN
Line 124:		Line 128:
	**[[4mak]] – EcCas2<br />		**[[4mak]] – EcCas2<br />
	**[[4p6i]], [[4qdl]] – EcCas1 + EcCas2<br />		**[[4p6i]], [[4qdl]] – EcCas1 + EcCas2<br />
		+	**[[6qy3]] – GsCas1 + EcCas2 + Csn2 – Cryo EM<br />
	**[[3s4l]] – MjCas3 – ''Methanocaldococcus jannaschii''<br />		**[[3s4l]] – MjCas3 – ''Methanocaldococcus jannaschii''<br />
	**[[4qqw]] – TfCas3 – ''Thermobifida fusca''<br />		**[[4qqw]] – TfCas3 – ''Thermobifida fusca''<br />
Line 159:		Line 164:
	**[[5wfe]] – EcCas1 + EcCas2 + IHF-a + IHF-b + DNA<br />		**[[5wfe]] – EcCas1 + EcCas2 + IHF-a + IHF-b + DNA<br />
	**[[5xvp]], [[5xvo]], [[5xvn]] – Cas1 + Cas2 + DNA – ''Enterococcus faecalis''<br />		**[[5xvp]], [[5xvo]], [[5xvn]] – Cas1 + Cas2 + DNA – ''Enterococcus faecalis''<br />
		+	**[[6qxt]], [[6qxf]] – GsCas1 (mutant) + EcCas2 + Csn2 + DNA – Cryo EM<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 - Cryo EM<br />
-	**[[6b48]], [[6b47]], [[6b46]], [[6b45]] – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + RNA<br />	+	**[[6b48]], [[6b47]], [[6b46]], [[6b45]] – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + RNA - Cryo EM<br />
-	**[[6b44]] – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + DNA<br />	+	**[[6b44]] – PaCsa6 + Csy1 + Csy2 + Csy3 + anti-crispr protein + DNA - Cryo EM<br />
		+	**[[6ne0]] – PaCsa6/Csy4 + Csy1 + Csy2 + Csy3 + DNA + RNA – Cryo EM<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]], [[5y36]] - SpCas9 (Csn1) (mutant) + RNA + DNA<br />	+	**[[4oo8]], [[4un3]], [[4un4]], [[4un5]], [[5fw1]], [[5fw2]], [[5fw3]], [[5fq5]], [[5b2r]], [[5b2s]], [[5b2t]], [[5y36]], [[6ia6]] - SpCas9 (Csn1) (mutant) + RNA + DNA<br />
		+	**[[5xbl]] - SpCas9 + associated protein + RNA <br />
		+	**[[6ifo]] - SpCas9 + AcriiA2 + RNA <br />
		+	**[[5vw1]] - SpCas9 + AcriiA4 + RNA <br />
		+	**[[6mcc]], [[5vzl]], [[6mcb]] - SpCas9 + AcriiA4 + RNA – Cryo EM<br />
		+	**[[5vgb]] - NmCas9 + AcriiC1 – Neisseria meningitidis <br />
		+	**[[6jdx]], [[6jdj], [[6j9m]]] - NmCas9 + AcriiC2 <br />
		+	**[[6j9n]] - NmCas9 + AcriiC3 <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 />
	**[[5axw]] - SaCas9 (Csn1) (mutant) + RNA + DNA <br />		**[[5axw]] - SaCas9 (Csn1) (mutant) + RNA + DNA <br />
		+	**[[6joo]] - Cas9 + RNA + DNA – Corynebacterium diphtheriae<br />
	**[[5b2o]], [[5b2p]], [[5b2q]] - FtCas9 (mutant) + RNA + DNA – ''Francisella tularensis''<br />		**[[5b2o]], [[5b2p]], [[5b2q]] - FtCas9 (mutant) + RNA + DNA – ''Francisella tularensis''<br />
		+	**[[6i1l]], [[6i1k]], [[6gtg]], [[6gtf]], [[6gte]], [[6gtd]], [[6gtc]] – FtCas12a (mutant) + RNA + DNA <br />
	**[[4u7u]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA<br />		**[[4u7u]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA<br />
