Exonuclease: Difference between revisions

From Proteopedia
Jump to navigation Jump to search
← Older editNewer edit →
Joel L. Sussman (talk | contribs)
ConfirmAccount, Editor, Journal, Mutation, Print3D, Tester, Bureaucrats, Administrators
7,927 edits
No edit summary
Michal Harel (talk | contribs)
31,761 edits
No edit summary
Line 26: Line 26:
**[[3hl8]], [[3hp9]] - EcExN-I + inhibitor<br />
**[[3hl8]], [[3hp9]] - EcExN-I + inhibitor<br />
**[[3c94]] - EcExN-I + DNA-binding C terminal peptide<br />
**[[3c94]] - EcExN-I + DNA-binding C terminal peptide<br />
**[[4jrp]], [[4jrq]] – EcExN-I + oligonucleotide<br />
**[[4jrp]], [[4jrq]], [[4js5]], [[4js4]], [[4hcc]], [[4hcb]] – EcExN-I + DNA<br />
**[[3qe9]] – hExN-I (mutant) + DNA – human<br />
**[[3qe9]], [[5v07]], [[5v08]], [[5v09]], [[5v0a]] – hExN-I (mutant) + DNA – human<br />
**[[3qea]], [[3qeb]] - hExN-I + DNA<br />
**[[3qea]], [[3qeb]], [[5v04]], [[5v05]], [[5v06]], [[5v0b]], [[5v0c]], [[5v0d]], [[5v0e]], [[5uzv] - hExN-I + DNA<br />
**[[4rg8]] – ExN-I (mutant) – ''Methylocaldum szegedienes''<br />
**[[4rg8]] – ExN-I (mutant) – ''Methylocaldum szegedienes''<br />
**[[5fiq]], [[5fis]] – ExN-I ExN domain – silkworm<br />


*ExN-III
*ExN-III
Line 60: Line 61:
**[[3h4r]] - EcExN-VIII C terminal (mutant)
**[[3h4r]] - EcExN-VIII C terminal (mutant)


*Phage ExN
*ExN-X
 
**[[4fzz]], [[4fzy]], [[4fzx]] - EcExN-X + DNA<br />
 
*5’ ExN or exodeoxyribonuclease


**[[1ut5]], [[1ut8]] – T5-5’-ExN + metal – Bacteriophage T5<br />
**[[1ut5]], [[1ut8]] – T5-5’-ExN + metal – Bacteriophage T5<br />
**[[1exn]], [[1xo1]] - T5-5’-ExN (mutant)<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 />
**[[1avq]] – BlExN λ (mutant) – Bacteriophage λ<br />
**[[3slp]], [[4wuz]] - BlExN λ + DNA<br />
**[[3slp]], [[4wuz]] - BlExN λ + DNA<br />
Line 69: Line 77:
**[[3k93]] – ExN – Haemophilus somnus
**[[3k93]] – ExN – Haemophilus somnus


*Exosome complex ExN
*Exosome complex ExN see [[Exosome]]
 
**[[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 />
**[[5c0y]] - yExN Rrp6 (mutant) + RNA<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]], [[5k36]], [[5c0x]] - yExN Rrp6, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4, Rrp6, Ski6, Dis3 + RNA<br />
**[[5jea]] - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + endolysin + RNA<br />
**[[5c0w]] - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + Lrp1 + RNA<br />
**[[5g06]] - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + endolysin <br />


*ssDNA-specific ExN
*ssDNA-specific ExN
Line 96: Line 87:
**[[5f56]] – DrExN + DNA + polypeptide<br />
**[[5f56]] – DrExN + DNA + polypeptide<br />


*3-5 ExN phoexo I
*3'-5' ExN  
 
**[[4yor]], [[4yot]], [[4you]] – PhExN phoexo I – ''Pyrococcus horikoshii''<br />
**[[4yov]], [[4yow]], [[4yox]], [[4yoy]] – PhExN phoexo I (mutant) + DNA<br />
**[[4qoz]], [[4l8r]] – hExN + histone RNA hairpin-binding protein + RNA<br />
 
*5’-3’ ExN


**[[4yor]], [[4yot]], [[4you]] – PhExN – ''Pyrococcus horikoshii''<br />
**[[6c33]] – MsExN – ''Mycobacterium smegmatis''<br />
**[[4yov]], [[4yow]], [[4yox]], [[4yoy]] – PhExN (mutant) + DNA<br />
**[[6c34]], [[6c35]], [[6c36]] – MsExN (mutant)<br />


*ExN Trex
*ExN Trex

Revision as of 12:24, 23 May 2018


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 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.
  • For phage ExN see Sand box 211.

in E. coli exonuclease I (PDB code 1fxx).[2] Water molecules shown as red spheres.

