Exonuclease

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.

3D Structures of exonuclease3D Structures of exonuclease

Updated June 2012

ExN-IExN-I

1fxx, 3c95 – EcExN-I – Escherichia coli
2qxf - EcExN-I + TMP
3hl8, 3hp9 - EcExN-I + inhibitor
3c94 - EcExN-I + DNA-binding C terminal peptide
3qe9 – hExN-I (mutant) + DNA – human
3qea, 3qeb - hExN-I + DNA

ExN-IIIExN-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-IVExN-IV

2jc4 – ExN-IV – Nisseria meningitides

ExN-VExN-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-VIIExN-VII

1vp7 – ExN-VII small subunit – Bordetella pertussis

ExN-VIIIExN-VIII

3h4r - EcExN-VIII C terminal (mutant)

Phage ExNPhage ExN

1ut5, 1ut8 – T5-5’-ExN + metal – Bacteriophage T5
1exn, 1xo1 - T5-5’-ExN (mutant)
1avq – BlExN λ (mutant) – Bacteriophage λ
3slp - BlExN λ + DNA
3sm4 - BlExN λ (mutant) + DNA
3k93 – ExN – Haemophilus somnus

Exosome complex ExNExosome 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)
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

Various ExNVarious ExN

1ir6, 2zxo, 2zxp, 2zxr – ExN Recj – Thermus thermophiles
1w0h – hExn Eri1 nuclease domain
1zbu - hExn Eri1
1zbh - hExn Eri1 (mutant) + DNA
1y97 – hExN Trex2
2o4g - mExN Trex1 + nucleotide – mouse
3mxj - mExN Trex1
2o4i, 3mxi, 3mxm, 3u3e, 3u6f - mExN Trex1 (mutant) + polynucleotide
2oa8 - mExN Trex1 + DNA
3b6o, 3b6p - mExN Trex1 + ion inhibitor
2w45 – H4ExN alkaline - Herpesvirus 4
2w4b - H4ExN alkaline (mutant)
3syy - LhExN alkaline – Laribacter hongkongensis
3sz4 - LhExN alkaline + AMP
3sz5 - LhExN alkaline + polynucleotide
3e2v – yExN - yeast