Abstract
Kindlin-2 belongs to a subfamily of FERM domain containing proteins, which plays key roles in activating integrin transmembrane receptors and mediating cell adhesion. Compared to conventional FERM domains, kindlin-2 FERM contains an inserted pleckstrin homology (PH) domain that specifically binds to phosphatidylinositol (3,4,5) trisphosphate (PIP3) and regulates the kindlin-2 function. We have determined the crystal structure of kindlin-2 PH domain at 1.9 Å resolution, which reveals a conserved PH domain fold with a highly charged and open binding pocket for PIP3 head group. Structural comparison with a previously reported solution structure of kindlin-2 PH domain bound to PIP3 head group reveals that upon PIP3 insertion, there is a significant conformational change of both the highly positively charged loop at the entry of the PIP3 binding pocket and the entire β barrel of the PH domain. We propose that such “induced-fit” type change is crucial for the tight binding of PIP3 to anchor kindlin-2 onto the membrane surface, thereby promoting its binding to integrins. Our results provide important structural insight into kindlin-2-mediated membrane anchoring and integrin activation.
Article PDF
Similar content being viewed by others
References
Adams, P.D., Afonine, P.V., Bunkóczi, G., Chen, V.B., Davis, I.W., Echols, N., Headd, J.J., Hung, L.W., Kapral, G.J., Grosse-Kunstleve, R.W., et al. (2010). PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213–221.
Anthis, N.J., Wegener, K.L., Ye, F., Kim, C., Goult, B.T., Lowe, E.D., Vakonakis, I., Bate, N., Critchley, D.R., Ginsberg, M.H., et al. (2009). The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. EMBO J 28, 3623–3632.
Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126–2132.
García-Alvarez, B., de Pereda, J.M., Calderwood, D.A., Ulmer, T.S., Critchley, D., Campbell, I.D., Ginsberg, M.H., and Liddington, R.C. (2003). Structural determinants of integrin recognition by talin. Mol Cell 11, 49–58.
Harburger, D.S., Bouaouina, M., and Calderwood, D.A. (2009). Kindlin-1 and -2 directly bind the C-terminal region of beta integrin cytoplasmic tails and exert integrin-specific activation effects. J Biol Chem 284, 11485–11497.
Hynes, R.O. (2002). Integrins: bidirectional, allosteric signaling machines. Cell 110, 673–687.
Kim, M., Carman, C.V., and Springer, T.A. (2003). Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins. Science 301, 1720–1725.
Lee, J.H., An, J.Y., Park, H., Kim, H.J., and Eom, S.H. (2011). Crystallization and preliminary x-ray crystallographic analysis of the human kindlin-2 PH domain. Acta Crystallogr Sect F Struct Biol Cryst Commun 67, 696–699.
Lemmon, M.A. (2008). Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol 9, 99–111.
Liu, J., Fukuda, K., Xu, Z., Ma, Y.Q., Hirbawi, J., Mao, X., Wu, C., Plow, E.F., and Qin, J. (2011). Structural basis of phosphoinositide binding to kindlin-2 protein pleckstrin homology domain in regulating integrin activation. J Biol Chem 286, 43334–43342.
Luo, B.H., Carman, C.V., and Springer, T.A. (2007). Structural basis of integrin regulation and signaling. Annu Rev Immunol 25, 619–647.
Ma, Y.Q., Qin, J., Wu, C., and Plow, E.F. (2008). Kindlin-2 (Mig-2): a co-activator of beta3 integrins. J Cell Biol 181, 439–446.
McCoy, A.J., Grosse-Kunstleve, R.W., Adams, P.D., Winn, M.D., Storoni, L.C., and Read, R.J. (2007). Phaser crystallographic software. J Appl Crystallogr 40, 658–674.
Milburn, C.C., Deak, M., Kelly, S.M., Price, N.C., Alessi, D.R., and van Aalten, D.M. (2003). Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change. Biochem J 375, 531–538.
Montanez, E., Ussar, S., Schifferer, M., Bösl, M., Zent, R., Moser, M., and Fässler, R. (2008). Kindlin-2 controls bidirectional signaling of integrins. Genes Dev 22, 1325–1330.
Moser, M., Legate, K.R., Zent, R., and Fässler, R. (2009). The tail of integrins, talin, and kindlins. Science 324, 895–899.
Moser, M., Nieswandt, B., Ussar, S., Pozgajova, M., and Fässler, R. (2008). Kindlin-3 is essential for integrin activation and platelet aggregation. Nat Med 14, 325–330.
Otwinowski, Z., and Minor, W. (1997). Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307–326.
Perera, H.D., Ma, Y.Q., Yang, J., Hirbawi, J., Plow, E.F., and Qin, J. (2011). Membrane binding of the N-terminal ubiquitin-like domain of kindlin-2 is crucial for its regulation of integrin activation. Structure 19, 1664–1671.
Plow, E.F., Qin, J., and Byzova, T. (2009). Kindling the flame of integrin activation and function with kindlins. Curr Opin Hematol 16, 323–328.
Qin, J., Vinogradova, O., and Plow, E.F. (2004). Integrin bidirectional signaling: a molecular view. PLoS Biol 2, e169.
Qu, H., Tu, Y., Shi, X., Larjava, H., Saleem, M.A., Shattil, S.J., Fukuda, K., Qin, J., Kretzler, M., and Wu, C. (2011). Kindlin-2 regulates podocyte adhesion and fibronectin matrix deposition through interactions with phosphoinositides and integrins. J Cell Sci 124, 879–891.
Rogalski, T.M., Mullen, G.P., Gilbert, M.M., Williams, B.D., and Moerman, D.G. (2000). The UNC-112 gene in Caenorhabditis elegans encodes a novel component of cell-matrix adhesion structures required for integrin localization in the muscle cell membrane. J Cell Biol 150, 253–264.
Shi, X., Ma, Y.Q., Tu, Y., Chen, K., Wu, S., Fukuda, K., Qin, J., Plow, E.F., and Wu, C. (2007). The MIG-2/integrin interaction strengthens cell-matrix adhesion and modulates cell motility. J Biol Chem 282, 20455–20466.
Siegel, D.H., Ashton, G.H., Penagos, H.G., Lee, J.V., Feiler, H.S., Wilhelmsen, K.C., South, A.P., Smith, F.J., Prescott, A.R., Wessagowit, V., et al. (2003). Loss of kindlin-1, a human homolog of the Caenorhabditis elegans actin-extracellular-matrix linker protein UNC-112, causes Kindler syndrome. Am J Hum Genet 73, 174–187.
Vinogradova, O., Velyvis, A., Velyviene, A., Hu, B., Haas, T., Plow, E., and Qin, J. (2002). A structural mechanism of integrin alpha(IIb)beta(3) “inside-out” activation as regulated by its cytoplasmic face. Cell 110, 587–597.
Zhang, Y., and Wang, H. (2012). Integrin signalling and function in immune cells. Immunology 135, 268–275.
Author information
Authors and Affiliations
Corresponding authors
Additional information
These authors contributed equally to the work.
Rights and permissions
About this article
Cite this article
Liu, Y., Zhu, Y., Ye, S. et al. Crystal structure of kindlin-2 PH domain reveals a conformational transition for its membrane anchoring and regulation of integrin activation. Protein Cell 3, 434–440 (2012). https://doi.org/10.1007/s13238-012-2046-1
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s13238-012-2046-1