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. 2012 May 31;3(6):434–440. doi: 10.1007/s13238-012-2046-1

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

Yan Liu 1, Yun Zhu 1, Sheng Ye 1,✉, Rongguang Zhang 1,✉
PMCID: PMC4875484  PMID: 22653426

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.

Keywords: kindlin-2, integrin, PH domain, crystal structure, cell adhesion, membrane

Footnotes

These authors contributed equally to the work.

Contributor Information

Sheng Ye, Email: yesheng@moon.ibp.ac.cn.

Rongguang Zhang, Email: rzhang@ibp.ac.cn.

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., et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr D Biol Crystallogr. 2010;66:213–221. doi: 10.1107/S0907444909052925. [DOI] [PMC free article] [PubMed] [Google Scholar]
  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., et al. The structure of an integrin/talin complex reveals the basis of inside-out signal transduction. EMBO J. 2009;28:3623–3632. doi: 10.1038/emboj.2009.287. [DOI] [PMC free article] [PubMed] [Google Scholar]
  3. Emsley P., Cowtan K. Coot: model-building tools for molecular graphics. Acta Crystallogr D Biol Crystallogr. 2004;60:2126–2132. doi: 10.1107/S0907444904019158. [DOI] [PubMed] [Google Scholar]
  4. García-Alvarez B., de Pereda J.M., Calderwood D.A., Ulmer T.S., Critchley D., Campbell I.D., Ginsberg M.H., Liddington R.C. Structural determinants of integrin recognition by talin. Mol Cell. 2003;11:49–58. doi: 10.1016/S1097-2765(02)00823-7. [DOI] [PubMed] [Google Scholar]
  5. Harburger D.S., Bouaouina M., Calderwood D.A. Kindlin-1 and -2 directly bind the C-terminal region of beta integrin cytoplasmic tails and exert integrin-specific activation effects. J Biol Chem. 2009;284:11485–11497. doi: 10.1074/jbc.M809233200. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Hynes R.O. Integrins: bidirectional, allosteric signaling machines. Cell. 2002;110:673–687. doi: 10.1016/S0092-8674(02)00971-6. [DOI] [PubMed] [Google Scholar]
  7. Kim M., Carman C.V., Springer T.A. Bidirectional transmembrane signaling by cytoplasmic domain separation in integrins. Science. 2003;301:1720–1725. doi: 10.1126/science.1084174. [DOI] [PubMed] [Google Scholar]
  8. Lee J.H., An J.Y., Park H., Kim H.J., Eom S.H. Crystallization and preliminary x-ray crystallographic analysis of the human kindlin-2 PH domain. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2011;67:696–699. doi: 10.1107/S1744309111013820. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Lemmon M.A. Membrane recognition by phospholipid-binding domains. Nat Rev Mol Cell Biol. 2008;9:99–111. doi: 10.1038/nrm2328. [DOI] [PubMed] [Google Scholar]
  10. Liu J., Fukuda K., Xu Z., Ma Y.Q., Hirbawi J., Mao X., Wu C., Plow E.F., Qin J. Structural basis of phosphoinositide binding to kindlin-2 protein pleckstrin homology domain in regulating integrin activation. J Biol Chem. 2011;286:43334–43342. doi: 10.1074/jbc.M111.295352. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Luo B.H., Carman C.V., Springer T.A. Structural basis of integrin regulation and signaling. Annu Rev Immunol. 2007;25:619–647. doi: 10.1146/annurev.immunol.25.022106.141618. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Ma Y.Q., Qin J., Wu C., Plow E.F. Kindlin-2 (Mig-2): a co-activator of beta3 integrins. J Cell Biol. 2008;181:439–446. doi: 10.1083/jcb.200710196. [DOI] [PMC free article] [PubMed] [Google Scholar]
  13. McCoy A.J., Grosse-Kunstleve R.W., Adams P.D., Winn M.D., Storoni L.C., Read R.J. Phaser crystallographic software. J Appl Crystallogr. 2007;40:658–674. doi: 10.1107/S0021889807021206. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Milburn C.C., Deak M., Kelly S.M., Price N.C., Alessi D.R., van Aalten D.M. Binding of phosphatidylinositol 3,4,5-trisphosphate to the pleckstrin homology domain of protein kinase B induces a conformational change. Biochem J. 2003;375:531–538. doi: 10.1042/bj20031229. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Montanez E., Ussar S., Schifferer M., Bösl M., Zent R., Moser M., Fässler R. Kindlin-2 controls bidirectional signaling of integrins. