Exonuclease: Difference between revisions

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'''Exonucleases''' (ExN) cleave nucleotides at the end of a polynucleotide chain<ref>PMID:14770007</ref>.  In ''E. coli'' there are ExN I to VIII.  ExN were found in human and yeast as well.
'''Exonucleases''' (ExN) cleave nucleotides at the end of a polynucleotide chain<ref>PMID:14770007</ref>.  In ''E. coli'' there are ExN I to VIII.  ExN were found in human and yeast as well.
<br />
<br />
* '''ExN-I''' cleaves single-stranded DNA.<br />
* '''ExN-I''' is a 5'-3' ExN cleaves double-stranded DNA<ref>PMID:27494243</ref>.<br />
* '''ExN-II''' is associated with DNA polymerase.<br />
* '''ExN-II''' is associated with DNA polymerase.<br />
* '''ExN-III''' cleaves double-stranded DNA.<br />
* '''ExN-III''' cleaves double-stranded DNA.<br />
* '''ExN-IV''' cleavage results in nucleoside monophosphate.<br />
* '''ExN-IV''' cleavage results in nucleoside monophosphate.<br />
* '''ExN-V''' cleaves linear double-stranded DNA.<br />
* '''ExN-V''' cleaves linear double-stranded DNA.<br />
* '''ExN-VIII''' requires a free 5’ OH group for reacting.<br />
* '''ExN-VIII''' degrades linear duplex DNA<ref>PMID:6309804</ref> and requires a free 5’ OH group for reacting.<br />
* '''ExN-X''' can degrade both single-stranded DNA and duplex DNA with 3'-5' polarity<ref>PMID:10514496</ref>
* '''Trex ExN''' degrades single-stranded DNA generated from processing of aberrant replication intermediates<ref>PMID:18045533</ref>
 
* For '''phage ExN''' see [[Sand box 211]].
* For '''phage ExN''' see [[Sand box 211]].


<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.  
<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.  
</StructureSection>


== 3D Structures of exonuclease ==
== 3D Structures of exonuclease ==
[[Exonuclease 3D structures]]


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


== References ==
== References ==

Latest revision as of 13:01, 20 June 2024


Exonucleases (ExN) cleave nucleotides at the end of a polynucleotide chain[1]. In E. coli there are ExN I to VIII. ExN were found in human and yeast as well.


  • ExN-I is a 5'-3' ExN cleaves double-stranded DNA[2].
  • ExN-II is associated with DNA polymerase.
  • ExN-III cleaves double-stranded DNA.
  • ExN-IV cleavage results in nucleoside monophosphate.
  • ExN-V cleaves linear double-stranded DNA.
  • ExN-VIII degrades linear duplex DNA[3] and requires a free 5’ OH group for reacting.
  • ExN-X can degrade both single-stranded DNA and duplex DNA with 3'-5' polarity[4]
  • Trex ExN degrades single-stranded DNA generated from processing of aberrant replication intermediates[5]

in E. coli exonuclease I (PDB code 1fxx).[6] Water molecules shown as red spheres.

3D Structures of exonuclease

Exonuclease 3D structures


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

Drag the structure with the mouse to rotate

ReferencesReferences

  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. ↑ Keijzers G, Liu D, Rasmussen LJ. Exonuclease 1 and its versatile roles in DNA repair. Crit Rev Biochem Mol Biol. 2016 Nov/Dec;51(6):440-451. PMID:27494243 doi:10.1080/10409238.2016.1215407
  3. ↑ Joseph JW, Kolodner R. Exonuclease VIII of Escherichia coli. II. Mechanism of action. J Biol Chem. 1983 Sep 10;258(17):10418-24 PMID:6309804
  4. ↑ Viswanathan M, Lovett ST. Exonuclease X of Escherichia coli. A novel 3'-5' DNase and Dnaq superfamily member involved in DNA repair. J Biol Chem. 1999 Oct 15;274(42):30094-100. PMID:10514496 doi:10.1074/jbc.274.42.30094
  5. ↑ Yang YG, Lindahl T, Barnes DE. Trex1 exonuclease degrades ssDNA to prevent chronic checkpoint activation and autoimmune disease. Cell. 2007 Nov 30;131(5):873-86. doi: 10.1016/j.cell.2007.10.017. PMID:18045533 doi:http://dx.doi.org/10.1016/j.cell.2007.10.017
  6. ↑ 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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