	**[[4qyz]], [[5h9f]], [[5h9e]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA<br />		**[[4qyz]], [[5h9f]], [[5h9e]] – EcCasA (Cse1) + CasB + CasC + CasD + CasE + RNA + DNA<br />
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	**[[1bam]] – BaENN – ''Bacillus amyloliquefaciens''<br />		**[[1bam]] – BaENN – ''Bacillus amyloliquefaciens''<br />
	**[[1bhm]], [[3bam]], [[2bam]], [[1esg]] - BaENN + DNA		**[[1bhm]], [[3bam]], [[2bam]], [[1esg]] - BaENN + DNA
		+
		+	*Bbvci ENN
		+
		+	**[[6mag]], [[6m9g]], [[6eg7]] – BbENN subunit 2 – ''Brevibacillus brevis''<br />
		+	**[[6maf]] – BbENN subunits 1+2 <br />
	*FokI ENN		*FokI ENN
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	*tRNA-splicing ENN		*tRNA-splicing ENN
		+	**[[2gw6]] – hENN subunit sen15 – NMR<br />
	**[[1a79]], [[1a76]], [[1a77]] - MjENN – ''Methanocaldococcus jannaschii''<br />		**[[1a79]], [[1a76]], [[1a77]] - MjENN – ''Methanocaldococcus jannaschii''<br />
	**[[2cv8]] - ENN – ''Sulfolobus tokodaii''<br />		**[[2cv8]] - ENN – ''Sulfolobus tokodaii''<br />
-	**[[2gw6]] – hENN subunit sen15 – NMR<br />
	**[[2gjw]] - AfENN + RNA –'' Archaeoglobus fulgidus''<br />		**[[2gjw]] - AfENN + RNA –'' Archaeoglobus fulgidus''<br />
	**[[1r0v]], [[1r11]] – AfENN		**[[1r0v]], [[1r11]] – AfENN
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	*Flap ENN		*Flap ENN
-	**[[1mc8]] - PhENN (mutant) <br />	+	**[[5zod]] - hENN <br />
-	**[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br />	+
	**[[3q8k]], [[3q8l]], [[3q8m]] - hENN + DNA<br />		**[[3q8k]], [[3q8l]], [[3q8m]] - hENN + DNA<br />
		+	**[[5zog]], [[5zof]], [[5zoe]] - hENN (mutant) + DNA<br />
	**[[5fv7]] - hENN + inhibitor<br />		**[[5fv7]] - hENN + inhibitor<br />
-	**[[1rxv]], [[1rxw]] - AfENN + DNA<br />
	**[[1ul1]] - hENN + PCNA <br />		**[[1ul1]] - hENN + PCNA <br />
		+	**[[1mc8]] - PhENN (mutant) <br />
		+	**[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br />
		+	**[[1rxv]], [[1rxw]] - AfENN + DNA<br />
	**[[2izo]] - SsENN + PCNA – ''Sulfolobus solfataricus''<br />		**[[2izo]] - SsENN + PCNA – ''Sulfolobus solfataricus''<br />
	**[[1a76]], [[1a77]] - MjENN <br />		**[[1a76]], [[1a77]] - MjENN <br />
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	*DNA mismatch ENN		*DNA mismatch ENN
-	**[[1odg]] - EcENN + DNA<br />
	**[[1h7u]] – hENN<br />		**[[1h7u]] – hENN<br />
		+	**[[6mfq]] – hENN Pms2<br />
	**[[5u5r]] – hENN + importin<br />		**[[5u5r]] – hENN + importin<br />
		+	**[[1odg]] - EcENN + DNA<br />
	*Vvn ENN		*Vvn ENN
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	*Structure-specific ENN		*Structure-specific ENN
