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Exonuclease

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* For '''phage ExN''' see [[Sand box 211]].
* For '''phage ExN''' see [[Sand box 211]].
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<scene name='46/466467/Cv/2'>Mg coordination site</scene> in ''E. coli'' exonuclease I (PDB code [[1fxx]]).<ref>PMID:11101894</ref> Water molecules shown as red spheres.
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<scene name='46/466467/Cv/3'>Mg coordination site</scene> in ''E. coli'' exonuclease I (PDB code [[1fxx]]).<ref>PMID:11101894</ref> Water molecules shown as red spheres.
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</StructureSection>
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== 3D Structures of exonuclease ==
== 3D Structures of exonuclease ==
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[[Exonuclease 3D structures]]
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Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
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</StructureSection>
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{{#tree:id=OrganizedByTopic|openlevels=0|
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*ExN-I
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**[[1fxx]], [[3c95]] – EcExN-I – ''Escherichia coli''<br />
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**[[2qxf]] - EcExN-I + TMP<br />
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**[[3hl8]], [[3hp9]] - EcExN-I + inhibitor<br />
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**[[3c94]] - EcExN-I + DNA-binding C terminal peptide<br />
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**[[4jrp]], [[4jrq]] – EcExN-I + oligonucleotide<br />
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**[[3qe9]] – hExN-I (mutant) + DNA – human<br />
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**[[3qea]], [[3qeb]] - hExN-I + DNA<br />
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**[[4rg8]] – ExN-I (mutant) – ''Methylocaldum szegedienes''<br />
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*ExN-III
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**[[2voa]] – AfExN-III (mutant) + DNA – ''Archaeoglobus fulgidus''<br />
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**[[3g1k]] - MtExN-III – ''Methanothermobacter thermaautotrophicus''<br />
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**[[3g3c]], [[3g4t]] - MtExN-III + DNA<br />
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**[[3fzi]], [[3g8v]], [[3g91]] - MtExN-III (mutant) <br />
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**[[3g00]], [[3g0r]], [[3g2c]], [[3g2d]], [[3g38]], [[3g3y]], [[3ga6]] - MtExN-III (mutant) + DNA<br />
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**[[3g0a]] - MtExN-III (mutant) + Mn<br />
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**[[1ako]] – EcExN-III
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*ExN-IV
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**[[2jc4]] – ExN-IV – ''Nisseria meningitides''
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*ExN-V
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**[[1w36]], [[3k70]] – EcExN-V α+β+γ + DNA hairpin<br />
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**[[3e1s]] - EcExN-V RECD subunit<br />
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**[[3gp8]] - DrExN-V RECD subunit + DNA – ''Deinococcus radiodurans''<br />
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**[[3gpl]] - DrExN-V RECD subunit + DNA + ADPNP
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*ExN-VII
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**[[1vp7]] – ExN-VII small subunit – ''Bordetella pertussis''
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*ExN-VIII
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**[[3h4r]] - EcExN-VIII C terminal (mutant)
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*Phage ExN
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**[[1ut5]], [[1ut8]] – T5-5’-ExN + metal – Bacteriophage T5<br />
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**[[1exn]], [[1xo1]] - T5-5’-ExN (mutant)<br />
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**[[1avq]] – BlExN λ (mutant) – Bacteriophage λ<br />
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**[[3slp]], [[4wuz]] - BlExN λ + DNA<br />
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**[[3sm4]] - BlExN λ (mutant) + DNA<br />
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**[[3k93]] – ExN – Haemophilus somnus
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*Exosome complex ExN
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**[[2ba1]] – AfExN Rrp41<br />
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**[[2br2]] – SsExN-I + ExN-II – ''Sulfolobus solfataricus''<br />
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**[[2jea]], [[2je6]], [[2jeb]] - SsExN-I (mutant) + ExN-II + RNA-binding protein 1<br />
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**[[2hbj]], [[2hbk]], [[2hbl]], [[2hbm]] – yExN Rrp6 (mutant) - yeast<br />
