Exonuclease: Difference between revisions

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Michal Harel, Alexander Berchansky, Joel L. Sussman

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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]]