This old version of Proteopedia is provided for student assignments while the new version is undergoing repairs. Content and edits done in this old version of Proteopedia after March 1, 2026 will eventually be lost when it is retired in about June of 2026.

Apply for new accounts at the new Proteopedia. Your logins will work in both the old and new versions.


Exonuclease

From Proteopedia

(Difference between revisions)
Jump to: navigation, search
Current revision (07:56, 25 June 2019) (edit) (undo)
 
(15 intermediate revisions not shown.)
Line 1: Line 1:
-
{{STRUCTURE_1fxx| PDB=1fxx | SIZE=400| SCENE= |right|CAPTION=E. coli exonuclease I complex with phosphate, glycerol and Mg+2 ion, [[1fxx]] }}
+
<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.<br />
+
 
 +
'''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''' cleaves single-stranded DNA.<br />
* '''ExN-I''' cleaves single-stranded DNA.<br />
* '''ExN-II''' is associated with DNA polymerase.<br />
* '''ExN-II''' is associated with DNA polymerase.<br />
Line 8: Line 10:
* '''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''' requires a free 5’ OH group for reacting.<br />
-
* '''ExN''' were found in human and yeast as well.
+
* For '''phage ExN''' see [[Sand box 211]].
 +
 
 +
<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.
== 3D Structures of exonuclease ==
== 3D Structures of exonuclease ==
 +
[[Exonuclease 3D structures]]
-
Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
+
</StructureSection>
-
 
+
-
===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
+
-
 
+
-
===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]] - 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) <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 />
+
-
[[4ifd]] - yExN Rrp6, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4, Rrp6, Ski6, Dis3 + RNA<br />
+
-
 
+
-
===Various 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 />
+
-
[[1y97]] – hExN Trex2<br />
+
-
[[3zdk]] – hExN Apollo<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 />
+
-
[[3b6o]], [[3b6p]] - mExN Trex1 + ion inhibitor<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 - yeast
+
-
 
+
 +
== References ==
 +
<references/>
[[Category:Topic Page]]
[[Category:Topic Page]]

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

Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman

Retrieved from "http://52.214.119.220/wiki/index.php/Exonuclease"
Personal tools