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**[[5c0y]] - yExN Rrp6 (mutant) + RNA<br />
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**[[2ja9]] – yExN Rrp40<br />
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**[[2vnu]] – yExN Rrp44 + DNA<br />
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**[[2wp8]] - yExN Rrp45, Ski6, Dis3<br />
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**[[2ioc]] - hExN Trex1 N terminal<br />
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**[[2nn6]] – hExN Rrp41, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4<br />
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**[[4wfc]] - yExN Rrp6 + Lrp1<br />
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**[[4wfd]] - yExN Rrp6 + Lrp1 + Dob1<br />
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**[[4ifd]], [[4oo1]], [[5k36]], [[5c0x]] - yExN Rrp6, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4, Rrp6, Ski6, Dis3 + RNA<br />
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**[[5jea]] - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + endolysin + RNA<br />
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**[[5c0w]] - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + Lrp1 + RNA<br />
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**[[5g06]] - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + endolysin <br />
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*ssDNA-specific ExN
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**[[5ght]] – TkExN – ''Thermococcus kodakarensis''<br />
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**[[5ghs]], [[5ghr]] – TkExN + polypeptide<br />
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**[[5f54]] – DrExN + dTMP<br />
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**[[5f55]] – DrExN + DNA<br />
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**[[5f56]] – DrExN + DNA + polypeptide<br />
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*3-5 ExN phoexo I
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**[[4yor]], [[4yot]], [[4you]] – PhExN – ''Pyrococcus horikoshii''<br />
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**[[4yov]], [[4yow]], [[4yox]], [[4yoy]] – PhExN (mutant) + DNA<br />
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*ExN Trex
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**[[1y97]] – hExN Trex2<br />
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**[[2o4g]] - mExN Trex1 + nucleotide – mouse<br />
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**[[3mxj]] - mExN Trex1<br />
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**[[2o4i]], [[3mxi]], [[3mxm]], [[3u3y]], [[3u6f]] - mExN Trex1 (mutant) + polynucleotide<br />
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**[[2oa8]] - mExN Trex1 + DNA<br />
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**[[4ynq]] - mExN Trex1 (mutant) + DNA<br />
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**[[3b6o]], [[3b6p]] - mExN Trex1 + ion inhibitor<br />
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*Other ExN
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**[[1ir6]], [[2zxo]], [[2zxp]], [[2zxr]] – ExN Recj – ''Thermus thermophiles''<br />
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**[[1w0h]] – hExn Eri1 nuclease domain <br />
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**[[1zbu]] - hExn Eri1<br />
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**[[1zbh]] - hExn Eri1 (mutant) + DNA<br />
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**[[5aho]] – hExN Apollo<br />
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**[[2w45]] – H4ExN alkaline - Herpesvirus 4<br />
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**[[2w4b]] - H4ExN alkaline (mutant)<br />
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**[[3syy]] - LhExN alkaline – ''Laribacter hongkongensis''<br />
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**[[3sz4]] - LhExN alkaline + AMP<br />
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**[[3sz5]] - LhExN alkaline + polynucleotide<br />
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**[[3e2v]] – yExN <br />
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**[[4lty]], [[4lu9]], [[4m0v]] – EcExN sbcD<br />
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}}
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== References ==
== References ==

Current revision

E. coli exonuclease I complex with phosphate, glycerol and Mg+2 ion (PDB code 1fxx)

Drag the structure with the mouse to rotate

References

  1. ↑ Mukherjee D, Fritz DT, Kilpatrick WJ, Gao M, Wilusz J. Analysis of RNA exonucleolytic activities in cellular extracts. Methods Mol Biol. 2004;257:193-212. PMID:14770007 doi:http://dx.doi.org/10.1385/1-59259-750-5:193
  2. ↑ Breyer WA, Matthews BW. Structure of Escherichia coli exonuclease I suggests how processivity is achieved. Nat Struct Biol. 2000 Dec;7(12):1125-8. PMID:11101894 doi:10.1038/81978

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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