Crystal structure of kindlin-2 PH domain reveals a conformational transition for its membrane anchoring and regulation of integrin activation

Yan Liu, Yun Zhu, Sheng Ye(), Rongguang Zhang()

PDF(708 KB)
PDF(708 KB)
Protein Cell ›› 2012, Vol. 3 ›› Issue (6) : 434-440. DOI: 10.1007/s13238-012-2046-1
COMMUNICATION
COMMUNICATION

Crystal structure of kindlin-2 PH domain reveals a conformational transition for its membrane anchoring and regulation of integrin activation

  • Yan Liu, Yun Zhu, Sheng Ye(), Rongguang Zhang()
Author information +
History +

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 ? 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.

Keywords

kindlin-2 / integrin / PH domain / crystal structure / cell adhesion / membrane

Cite this article

Download citation ▾
Yan Liu, Yun Zhu, Sheng Ye, Rongguang Zhang. Crystal structure of kindlin-2 PH domain reveals a conformational transition for its membrane anchoring and regulation of integrin activation. Prot Cell, 2012, 3(6): 434‒440 https://doi.org/10.1007/s13238-012-2046-1

References

[1] 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., . (2010). PHENIX: a comprehensive Python- based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr 66, 213-221 .10.1107/S0907444909052925
[2] 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., . (2009). The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. EMBO J 28, 3623-3632 .10.1038/emboj.2009.287
[3] Emsley, P., and Cowtan, K. (2004). Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr 60, 2126-2132 .10.1107/S0907444904019158
[4] 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 .10.1016/S1097-2765(02)00823-7
[5] 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 .10.1074/jbc.M809233200
[6] Hynes, R.O. (2002). Integrins: bidirectional, allosteric signaling machines. Cell 110, 673-687 .10.1016/S0092-8674(02)00971-6
[7] Kim, M., Carman, C.V., and Springer, T.A. (2003). Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins. Science 301, 1720-1725 .10.1126/science.1084174
[8] 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 .10.1107/S1744309111013820
[9] Lemmon, M.A. (2008). Membrane recognition by phospholipid- binding domains. Nat Rev Mol Cell Biol 9, 99-111 .10.1038/nrm2328
[10] 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 .10.1074/jbc.M111.295352
[11] Luo, B.H., Carman, C.V., and Springer, T.A. (2007). Structural basis of integrin regulation and signaling. Annu Rev Immunol 25, 619-647 .10.1146/annurev.immunol.25.022106.141618
[12] 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 .10.1083/jcb.200710196
[13] 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 .10.1107/S0021889807021206
[14] 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 .10.1042/BJ20031229
[15] Montanez, E., Ussar, S., Schifferer, M., B?sl, M., Zent, R., Moser, M., and F?ssler, R. (2008). Kindlin-2 controls bidirectional signaling of integrins. Genes Dev 22, 1325-1330 .10.1101/gad.469408
[16] Moser, M., Legate, K.R., Zent, R., and F?ssler, R. (2009). The tail of integrins, talin, and kindlins. Science 324, 895-899 .10.1126/science.1163865
[17] Moser, M., Nieswandt, B., Ussar, S., Pozgajova, M., and F?ssler, R. (2008). Kindlin-3 is essential for integrin activation and platelet aggregation. Nat Med 14, 325-330 .10.1038/nm1722
[18] Otwinowski, Z., and Minor, W. (1997). Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol 276, 307-326 .10.1016/S0076-6879(97)76066-X
[19] 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 .10.1016/j.str.2011.08.012
[20] 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 .10.1097/MOH.0b013e32832ea389
[21] Qin, J., Vinogradova, O., and Plow, E.F. (2004). Integrin bidirectional signaling: a molecular view. PLoS Biol 2, e169.10.1371/journal.pbio.0020169
[22] 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 .10.1242/jcs.076976
[23] 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 .10.1083/jcb.150.1.253
[24] 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. 10.1074/jbc.M611680200
[25] 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., . (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 .10.1086/376609
[26] 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 .10.1016/S0092-8674(02)00906-6
[27] Zhang, Y., and Wang, H. (2012). Integrin signalling and function in immune cells. Immunology 135, 268-275 .10.1111/j.1365-2567.2011.03549.x
AI Summary AI Mindmap
PDF(708 KB)

Accesses

Citations

Detail

Sections
Recommended

/