PCTAIRE1 (PCTK1/CDK16) protein kinase in complex with indirubin E804

Krojer, T., Sharpe, T.D., Roos, A., Savitsky, P., Amos, A., Ayinampudi, V., Berridge, G., Fedorov, O., Keates, T., Phillips, C., Burgess-Brown, N., Zhang, Y., Pike, A.C.W., Muniz, J., Vollmar, M., Thangaratnarajah, C., Rellos, P., Ugochukwu, E., Filippakopoulos, P., Lee, W.H., Marsden, B.D., Liu, Q., Yue, W., Das, S., von Delft, F., Edwards, A., Arrowsmith, C.H., Weigelt, J., Bountra, C., Knapp, S., Bullock, A

PDB Code: 3MTL (deposited on 30.Apr.10)

Datapack version: 1 (built on 1.Apr.11; last revised on 04.Apr.11)

Description

PCTAIRE1, also known as PCTK1 or CDK16, belongs to the CDK family of protein kinases. The PCTAIRE protein kinases comprise a distinct subfamily and are so named for the presence of a serine to cysteine substitution in the conserved PSTAIRE amino acid motif found in prototypic CDK kinases. Three members of this kinase subfamily, PCTAIRE1-3, have been identified in humans. The three PCTAIRE kinases are 65% identical to one another (80% within the catalytic domain) (Meyerson et al., 1992), (Okuda et al., 1992). For many years no cyclin interaction partners were identified for the PCTAIREs and it was speculated that conserved sequences in the N-terminus provided the activation that cyclins normally provide to the rest of the CDK family (Graeser et al., 2002; Cole 2009).

The human PCTAIRE1 gene maps to the X chromosome (Xp11.3 p11.23), a chromosomal region associated with a growing number of diseases with a genetic basis. PCTAIRE1 is widely expressed with high levels in brain and testis (Besset et al., 1999; Rhee and Wolgemuth, 1995). Little is known about the function of this kinase and diverse roles have been suggested including as a negative regulator of insulin-responsive glucose transport (Tang et al., 2006), a modulator of exocytosis, (Liu et al., 2006), a control factor for neurite outgrowth (Graeser et al., 2002) and for membrane traffic through the early secretory pathway (Palmer et al., 2005). ;So far no mouse model has been established to confirm any of the proposed functions. ES cells lacking PCTAIRE1 have been generated but no germline transmission could be achieved, which could point to an essential role of PCTAIRE 1 in the formation of viable sperm (Graeser et al., 2002).

Here we present the structure of the kinase domain of PCTAIRE1 refined at 2.4 Å resolution. Following the deposition of the structure, it was reported that a novel protein, cyclin Y, was the likely interaction partner for PCTAIRE1 (ou et al., 2010).

Structural Features

Overall structure : The kinase domain of PCTAIRE1 was crystallised in the presence of the kinase inhibitor Indirubin E804. The structure shows the typica CDK insert which packs against the αG helix as well as a PCTAIRE-family specific C-terminal extension. Some disorder was suggested by the weak electron density around parts of the activation loop and αC helix.

(TIP 1: the background colour can be changed to [WHITE] or [BLACK] )

(TIP 2: reset the view )

Structural comparison: Comparison with the CDK2 - cyclinA structure (1QMZ) shows the general conservation of the CDK fold , but highlights the inactive catalytic state of the PCTAIRE1 kinase. This is most evident at the cyclin interface where the αC helix in PCTAIRE1 is largely unstructured and reduced to a single turn.

Activation site region: The PCTAIRE motif adopts an extended and somewhat flexible conformation. At the end of the motif the catalytic αC-β3 salt bridge is formed by E393. However, the activation segments shows an inactive DGF-out conformation despite binding to a typical type I inhibitor.

Inhibitor binding: Indirubin E804 binds as an ATP-competitive inhibitor and forms three hydrogen bonds with the hinge region. With the rearrangement of the DFG motif, the compound shows excellent shape complementarity to the ATP pocket.

Note: The target annotations and structure descriptions within this datapack are compiled by our Principal Investigators and are not peer-reviewed. If you find anything in the annotations that is not accurate, please notify us using the our on-line feedback page or send an e-mail to isee@sgc.ox.ac.uk.

References

Besset, V., Rhee, K., and Wolgemuth, D.J. (1999). The cellular distribution and kinase activity of the Cdk family member Pctaire1 in the adult mouse brain and testis suggest functions in differentiation. Cell Growth Differ 10, 173-181.

Cole, A.R. (2009). PCTK proteins: the forgotten brain kinases? Neurosignals. 17, 288-97.

Graeser, R., Gannon, J., Poon, R.Y., Dubois, T., Aitken, A., and Hunt, T. (2002). Regulation of the CDK-related protein kinase PCTAIRE-1 and its possible role in neurite outgrowth in Neuro-2A cells. J. Cell Science 115, 3479-3490.

Liu, Y., Cheng, K., Gong, K., Fu, A.K., and Ip, N.Y. (2006). Pctaire1 phosphorylates N-ethylmaleimide-sensitive fusion protein: implications in the regulation of its hexamerization and exocytosis. J. Biol. Chem. 281, 9852-9858.

Meyerson, M., Enders, G.H., Wu, C.L., Su, L.K., Gorka, C., Nelson, C., Harlow, E., and Tsai, L.H. (1992). A family of human cdc2-related protein kinases. EMBO J. 11, 2909-2917.

Okuda, T., Cleveland, J.L., and Downing, J.R. (1992). PCTAIRE-1 and PCTAIRE-3, two members of a novel cdc2/CDC28-related protein kinase gene family. Oncogene 7, 2249-2258.

Palmer, K.J., Konkel, J.E., and Stephens, D.J. (2005). PCTAIRE protein kinases interact directly with the COPII complex and modulate secretory cargo transport. J. Cell Science 118, 3839-3847.

Rhee, K., and Wolgemuth, D.J. (1995). Cdk family genes are expressed not only in dividing but also in terminally differentiated mouse germ cells, suggesting their possible function during both cell division and differentiation. Dev Dyn 204, 406-420.

Tang, X., Guilherme, A., Chakladar, A., Powelka, A.M., Konda, S., Virbasius, J.V., Nicoloro, S.M., Straubhaar, J., and Czech, M.P. (2006). An RNA interference-based screen identifies MAP4K4/NIK as a negative regulator of PPARgamma, adipogenesis, and insulin-responsive hexose transport. Proc. Natl. Acad. Sci. USA 103, 2087-2092.

Ou, C.Y., Poon, V.Y., Maeder, C.I., Watanabe, S., Lehrman, E.K., Fu, A.K., Park, M., Fu, W.Y., Jorgensen, E.M., Ip, N.Y., Shen, K. (2010). Two cyclin-dependent kinase pathways are essential for polarized trafficking of presynaptic components. Cell. 141, 846-58.

Download Standalone iSee datapack: You can download and view all the Information of a datapack offline including information not available in the web version (where applicable). You will also need to download and install the ICM-Browser to view the standalone datapacks.

 
Datapack created using Molsoft ICM and Molsoft Browser technologies. (Patent Pending)