Endonuclease

From Proteopedia

Revision as of 09:05, 23 June 2013

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. Some ENNs are encoded within introns thus facilitating their mobility. These ENNs or inteins are designated I-ENN. See also

• Apurinic/Apyrimidinic Endonuclease-1
  
• DNA repair protein human endonuclease VIII-like 1 (NEIL1) .

3D structures of endonuclease

Updated on 23-June-2013

Endonuclease

ENN-I

1bix - hENN – human
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

ENN-III

2abk, 1ako - EcENN – Escherichia coli
1orn, 1orp, 1p59 - GsENN + DNA – Geobacillus stearothermophilus

ENN-IV

1qtw - EcENN
2nqh - EcENN (mutant)
1qum – EcENN + DNA
2nqj, 2nq9 - EcENN (mutant) + DNA
1xp3 - ENN – Bacillus anthracis
3aal - GkENN – Geobacillus kaustophilus
3aam - TtENN – Thermus thermophilus

ENN-V

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

1q39, 1q39 - EcENN
1q3b, 1q3c - EcENN (mutant)
1tdh – hENN
1bix – hENN + DNA
1k3x, 2ea0, 1k3w, 1k3x, 2ea0, 2opf, 2oq4 - EcENN + DNA
2opf, 2oq4 - EcENN (mutant) + 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 - EcENN + DNA
1bss, 1b96, 1b97, 1stx, 1suz, 1sx5, 1sx8, 2ge5 - EcENN (mutant) + DNA

BamHI ENN

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

FokI ENN

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

PvuII ENN

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

tRNA-splicing ENN

1a79, 1a76, 1a77 - MjENN – Methanocaldococcus jannaschii
2cv8 - ENN – Sulfolobus tokodaii
2gw6 – hENN subunit sen15 – NMR
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

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

1mc8 - ENN (mutant) – Pyrococcus horikoshii
3ory– ENN – Desulfurococcus amylolyticus
3q8k, 3q8l, 3q8m - hENN + DNA
1rxv, 1rxw - AfENN + DNA
1ul1 - hENN + PCNA
2izo - SsENN + PCNA – Sulfolobus solfataricus
1a76, 1a77 - MjENN
1b43 – PfENN – Pyrococcus furiosus
1rxz - AfENN + PCNA

DNA mismatch ENN

1odg - EcENN + DNA

Vvn ENN

1ouo – VvENN – Vibrio vulnificus
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
3bzj, 3c0l, 3c0q - TtENN (mutant)

NotI ENN

3bvq - NoENN – Nocardia otitidiscaviarum
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
3or3 – HpENN88 + DNA

PacI ENN

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

Crossover junction ENN

2kpf - ENN – mouse

OkrAI ENN

3odh - ENN + DNA – Oceanobacter kriegii

BspD6I ENN

2ewf - ENN – Bacillus

ThaI ENN

3ndh - TaENN + 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 - CrENN (mutant) + DNA
2o7m - CrENN

I-CeuI ENN

2ex5 - ENN (mutant) + DNA – Chlamydomonas eugametos

I-DmoI ENN

1b24, 2vs7, 2vs8 - DmENN + DNA – Desulfurococcus mobilis
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 - yENN + DNA
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
2l8l - MtENN

I-MsoI ENN

1m5x, 3fd2 – MoENN + DNA – Monomastix
3ko2 – MoENN (mutant) + DNA

I-GzeMII ENN

4efj – ENN + DNA – Gibberella zeae