		+	**[[4zou]] – hENN SLX4 subunit BTB domain<br />
		+	**[[4uyi]] – hENN SLX4 subunit BTB domain (mutant)<br />
	**[[4xm5]] – CgENN SLX1 subunit – ''Candida glabrata''<br />		**[[4xm5]] – CgENN SLX1 subunit – ''Candida glabrata''<br />
	**[[4xlg]] – CgENN SLX1 (mutant)+SLX4 subunits<br />		**[[4xlg]] – CgENN SLX1 (mutant)+SLX4 subunits<br />
	**[[4zdt]] – fyENN SLX1+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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	**[[5h0o]], [[5h0m]] – ENN – Geobacillus virus E2<br />		**[[5h0o]], [[5h0m]] – ENN – Geobacillus virus E2<br />
	**[[5cxr]] – ENN + pyrazole derivative – Influenza virus <br />		**[[5cxr]] – ENN + pyrazole derivative – Influenza virus <br />
		+	**[[6j9l]]] - NmENN + AcriiC2 <br />
	*UV damage ENN		*UV damage ENN
Line 405:		Line 430:
	*Crossover junction ENN		*Crossover junction ENN
-	**[[2kpf]] - mENN – mouse<br />
	**[[2ziw]], [[2zix]], [[2ziu]] – hENN EME1 + Mus81<br />		**[[2ziw]], [[2zix]], [[2ziu]] – hENN EME1 + Mus81<br />
	**[[2ziv]] – hENN EME1 (mutant) + Mus81<br />		**[[2ziv]] – hENN EME1 (mutant) + Mus81<br />
	**[[4p0p]], [[4p0q]], [[4p0r]], [[4p0s]] – hENN EME1 + Mus81 + DNA<br />		**[[4p0p]], [[4p0q]], [[4p0r]], [[4p0s]] – hENN EME1 + Mus81 + DNA<br />
		+	**[[2kpf]] - mENN – mouse<br />
	*OkrAI ENN		*OkrAI ENN
Line 465:		Line 490:
	*Apurinic-apyrimidinic ENN		*Apurinic-apyrimidinic ENN
-	**[[5cfg]] – hENN <br />	+	**[[5cfg]], [[6mk3]], [[6mkk]], [[6mkm]], [[6mko]] – hENN <br />
-	**[[5dff]], [[5dfh]], [[5dfi]], [[5dfj]], [[5dg0]], [[5wn5]], [[5wn4]], [[5wn3]], [[5wn2]], [[5wn1]], [[5wn0]] – hENN + DNA<br />	+	**[[5dff]], [[5dfh]], [[5dfi]], [[5dfj]], [[5dg0]], [[5wn5]], [[5wn4]], [[5wn3]], [[5wn2]], [[5wn1]], [[5wn0]], [[6bos]] – hENN + DNA<br />
		+	**[[6bot]], [[6boq]], [[6bor]], [[6bou]], [[6bov]], [[6bow]] – hENN (mutant) + DNA<br />
	*'''Intron-encoded endonuclease'''		*'''Intron-encoded endonuclease'''
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	**[[1bp7]], [[1g9y]], [[1g9z]], [[1n3e]], [[1n3f]], [[2vbj]], [[2vbl]], [[2vbn]], [[2vbo]], [[4aqu]], [[4aqx]] - CrENN + DNA <br />		**[[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 />	+	**[[1u0c]], [[1u0d]], [[1t9i]], [[1t9j]], [[2i3p]], [[2i3q]], [[4aab]], [[4aad]], [[4aae]], [[4aaf]], [[4aag]], [[6fb9]], [[6fb8]], [[6fb7]], [[6fb6]], [[6fb5]], [[6fb2]], [[6fb1]], [[6fb0]] - CrENN (mutant) + DNA<br />
	**[[2o7m]] - CrENN		**[[2o7m]] - CrENN
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	*I-tRNA ENN		*I-tRNA ENN
-	**[[4fz2]] – MoENN – ''Candidatus micrarchaeum''<br />	+	**[[4fz2]] – ENN – ''Candidatus micrarchaeum''<br />
	*I-Cvui ENN		*I-Cvui ENN

