Exonuclease

spinqualitylabelsall models E. coli exonuclease I complex with phosphate, glycerol and Mg+2 ion (PDB code 1fxx) Show:Asymmetric Unit Biological Assembly Drag the structure with the mouse to rotate   Export Animated Image   Print3D Exonucleases (ExN) cleave nucleotides at the end of a polynucleotide chain. 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. Mg coordination site in E. coli exonuclease I (PDB code 1fxx). Water molecules shown as red spheres.

3D Structures of exonuclease

Updated on 25-August-2017

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• ExN-I
  • Sand box 211, 1fxx – EcExN-I – Escherichia coli
    
  • 2qxf - EcExN-I + TMP
    
  • 3hl8, 3hp9 - EcExN-I + inhibitor
    
  • 3c94 - EcExN-I + DNA-binding C terminal peptide
    
  • 4jrp, 4jrq – EcExN-I + oligonucleotide
    
  • 3qe9 – hExN-I (mutant) + DNA – human
    
  • 3qea, 3qeb - hExN-I + DNA
    
  • 4rg8 – ExN-I (mutant) – Methylocaldum szegedienes
    
• ExN-III
  • 2voa – AfExN-III (mutant) + DNA – Archaeoglobus fulgidus
    
  • 3g1k - MtExN-III – Methanothermobacter thermaautotrophicus
    
  • 3g3c, 3g4t - MtExN-III + DNA
    
  • 3fzi, 3g8v, 3g91 - MtExN-III (mutant)
    
  • 3g00, 3g0r, 3g2c, 3g2d, 3g38, 3g3y, 3ga6 - MtExN-III (mutant) + DNA
    
  • 3g0a - MtExN-III (mutant) + Mn
    
  • 1ako – EcExN-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)
• Phage ExN
  • 1ut5, 1ut8 – T5-5’-ExN + metal – Bacteriophage T5
    
  • 1exn, 1xo1 - T5-5’-ExN (mutant)
    
  • 1avq – BlExN λ (mutant) – Bacteriophage λ
    
  • 3slp, 4wuz - BlExN λ + DNA
    
  • 3sm4 - BlExN λ (mutant) + DNA
    
  • 3k93 – ExN – Haemophilus somnus
• Exosome complex ExN
  • 2ba1 – AfExN Rrp41
    
  • 2br2 – SsExN-I + ExN-II – Sulfolobus solfataricus
    
  • 2jea, 2je6, 2jeb - SsExN-I (mutant) + ExN-II + RNA-binding protein 1
    
  • 2hbj, 2hbk, 2hbl, 2hbm – yExN Rrp6 (mutant) - yeast
    
  • 5c0y - yExN Rrp6 (mutant) + RNA
    
  • 2ja9 – yExN Rrp40
    
  • 2vnu – yExN Rrp44 + DNA
    
  • 2wp8 - yExN Rrp45, Ski6, Dis3
    
  • 2ioc - hExN Trex1 N terminal
    
  • 2nn6 – hExN Rrp41, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4
    
  • 4wfc - yExN Rrp6 + Lrp1
    
  • 4wfd - yExN Rrp6 + Lrp1 + Dob1
    
  • 4ifd, 4oo1, 5k36, 5c0x - yExN Rrp6, Rrp45, Rrp42, Rrp40, Prp43, Rrp46, Mtr3, Csl4, Rrp4, Rrp6, Ski6, Dis3 + RNA
    
  • 5jea - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + endolysin + RNA
    
  • 5c0w - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + Lrp1 + RNA
    
  • 5g06 - yExN Rrp45, Rrp42, Rrp43, Rrp40, Rrp46, Mtr3, Csl4, Rrp4, Ski6, Dis3 + endolysin
    
• ssDNA-specific ExN
  • 5ght – TkExN – Thermococcus kodakarensis
    
  • 5ghs, 5ghr – TkExN + polypeptide
    
  • 5f54 – DrExN + dTMP
    
  • 5f55 – DrExN + DNA
    
  • 5f56 – DrExN + DNA + polypeptide
    
• 3-5 ExN phoexo I
  • 4yor, 4yot, 4you – PhExN – Pyrococcus horikoshii
    
  • 4yov, 4yow, 4yox, 4yoy – PhExN (mutant) + DNA
    
• 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
    

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