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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 [[Apurinic/Apyrimidinic Endonuclease-1]].


==3D structures of endonuclease==
== Function ==


'''Endonuclease'''
'''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. 
*'''ENN-III''' is a bifunctional DNA glycosylase that removes oxidized pyrimidines from DNA<ref>PMID:30959406</ref>.
*'''ENN-IV''' cleaves the DNA backbone 5' of AP sites<ref>PMID:10458614</ref>.
*'''ENN-V''' removes deaminated bases from DNA<ref>PMID:23263163</ref>.
*'''ENN-VII''' recognizes mixmatches in DNA recombinational heteroduplexes and performs their incision<ref>PMID:21237725</ref>.
*'''ENN-VIII''' removes radiolysis thymine products from phage DNA and cleaves the DNA at AP sites<ref>PMID:9405426</ref>.
*'''Structure-specific ENN''' specific for DNA secondary structure rather than for its sequence<ref>PMID:28327556</ref>.
*'''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]]
*CRISPR type I-A (Cascade) - see [[CRISPR subtype I-A]]
*CRISPR type I-B (Cascade) - see [[CRISPR subtype I-B]]
*CRISPR type I-C (Cascade) - see [[CRISPR subtype I-C]]
*CRISPR type I-E (Cascade) - see [[CRISPR type I-E (Cascade)|CRISPR subtype I-E]]
*(CRISPR type I-F (Csy1, Csy2, Csy3) - see [[CRISPR subtype I-F]]
*CRISPR type III-A (Csm complex) - see [[CRISPR subtype III-A (Csm complex)]]
*CRISPR type II-A - see [[CRISPR-Cas9]]
*CRISPR type V (Cpf1, C2c1, C2c3) - see [[CRISPR type V]]
*CRISPR type VI (Cas13a (previously known as C2c2), Cas13b, Cas13c, Cas13d) - see [[CRISPR type VI]]
See also<br />
* [[Apurinic-Apyrimidinic Endonuclease-1]]<br />
* For EcoRV ENN see [[Student Projects for UMass Chemistry 423 Spring 2012-3]]<br />
* For NEI ENN see [[DNA repair protein human endonuclease VIII-like 1 (NEIL1)]].


''ENN-I''
== Relevance ==


[[1bix]] - hENN – human<br />
Sickle cell anemia is caused by mutation in the recognition site of MstII ENN.
[[1cfr]] – ENN – ''Citrobacter freundii''<br />
[[1af5]] - CrENN – ''Chlamydomonas reinhardtii''<br />
[[1fzr]], [[1m0d]], [[1m0i]], [[3cae]] – T7ENN - Enterobacteria phage T7<br />
[[2g7e]], [[2g7f]] – VcENN – ''Vibrio cholera''<br />
[[2vnd]] - VcENN (mutant) <br />
[[2pu3]] - VsENN – ''Vibrio salmonicida''


''ENN-II''
== Disease ==


[[1pvi]], [[1pvu]] - ENN – ''Proteus vulgaris''<br />
Mutation in UV-specific ENN causes Xeroderma pigmentosa. Mutations in tRNA-splicing ENN cause pontocerebellar hypoplasia.
[[2wsh]] - T4ENN (mutant) - Enterobacteria phage T4


== Structural highlights ==
<scene name='49/496318/Cv/1'>E. coli EcoRV endonuclease dimer with DNA</scene>


''ENN-III''
<scene name='49/496318/Cv/2'>DNA-protein binding</scene> (PDB code [[1rva]]).


[[2abk]], [[1ako]] - EcENN  – ''Escherichia coli''<br />
==3D structures of endonuclease==
[[1orn]], [[1orp]], [[1p59]] - GsENN + DNA – ''Geobacillus stearothermophilus''
[[Endonuclease 3D structures]]
 
''ENN-IV''
 
[[1qtw]] - EcENN  <br />
[[2nqh]] - EcENN (mutant) <br />
[[1qum]] – EcENN + DNA<br />
[[2nqj]], [[2nq9]] - EcENN (mutant) + DNA<br />
[[1xp3]] - ENN – ''Bacillus anthracis''<br />
[[3aal]] - GkENN – ''Geobacillus kaustophilus''<br />
[[3aam]] - TtENN – ''Thermus thermophilus''
 