---

Revision as of 11:08, 19 June 2019

spinqualitylabelsall models E. coli EcoRV endonuclease dimer (magenta, green) complex with DNA, (PDB code 1rva) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image Contents 1 Function 2 Relevance 3 Disease 4 Structural highlights 5 3D structures of endonuclease Function 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[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 CRISPR-Cas CRISPR-Cas Part II Cas9 CRISPR-Cas9 CRISPR type I-E (Cascade) CRISPR type V CRISPR subtype I-A CRISPR subtype I-B CRISPR subtype I-C CRISPR subtype I-F CRISPR subtype III-A (Csm complex) CRISPR subtype III-B (Cmr complex) CRISPR subtype V (Cpf1) CRISPR type VI CRISPR type V (Cpf1) 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]. See also Apurinic-Apyrimidinic Endonuclease-1 For EcoRV ENN see Student Projects for UMass Chemistry 423 Spring 2012-3 For NEI ENN see DNA repair protein human endonuclease VIII-like 1 (NEIL1). Relevance Sickle cell anemia is caused by mutation in the recognition site of MstII ENN. Disease Mutation in UV-specific ENN causes Xeroderma pigmentosa. Mutations in tRNA-splicing ENN cause pontocerebellar hypoplasia. Structural highlights (PDB code 1rva). 3D structures of endonuclease Endonuclease 3D structures

3D structures of endonuclease

Updated on 19-June-2019 {{#tree:id=OrganizedByTopic|openlevels=0|

• ENN-I

• • 1bix - hENN – human
    
  • 5um9, 5kse, 5k97 – hENN (mutant) + DNA
    
  • 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
    
  • 4unf – DrENN-1 – Deinococcus radiodurans
    
  • 4uob – DrENN-3
    

• 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

• • 4nsp – hENN catalytic domain
    
  • 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
    

• ENN-VII

• • 1en7, 1e7d - T4ENN
    
  • 1e7l - T4ENN (mutant)
    
  • 2qnc, 2qnf - T4ENN (mutant) + DNA

• ENN-VIII

• • 1tdh – hENN
    
  • 1bix – hENN + DNA
    
  • 1q39, 1q39 - EcENN
    
  • 1q3b, 1q3c - EcENN (mutant)
    
  • 1k3x, 2ea0, 1k3w, 1k3x, 2ea0, 2opf, 2oq4 - EcENN + DNA
    
  • 2opf, 2oq4, 6fbu - 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
    
  • 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
    

• 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
    

• 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, 5hlk - EcENN + DNA
    
  • 1bss, 1b96, 1b97, 1stx, 1suz, 1sx5, 1sx8, 2ge5 - EcENN (mutant) + DNA
    
  • 5f8a - EcENN + DNA + Lu
    

• BamHI ENN

• • 1bam – BaENN – Bacillus amyloliquefaciens
    
  • 1bhm, 3bam, 2bam, 1esg - BaENN + DNA

• Bbvci ENN

• • 6mag, 6m9g, 6eg7 – BbENN subunit 2 – Brevibacillus brevis
    
  • 6maf – BbENN subunits 1+2
    

• FokI ENN

• • 1fok – PoENN + DNA – Planomicrobium okeanokoites
    
  • 2fok – PoENN

• LAGLIDAD ENN

• • 4z1x – fyENN + DNA – fission yeast
    
  • 5e5o – ENN + DNA – Sordaria macropora
    

• PvuII ENN

• • 3pvi - PvENN (mutant) + DNA – Proteus vulgaris
    
  • 1k0z, 1h56, 3ksk - PvENN
    
  • 1ni0 - PvENN (mutant)
    
  • 2pvi, 1eyu, 1f0o - PvENN + DNA

• 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

• 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

• • 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
    

• DNA mismatch ENN

• • 1h7u – hENN
    
  • 6mfq – hENN Pms2
    
  • 5u5r – hENN + importin
    
  • 1odg - EcENN + DNA
    

• Vvn ENN

• • 1ouo – VvENN – Vibrio vulnificus
    
  • 1oup, 2ivk - VvENN + DNA

• Structure-specific ENN

• • 4zou – hENN SLX4 subunit BTB domain
    
  • 4uyi – hENN SLX4 subunit BTB domain (mutant)
    
