Table 2.
Proteins of the PD-(D/E)-XK family that are structurally homologous to λ exo.a
| Protein Name (organism) | Oligomeric state | PDB code | #residues | %ident. | rmsd (Å) | Ligands | Reference |
|---|---|---|---|---|---|---|---|
| LHK-exo (L. Hongkongensis) | 3-mer ring | 3sz5 | 186 | 27 | 1.3 | dT4-Mg2+ | Yang et al. (2011) |
| Phage exo (H. somnus) | 3-mer ring | 3k93 | 184 | 18 | 2.4 | ||
| Cas4 (Mimivirus Virophage) | dimer | 5yeu | 186 | 20 | 2.8 | Mg2+ | Dou et al. (2018) |
| Epstein-Barr virus nuclease | monomer | 2w4b | 188 | 12 | 2.9 | Buisson et al. (2009) | |
| KSHV-SOX | monomer | 3pov | 179 | 16 | 3.1 | dsDNA | Bagnéris et al. (2011) |
| KSHV-SOX | monomer | 5hsw | 179 | 14 | 2.9 | 31-mer RNA | Lee et al. (2017) |
| Cas4 (S. solfataricus) | 2×5-ring | 4ic1 | 152 | 10 | 3.3 | Mn2+ | Lemak et al. (2013) |
| Exonuclease (E. rectale) | 3-mer ring | 3loa | 167 | 9 | 3.4 | Zn2+ | |
| RecE exo (E. coli rac) | 4-mer ring | 3h4r | 153 | 10 | 3.4 | Zhang et al. (2009) | |
| HsMGME1 (mitochondrial) | monomer | 5zyu | 150 | 9 | 3.6 | ssDNA-Mn2+ | Yang et al. (2018) |
| Dna2 nuclease (Mouse) | monomer | 5eax | 157 | 8 | 3.9 | ssDNA | Zhou et al. (2015) |
| Cas4 nuc (P. calidifontis) | monomer | 4r5q | 138 | 12 | 3.5 | Mg2+ | |
| RecB (E. coli) | heterotrim. | 1w36 | 132 | 9 | 3.7 | Ca2+ | Singleton et al. (2004) |
| AddA (B. subtilis) | heterodim | 4ceh | 113 | 15 | 3.1 | Krajewski et al. (2014) | |
| eIF3d (N. vitripennis) | monomer | 5k4d | 159 | 8 | 3.6 | Lee et al. (2016) | |
| Rai1 nuc (A. gossypii) | monomer | 5bud | 143 | 8 | 4.1 | pU5-Mn2+ | Wang et al. (2015) |
| HJC resolvase (P. furiosis) | dimer | 1gef | 90 | 14 | 3.2 | Nishino et al. (2001) | |
| Dom3Z (DXO, human) | monomer | 4j7l | 144 | 9 | 4.0 | RNA-Mg2+ | Jiao et al. (2013) |
| tRNA splicing (M. jannaschii) | dimer | 1a79 | 93 | 11 | 3.6 | Li et al. (1998) | |
| NucS/EndoMS (E. kodakaren) | dimer | 5gke | 80 | 16 | 3.8 | dsDNA | Nakae et al. (2016) |
| FAN1 nuclease (mouse) | monomer | 4rib | 93 | 9 | 2.4 | 5′P-FlapDNA | Wang et al. (2014) |
The listed protein structures are selected from a Dali Search with the structure of λ exo (Chain B of 3SM4) as the query. They are listed in order of decreasing Z-score from the Dali search. In cases where there are multiple PDB entries for the same protein, the structure with the most functionally comparable ligand is listed. Only some of the protein hits from the search are listed, to minimize redundancy of similar proteins. The following structures form ring-shaped oligomers for processing dsDNA breaks (like λ exo): LHK-exo, H. somnus exo, E. rectale exo, and RecE. EBV nuclease and KSHV-SOX perform the same function, but do so as monomers. RecB and AddA have nuclease domains that are homologous to λ exo, and function as larger helicase/nuclease complexes for processing dsDNA breaks. eIF3d, Rai1, and Dom3Z all act on 5′-caps of mRNA substrates.