STK40 Is a Pseudokinase that Binds the E3 Ubiquitin Ligase COP1

Abstract

Serine/threonine kinase 40 (STK40) was originally identified as a distant homolog of Tribbles-family proteins. Despite accumulating data attesting to the importance of STK40 in a variety of different physiologic processes, little is known about its biological activity or mechanism of action. Here, we show that STK40 interacts with Constitutive Photomorphogenic Protein 1 (COP1), relying primarily on a C-terminal sequence analogous to the motif found in Tribbles proteins. In order to further elucidate structure-function relationships in STK40, we determined the crystal structure of the STK40 kinase homology domain at 2.5 Å resolution. The structure, together with ATP-binding assay results, show that STK40 is a pseudokinase, in which substitutions of conserved residues within the kinase domain prevent ATP binding. Although the structure of the kinase homology domain diverges from the analogous region of Trib1, the results reported here suggest functional parallels between STK40 and Tribbles-family proteins as COP1 adaptors.

Keywords: ATP binding; COP1; E3 ligase; RFWD2; SINK-homologous kinase; STK40; SgK495; Tribbles; X-ray crystallography; pseudokinase.

Figure 1. STK40 binds to COP1 in human cells

(A) Schematic diagrams of human STK40 constructs used in the accompanying binding studies. The putative COP1 binding motif in full-length STK40 (SSLSGPLQVVPDI) is aligned with that of Trib1 with the critical VP colored in cyan. (B) Results of tandem immunoprecipitation experiments in HeLa cells using STK40 as “bait.” The number of unique endogenous COP1 peptides recovered from the cytoplasmic fraction is listed for each of three independent experiments. Endogenous COP1 peptides recovered from the nuclear fraction are in parentheses. (C) Flag-STK40 immunoprecipitations carried out in 293T cells. N-terminal Flag-tagged FL, KHD and STK40 proteins were recovered using anti-Flag resin. A Flag-GFP-fused peptide derived from STK40 (“PEP,” amino acids 339–351) was also recovered using anti-FLAG resin. The cleared lysates (Input) and the immunoprecipitates (Flag IP) were western blotted and probed with anti-Flag (top) and anti-COP1 antibodies (bottom). The position of endogenous COP1 is indicated by a black arrow. (D) Fluorescence polarization assay measuring the binding affinity of the human COP1 WD40 β propeller (386–731) for the STK40 peptide FITC-SSLSGPLQVVPD. The change in fluorescence polarization is plotted as a function of COP1 protein concentration. Trib1 peptide (FITC-SEIGTSGQIVPEY) is included for comparison. (E) Competition assay comparing binding affinities of STK40 proteins, including the KHD, KHD+20 and STK40 peptides (wild-type PEP and the two STK40 VP mutants labeled m1, m2) to the COP1 WD40 domain. Displacement of the consensus STK40 peptide FITC-SSLSGPLQVVPD was monitored using fluorescence polarization. The change in polarization is plotted for the indicated competitor as a function of unlabeled competitor concentration.

Figure 2. Crystal structure of STK40

(A) Domain organization of STK40 full-length protein with a short N-terminus (1–21), serine/threonine kinase homology domain (KHD, 22–339), and C-terminus (340–435). The crystal structure includes the entire KHD. The N-lobe is colored in green and the C-lobe is in blue (aa 156–336). Within the N-lobe, the glycine-rich P-loop is colored in grey (40–47), the αC helix is in cyan (84–98), and the hinge region is in red (142–155). Within the C-lobe, the catalytic loop is colored in yellow (191–202) and the activation loop is in magenta (215–243). (B) Ribbon diagram of the crystal structure of STK40 KHD using the same color scheme. (C,D) Least squares superposition (LSQ) of STK40 N-lobe (green, residues 35–71) on the N-lobe of PKA (wheat, residues 42–75) and on the N-lobe of Trib1 (light pink, residues 94–123). Coot least squares alignment (LSQ) was used for superpositions. RMSD values are listed.

Figure 3. Atypical sequence insertions in STK40 structure

(A) Structural and sequence alignment of the β4–β5 loop extension. Left: STK40 N-lobe (chain D) β4–β5 loop (green) is aligned to the PKA short connecting loop (wheat), with residues of the predicted NLS represented as sticks. Right: Sequence insertion of STK40 aligned to selected active kinases: PKA (pdb code:1ATP), EGFR (1M14), Chk1 (1IA8), CaMKII (2VZ6), Aurora-A (2WTV), CASK (3MFS) and pseudokinases: Trib1 (5CEK), VRK3 (2JII), TYK2 (3ZON), HER3 (4RIW), ILK (3REP), STRADα (3GNI), ROP2 (2W1Z). Brackets indicate predicted nuclear localization signal (NLS). (B) Sequence alignment of hinge loop insertion. Residues flanking the unique hinge insertion in STK40 are aligned to analogous residues in known structures as in (A). (C) Structure of the hinge region of STK40 (red arrow) compared to the hinge region (red arrow on PKA) and the C-terminal tail of PKA (cyan). Coot secondary structure alignment (SSM) was used for superpositions.

Figure 4. Degradation of the STK40 ATP binding pocket

(A) Multiple sequence alignment of canonical kinase motifs. The STK40 sequence (bottom) is aligned to the active kinases PKA, EGFR, Chk1, CamKII, Aurora-A, and CASK, and the pseudokinases: Trib1, VRK3, TYK2 pseudokinase domain, HER3, ILK, STRADα, and ROP2. Identical residues are highlighted in cyan. Divergent residues in STK40 are indicated by red dots. (B) Comparison of ATP binding pockets among PKA (wheat), STK40 (green), and Trib1 (light pink). Superposition of STK40 and Trib1 on PKA was performed using SSM in Coot. The position of ATP in STK40 and Trib1 is modeled based on its position in the aligned, ATP-bound structure of PKA (PDB code 1ATP). ATP, A70 (PKA), Q64 (STK40) and R118 (Trib1) are represented as spheres. (C–D) Thermal shift assay. (C) Shift in melting temperature (ΔTm) of the STK40 kinase-homology domain (aa 22–339, black bars), MELK kinase (aa 1–342, white bars), and the Trib1 kinase-homology domain (aa 84–342, grey bars) upon addition of ATP as ligand. Ligand concentration varies from 0–1 mM as indicated on the x-axis. (D) Thermal shift using the ATP analogue staurosporine, titrated from 0–30 µM. Graphs were produced in GraphPad Prism, plotting the mean and standard deviation of T_m from three independent experiments.