  • 4xm5 – CgENN SLX1 subunit – Candida glabrata
    
  • 4xlg – CgENN SLX1 (mutant)+SLX4 subunits
    
  • 4zdt – fyENN SLX1+SLX4 subunits
    

• 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

• HNH ENN

• • 4h6d – ENN – Geobacter metallireducens
    
  • 5h0o, 5h0m – ENN – Geobacillus virus E2
    
  • 5cxr – ENN + pyrazole derivative – Influenza virus
    
  • 6j9l] - NmENN + AcriiC2
    

• 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 – BpENN – Bacillus pumilus
    
  • 5hnf, 5hnh, 5hlt – BpENN + DNA
    

• Sau3AI ENN

• • 2reu – SaENN C terminal – Staphylococcus aureus
    
  • 4pxg – SaENN (mutant)
    

• HpyI ENN

• • 3fc3, 3gox – HpENN99 + DNA – Helicobacter pylori
    
  • 3or3 – HpENN88 + DNA

• PacI ENN

• • 3ldy, 3m7k - PaENN + DNA – Psdeudomonas alcaligenes

• Crossover junction ENN

• • 2ziw, 2zix, 2ziu – hENN EME1 + Mus81
    
  • 2ziv – hENN EME1 (mutant) + Mus81
    
  • 4p0p, 4p0q, 4p0r, 4p0s – hENN EME1 + Mus81 + DNA
    
  • 2kpf - mENN – mouse
    

• 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
    

• Mazf3 ENN

• • 5uct, 5cca - MtENN – Mycobacterium tuberculosis
    

• Vapc ENN

• • 5wzf, 5wz4 – MtENN-20
    
  • 5ed0, 5ecy – SfENN – Shigella flexneri
    
  • 5ecy, 5ecw, 5ecd – SfENN (mutant)
    

• Muts2 ENN

• • 4och, 4od6 - DrENN SMR domain
    

• Endoms ENN

• • 5gkj – TkENN (mutant) – Thermococcus kodakarensis
    
  • 5gke, 5gkf, 5gkg, 5gkh, 5gki – TkENN (mutant) + DNA
    

• ENN G

• • 5gkc, 4qn0 – CeENN (mutant) – Caenorhabdfitis elegans
    
  • 5gkp – CeENN (mutant) + DNA
    

• ENN S

• • 5ybb – ENN + R-M system + DNA – Caldanaerobacter subterraneus
    

• ENN V

• • 5aoy – mENN (mutant)
    
  • 4xpu – EcENN
    

• Apurinic-apyrimidinic ENN

• • 5cfg, 6mk3, 6mkk, 6mkm, 6mko – hENN
    
  • 5dff, 5dfh, 5dfi, 5dfj, 5dg0, 5wn5, 5wn4, 5wn3, 5wn2, 5wn1, 5wn0, 6bos – hENN + DNA
    
  • 6bot, 6boq, 6bor, 6bou, 6bov, 6bow – hENN (mutant) + DNA
    

• 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, 6fb9, 6fb8, 6fb7, 6fb6, 6fb5, 6fb2, 6fb1, 6fb0 - 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, 5ak9, 5a0w, 5o6g, 5o6i - DmENN + DNA – Desulfurococcus mobilis
    
  • 5akf, 5akm, 5akn - DmENN (mutant) + DNA
    
  • 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, 5a0m - yENN + DNA
    
  • 3oor - yENN (mutant) + DNA

• I-PkoII ENN

• • 2cw7, 2cw8 – TkENN

• 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)
    
  • 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 – ENN – Candidatus micrarchaeum
    

• I-Cvui ENN

• • 5a78, 5a72, 5a74, 5a77, 5a78 – ENN + DNA – Chlorella vulgaris
    

}}

References

1. ↑ 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
2. ↑ 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
3. ↑ 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