''ENN-V''
 
[[1eni]], [[1enj]], [[1enk]], [[2end]] - T4ENN  <br />
[[1vas]] - T4ENN + DNA<br />
[[2w35]], [[2w36]] - TmENN + DNA – ''Thermotoga maritima''<br />
[[3hd0]] - TmENN <br />
[[3ga2]] - BsENN (mutant) – ''Bacillus subtilis''<br />
[[3goc]] - ENN – ''Streptomyces avermitilis''
 
''ENN-VII''
 
[[1en7]], [[1e7d]] - T4ENN <br />
[[1e7l]] - T4ENN (mutant) <br />
[[2qnc]], [[2qnf]] - T4ENN (mutant) + DNA
 
 
''ENN-VIII''
 
[[1q39]], [[1q39]] -  EcENN  <br />
[[1q3b]], [[1q3c]] -  EcENN  (mutant) <br />
[[1bix]] – hENN + DNA<br />
[[1k3x]], [[2ea0]], [[1k3w]], [[1k3x]], [[2ea0]], [[2opf]], [[2oq4]] - EcENN + DNA <br />
[[2opf]], [[2oq4]] - EcENN (mutant) + DNA
 
''EcoRI ENN''
 
[[1qc9]], [[1wtd]] - EcENN<br />
[[1eri]], [[1ckq]], [[1cl8]], [[1qps]], [[1wte]] – EcENN + DNA<br />
[[1qrh]], [[1qri]], [[2oxv]] - EcENN (mutant) + DNA
 
''EcoRII ENN''
 
[[1na6]] – EcENN<br />
[[3hqf]], [[3hqg]] - EnENN + DNA
 
''EcoRV ENN''
 
[[1rve]], [[1az3]] – EcENN<br />
[[1az4]] - EcENN (mutant) <br />
[[2rve]], [[4rve]], [[1rva]], [[1rvb]], [[1rvc]], [[1az0]], [[1bsu]], [[1bua]], [[1bgb]], [[1rv5]], [[1b94]], [[1b95]], [[1eo3]], [[1eo4]], [[1eon]], [[1eoo]], [[1eop]], [[2b0d]], [[2b0e]] - EcENN + DNA<br />
[[1bss]], [[1b96]], [[1b97]], [[1stx]], [[1suz]], [[1sx5]], [[1sx8]], [[2ge5]] - EcENN (mutant) + DNA
 
''BamHI ENN''
 
[[1bam]] – BaENN – ''Bacillus amyloliquefaciens''<br />
[[1bhm]], [[3bam]], [[2bam]], [[1esg]] - BaENN + DNA
 
''FokI ENN''
 
[[1fok]] – PoENN + DNA – ''Planomicrobium okeanokoites''<br />
[[2fok]] – PoENN
 
''PvuII ENN''
 
[[3pvi]] - PvENN (mutant) + DNA – ''Proteus vulgaris''<br />
[[1k0z]], [[1h56]], [[3ksk]] - PvENN<br />
[[1ni0]] - PvENN (mutant) <br />
[[2pvi]], [[1eyu]], [[1f0o]] - PvENN + DNA
 
''tRNA-splicing ENN''
 
[[1a79]], [[1a76]], [[1a77]] - ENN  – ''Methanocaldococcus jannaschii''<br />
[[2cv8]] - ENN  – ''Sulfolobus tokodaii''<br />
[[2gw6]] – hENN subunit sen15 – NMR<br />
[[2gjw]] - AfENN + RNA –'' Archaeoglobus fulgidus''<br />
[[1r0v]], [[1r11]] – AfENN
[[2ohc]], [[2ohe]] - ENN – ''Thermoplasma acidophilum''<br />
[[2zyz]] – ENN – ''Pyrobaculum aerophilum''<br />
[[3iey]] - ENN + NEQ261 – ''Nanoarchaeum equitans''<br />
[[3ajv]] - ApENN  (mutant) – ''Aeropyrum pernix''<br />
[[3p1y]] - ApENN /AfENN<br />
[[3p1z]] - ApENN  + protein
 
''VSR ENN''
 
[[1vsr]] – EcENN<br />
[[1cw0]] - EcENN + DNA
 
''BglI ENN''
 
