Sequence, structure and functional diversity of PD-(D/E)XK phosphodiesterase superfamily

Abstract

Proteins belonging to PD-(D/E)XK phosphodiesterases constitute a functionally diverse superfamily with representatives involved in replication, restriction, DNA repair and tRNA–intron splicing. Their malfunction in humans triggers severe diseases, such as Fanconi anemia and Xeroderma pigmentosum. To date there have been several attempts to identify and classify new PD-(D/E)KK phosphodiesterases using remote homology detection methods. Such efforts are complicated, because the superfamily exhibits extreme sequence and structural divergence. Using advanced homology detection methods supported with superfamily-wide domain architecture and horizontal gene transfer analyses, we provide a comprehensive reclassification of proteins containing a PD-(D/E)XK domain. The PD-(D/E)XK phosphodiesterases span over 21 900 proteins, which can be classified into 121 groups of various families. Eleven of them, including DUF4420, DUF3883, DUF4263, COG5482, COG1395, Tsp45I, HaeII, Eco47II, ScaI, HpaII and Replic_Relax, are newly assigned to the PD-(D/E)XK superfamily. Some groups of PD-(D/E)XK proteins are present in all domains of life, whereas others occur within small numbers of organisms. We observed multiple horizontal gene transfers even between human pathogenic bacteria or from Prokaryota to Eukaryota. Uncommon domain arrangements greatly elaborate the PD-(D/E)XK world. These include domain architectures suggesting regulatory roles in Eukaryotes, like stress sensing and cell-cycle regulation. Our results may inspire further experimental studies aimed at identification of exact biological functions, specific substrates and molecular mechanisms of reactions performed by these highly diverse proteins.

Mutational Analysis of the Binding Pockets of the Diketo Acid Inhibitor L-742,001 in the Influenza Virus PA Endonuclease

“…The catalytic core houses one or two divalent metal ions (Mg 2ϩ or Mn 2ϩ ), coordinated by a histidine (His41), a cluster of acidic residues (Glu80, Asp108, and Glu119), and a conserved lysine (Lys134) implemented in catalysis (14,15). PA-Nter shares structural characteristics with other nucleases of the PD-(D/E)XK superfamily, which also includes most type II restriction endonucleases (16). Recently, structural similarity was reported for the catalytic domains of PA-Nter and the Prp8 endonuclease component of the yeast spliceosome (17).…”

Functional Diversity of Cytotoxic tRNase/Immunity Protein Complexes from Burkholderia pseudomallei

“…This ␤-hairpin constitutes much of the binding interface with the cognate immunity protein, and its sequence varies between family members (27). Analogous insertions into the PD(D/E)XK core have been detected in other superfamily members (23), again underscoring the flexibility of the core fold.…”

“…The canonical PD(D/E)XK active site found in type II restriction endonucleases is built from a conserved Asp residue at the N terminus of ␤2 and the (D/E)XK sub-motif within ␤3 of the core (23,36). However, there are several variations in the active-site configuration, with catalytic residues migrating to other secondary structure elements during evolution (23,37,38). For the CdiA-CT E479 nuclease domain, Asp-229 and Asp-243 occupy canonical positions within ␤2 and ␤3, but Glu-204 and His-275 are contributed by ␣1 and ␣2, respectively.…”

“…The C-terminal tRNase domain of CdiA-CT E479 is built upon an ␣/␤-fold characteristic of PD(D/E)XK nucleases. The PD(D/E)XK superfamily includes most restriction endonucleases and other enzymes involved in DNA recombination and repair (23). A DALI server (24) search reveals that the type V toxin domain from B. pseudomallei 1026b is the closest structural homolog of CdiA-CT E479 .…”

“…Although most PD (D/E)XK nucleases are DNA-specific phosphodiesterases, our findings indicate that these enzymes are commonly used as toxic RNases in bacterial competition. Because PD(D/E)XK nucleases can be difficult to identify through sequence analyses (23,25), it is possible that many other uncharacterized CDI toxins also belong to the superfamily.…”