Exonuclease: Difference between revisions

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{{STRUCTURE_1w36|  PDB=1w36  | SIZE=400| SCENE= |right|CAPTION=E. coli exonuclease V complex with DNA hairpin, [[1w36]] }}
<StructureSection load='' size='350' side='right' scene='46/466467/Cv/1' caption='E. coli exonuclease I complex with phosphate, glycerol and Mg+2 ion (PDB code [[1fxx]]) '>


'''Exonucleases''' (ExN) cleave nucleotides at the end of a polynucleotide chain.  In E. coli there are ExN I to VIII.  ExN-I cleaves single-stranded DNA; 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 requires a free 5’ OH group for reacting.  ExN were found in human and yeast as well.


{{TOC limit|limit=2}}
'''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 />
* '''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-III''' cleaves double-stranded DNA.<br />
* '''ExN-IV''' cleavage results in nucleoside monophosphate.<br />
* '''ExN-V''' cleaves linear double-stranded DNA.<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>


== 3D Structures of exonuclease ==
* For '''phage ExN''' see [[Sand box 211]].


===ExN-I===
<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.
[[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


===ExN-III===
== 3D Structures of exonuclease ==
 
[[Exonuclease 3D structures]]
[[2voa]] – ExN-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
 
===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===
</StructureSection>


[[3h4r]] - EcExN-VIII C terminal (mutant)
== References ==
<references/>


[[1ut5]], [[1ut8]] – 5’-ExN + metal – Bacteriophage T5


[[Category:Topic Page]]
[[Category:Topic Page]]

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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