[[1dmu]], [[1d2i]] – BsENN + DNA <br />
[[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''<br />
[[1iaw]] - LaENN + DNA
 
''NgoMIV ENN''
 
[[1fiu]], [[4abt]] - ENN + DNA – ''Neisseria gonorrheae''
 
''BsoBI ENN''
 
[[1dc1]] - GsENN + DNA
 
''Bse634I ENN''
 
[[1knv]] – GsENN<br />
[[3v1z]] – GsENN + DNA<br />
[[3v20]], [[3v21]] - GsENN (mutant) + DNA
 
''HincII ENN''
 
[[1kc6]], [[1tw8]], [[1xhu]], [[1xhv]], [[1tx3]], [[2gie]] - HiENN + DNA – ''Haemophilus influenza''<br />
[[2gig]], [[2gih]], [[2gii]], [[2gij]], [[3e3y]], [[3e40]], [[3e41]], [[3e42]], [[3e43]], [[3e44]], [[3e45]], [[3ebc]] - HiENN (mutant) + DNA<br />
[[2aud]] – HiENN
 
''HinDIII ENN''
 
[[2e52]], [[3a4k]] - HiENN + DNA
 
''HinP1I ENN''
 
[[1ynm]] – HiENN<br />
[[2fkc]], [[2fkh]], [[2fl3]], [[2flc]] - HiENN + DNA
 
''Flap ENN''
 
[[1mc8]] - ENN (mutant) – ''Pyrococcus horikoshii''<br />
[[3ory]]– ENN – ''Desulfurococcus amylolyticus''<br />
[[3q8k]], [[3q8l]], [[3q8m]] - hENN + DNA<br />
[[1rxv]], [[1rxw]] - AfENN + DNA
 
''DNA mismatch ENN''
 
[[1odg]] - EcENN + DNA
 
''Vvn ENN''
 
[[1ouo]] – VvENN – ''Vibrio vulnificus''<br />
[[1oup]], [[2ivk]] - VvENN + DNA
 
''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''
 
''NHN ENN''
 
[[2qgp]] – ENN – ''Geobacter metallireducens''
 
''UV damage ENN''
 
[[2j6v]], [[3bzg]], [[3c0s]] – TtENN <br />
[[3bzj]], [[3c0l]], [[3c0q]] - TtENN (mutant)
 
''NotI ENN''
 
[[3bvq]] - NoENN – ''Nocardia otitidiscaviarum''<br />
[[3c25]] - NoENN + DNA
 
''BpujI ENN''
 
[[2vla]], [[3s1s]] – ENN – ''Bacillus pumilus''
 
''Sau3AI ENN''
 
[[2reu]] – ENN C terminal – ''Staphylococcus aureus''
 
''HpyI ENN''
 
[[3fc3]], [[3gox – HpENN99 + DNA – ''Helicobacter pylori''<br />
[[3or3]] – HpENN88 + DNA
 
''PacI ENN''
 
[[3ldy]], [[3m7k]] - PaENN + DNA – ''Psdeudomonas alcaligenes''
 
''Crossover junction ENN''
 
[[2kpf]] - ENN – mouse
 
''OkrAI ENN''
 
[[3odh]] - ENN + DNA – ''Oceanobacter kriegii''
 
'''Intron-encoded endonuclease'''
 
''I-PpoI ENN''
 
[[1a74]], [[1ipp]], [[1a73]], [[1cz0]] - PpENN + DNA – ''Physarum polycephalum''<br />
[[1cyq]], [[1evw]], [[2o6m]] - PpENN (mutant) + DNA<br />
[[1evx]] - PpENN
 
''I-CreI ENN''
 
[[1bp7]], [[1g9y]], [[1g9z]], [[1n3e]], [[1n3f]], [[2vbj]], [[2vbl]], [[2vbn]], [[2vbo]] - 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]] – ENN – ''Pyrococcus furiosus''
 
''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''
</StructureSection>


[[1m5x]], [[3fd2]] – MoENN + DNA – ''Monomastix''<br />
== References ==
[[3ko2]] – MoENN (mutant) + DNA
<references/>


''I-GzeMII ENN''


[[4efj]] – ENN + DNA – ''Gibberella zeae''
[[Category:Topic Page]]
[[Category:Endonuclease]]

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