Exonuclease: Difference between revisions

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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-<StructureSection load='1fxx' 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]]) '>
+<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<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''' 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''' 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]].
-<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 ==
+[[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 />
-**[[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]] - yExN Rrp6, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4, Rrp6, Ski6, Dis3 + RNA<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 />
-**[[1y97]] – hExN Trex2<br />
-**[[5aho]] – 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 <br />
-**[[4lty]], [[4lu9]], [[4m0v]] – EcExN sbcD<br />
-}}
 == References ==