A novel protein kinase-like domain in a selenoprotein, widespread in the tree of life

Abstract

Selenoproteins serve important functions in many organisms, usually providing essential oxidoreductase enzymatic activity, often for defense against toxic xenobiotic substances. Most eukaryotic genomes possess a small number of these proteins, usually not more than 20. Selenoproteins belong to various structural classes, often related to oxidoreductase function, yet a few of them are completely uncharacterised.Here, the structural and functional prediction for the uncharacterised selenoprotein O (SELO) is presented. Using bioinformatics tools, we predict that SELO protein adopts a three-dimensional fold similar to protein kinases. Furthermore, we argue that despite the lack of conservation of the "classic" catalytic aspartate residue of the archetypical His-Arg-Asp motif, SELO kinases might have retained catalytic phosphotransferase activity, albeit with an atypical active site. Lastly, the role of the selenocysteine residue is considered and the possibility of an oxidoreductase-regulated kinase function for SELO is discussed.The novel kinase prediction is discussed in the context of functional data on SELO orthologues in model organisms, FMP40 a.k.a.YPL222W (yeast), and ydiU (bacteria). Expression data from bacteria and yeast suggest a role in oxidative stress response. Analysis of genomic neighbourhoods of SELO homologues in the three domains of life points toward a role in regulation of ABC transport, in oxidative stress response, or in basic metabolism regulation. Among bacteria possessing SELO homologues, there is a significant over-representation of aquatic organisms, also of aerobic ones. The selenocysteine residue in SELO proteins occurs only in few members of this protein family, including proteins from Metazoa, and few small eukaryotes (Ostreococcus, stramenopiles). It is also demonstrated that enterobacterial mchC proteins involved in maturation of bactericidal antibiotics, microcins, form a distant subfamily of the SELO proteins.The new protein structural domain, with a putative kinase function assigned, expands the known kinome and deserves experimental determination of its biological role within the cell-signaling network.

Figure 1. CLANS graph visualizing PSI-BLAST-detected significant (dark grey) and sub-significant (light grey) similarities among protein kinase-like proteins.

Red: UPF0061 (SELO) family, Light green: pkinase and pkinase_Tyr, Dark blue: APH phosphotransferase, Magenta: PIP5K, Grey: alpha_kinase. Pink: PI3_PI4, Light blue: Act_Frag_cataly, Yellow: PPDK_N, Dark green: Kdo, Orange: UL97.

Figure 2. Phylogenetic tree (PhyML) of the representative SELO proteins.

Tree branch coloring: Red: Bacteria, Dark green: Plants, Light green: Green algae, Orange: Chromoalveolata, Magenta: Excavates, Yellow: vertebrates, Blue: non-vertebrate Metazoa, Brown: Fungi. Inner ring: presence of Cys or Sec at C-terminus: CXX> motif: green; UXX> motif: red. Outer ring: presence of additional Cys residues prior to the [CU]XX> motif: CXX[CU]XX>: magenta, CX[CU]XX>: blue, CX(3–10)[CU]XX>: black. Identifiers: NCBI gi numbers. The tree is built using the alignment shown in Figure S3.

Figure 3. Multiple sequence alignment of selected SELO proteins (representatives of branches identified in the tree in Fig. 2 ).

mchC protein is the penultimate sequence. Secondary structure prediction for human SELO protein is shown. Secondary structure elements named as in PKA, according to Knighton . “x” denotes putative residues belonging to the C-spine (catalytic), “+” denotes putative R-spine (regulatory) residues. Exclamation signs denote potential phosphorylation sites in the activation loop. Locations of predicted key catalytic residues shown, in standard PKA numbering (e.g. H166). Identifiers: NCBI gi numbers.

Figure 4. Sequence logos for the conserved motifs of the SELO family (using the 143 representative sequences), in “classic” protein kinases (Pfam family pkinase, PF00069), and in the mchC group.

Figure 5. Active site details in the model of the kinase domain of the human SELO protein.

Top. Schematic representation. Comparison of binding of an ATP molecule and two Mg²⁺ ions in SELO model (upper residue labels) and in the PKA structure (lower labels). Bottom. As in top panel, wireframe model of the predicted active site of human SELO with ATP and two Mg²⁺ ions.