E. coli exonuclease I complex with phosphate, glycerol and Mg+2 ion (PDB code 1fxx)

Drag the structure with the mouse to rotate

3D Structures of exonuclease3D Structures of exonuclease

Updated on 23-May-2018 {{#tree:id=OrganizedByTopic|openlevels=0|

  • ExN-I
  • ExN-III
  • ExN-IV
    • 2jc4 – ExN-IV – Nisseria meningitides
  • ExN-V
    • 1w36, 3k70 – EcExN-V α+β+γ + DNA hairpin
    • 3e1s - EcExN-V RECD subunit
    • 3gp8 - DrExN-V RECD subunit + DNA – Deinococcus radiodurans
    • 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
  • 5’ ExN or exodeoxyribonuclease
    • 1ut5, 1ut8 – T5-5’-ExN + metal – Bacteriophage T5
    • 1exn, 1xo1 - T5-5’-ExN (mutant)
    • 5hmm - EpT5-5’-ExN + metal – Escherichia phage T5
    • 5hml - EpT5-5’-ExN (mutant) + metal
    • 5hnk, 5hp4 - EpT5-5’-ExN (mutant) + metal + DNA
    • 1avq – BlExN λ (mutant) – Bacteriophage λ
    • 3slp, 4wuz - BlExN λ + DNA
    • 3sm4 - BlExN λ (mutant) + DNA
    • 3k93 – ExN – Haemophilus somnus
  • ssDNA-specific ExN
    • 5ght – TkExN – Thermococcus kodakarensis
    • 5ghs, 5ghr – TkExN + polypeptide
    • 5f54 – DrExN + dTMP
    • 5f55 – DrExN + DNA
    • 5f56 – DrExN + DNA + polypeptide
  • 3'-5' ExN
    • 4yor, 4yot, 4you – PhExN phoexo I – Pyrococcus horikoshii
    • 4yov, 4yow, 4yox, 4yoy – PhExN phoexo I (mutant) + DNA
    • 4qoz, 4l8r – hExN + histone RNA hairpin-binding protein + RNA
  • 5’-3’ ExN
  • ExN Trex
    • 1y97 – hExN Trex2
    • 2o4g - mExN Trex1 + nucleotide – mouse
    • 3mxj - mExN Trex1
    • 2o4i, 3mxi, 3mxm, 3u3y, 3u6f - mExN Trex1 (mutant) + polynucleotide
    • 2oa8 - mExN Trex1 + DNA
    • 4ynq - mExN Trex1 (mutant) + DNA
    • 3b6o, 3b6p - mExN Trex1 + ion inhibitor
  • Other ExN
    • 1ir6, 2zxo, 2zxp, 2zxr – ExN Recj – Thermus thermophiles
    • 1w0h – hExn Eri1 nuclease domain
    • 1zbu - hExn Eri1
    • 1zbh - hExn Eri1 (mutant) + DNA
    • 5aho – hExN Apollo
    • 2w45 – H4ExN alkaline - Herpesvirus 4
    • 2w4b - H4ExN alkaline (mutant)
    • 3syy - LhExN alkaline – Laribacter hongkongensis
    • 3sz4 - LhExN alkaline + AMP
    • 3sz5 - LhExN alkaline + polynucleotide
    • 3e2v – yExN
    • 4lty, 4lu9, 4m0v – EcExN sbcD

}}

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

Michal Harel, Alexander Berchansky, Joel L. Sussman
Retrieved from "https://proteopedia.openfox.io/wiki/index.php?title=Exonuclease&oldid=2904576"