Exonuclease: Difference between revisions

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Proteopedia Page Contributors and Editors (what is this?)Proteopedia Page Contributors and Editors (what is this?)

Michal Harel, Alexander Berchansky, Joel L. Sussman

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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.
 <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]].
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 </StructureSection>
-== 3D Structures of exonuclease ==
-Updated on {{REVISIONDAY2}}-{{MONTHNAME|{{REVISIONMONTH}}}}-{{REVISIONYEAR}}
-{{#tree:id=OrganizedByTopic|openlevels=0|
-*ExN-I
-**[[3qea]], [[3qeb]], [[5v04]], [[5v05]], [[5v06]], [[5v0b]], [[5v0c]], [[5v0d]], [[5v0e]], [[5uzv]] - hExN-I + DNA - human<br />
-**[[3qe9]], [[5v07]], [[5v08]], [[5v09]], [[5v0a]] – hExN-I (mutant) + DNA – human<br />
-**[[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]], [[4js5]], [[4js4]], [[4hcc]], [[4hcb]] – EcExN-I + DNA<br />
-**[[4rg8]] – ExN-I (mutant) – ''Methylocaldum szegedienes''<br />
-**[[5fiq]], [[5fis]] – ExN-I ExN domain – silkworm<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)
-*ExN-X
-**[[4fzz]], [[4fzy]], [[4fzx]] - EcExN-X + DNA<br />
-*5’ ExN or exodeoxyribonuclease
-**[[1ut5]], [[1ut8]] – T5-5’-ExN + metal – Bacteriophage T5<br />
-**[[1exn]], [[1xo1]] - T5-5’-ExN (mutant)<br />
-**[[5hmm]] - EpT5-5’-ExN + metal – Escherichia phage T5<br />
-**[[5hml]] - EpT5-5’-ExN (mutant) + metal <br />
-**[[5hnk]], [[5hp4]] - EpT5-5’-ExN (mutant) + metal + DNA<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 see [[Exosome]]
-*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
-**[[4qoz]], [[4l8r]] – hExN + histone RNA hairpin-binding protein + RNA<br />
-**[[4yor]], [[4yot]], [[4you]] – PhExN phoexo I – ''Pyrococcus horikoshii''<br />
-**[[4yov]], [[4yow]], [[4yox]], [[4yoy]] – PhExN phoexo I (mutant) + DNA<br />
-*5’-3’ ExN
-**[[6c33]] – MsExN – ''Mycobacterium smegmatis''<br />
-**[[6c34]], [[6c35]], [[6c36]] – MsExN (mutant)<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]], [[5ywv]], [[5ywu]], [[5ywt]], [[5yws]] - mExN Trex1 + DNA<br />
-**[[4ynq]] - mExN Trex1 (mutant) + DNA<br />
-**[[3b6o]], [[3b6p]] - mExN Trex1 + ion inhibitor<br />
-**[[6a45]] - mExN Trex2<br />
-**[[6a4b]], [[6a47]] - mExN Trex2 + DNA<br />
-**[[6a46]] - mExN Trex2 + nucleotide<br />
-*Other ExN
-**[[1w0h]] – hExn Eri1 nuclease domain <br />
-**[[1zbu]] - hExn Eri1<br />
-**[[1zbh]] - hExn Eri1 (mutant) + DNA<br />
-**[[5aho]] – hExN Apollo<br />
-**[[5zyw]] – hExN mitochondrial genome repair 1<br />
-**[[5zyv]], [[5zyu]], [[5zyt]] – hExN mitochondrial genome repair 1 + DNA<br />
-**[[3e2v]] – yExN <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 />
-**[[4lty]], [[4lu9]], [[4m0v]] – EcExN sbcD<br />
-**[[6m9k]] - ExN + recombination protein BET – Escherichia phage λ<br />
-**[[1ir6]], [[2zxo]], [[2zxp]], [[2zxr]] – ExN Recj – ''Thermus thermophiles''<br />
-}}
 == References ==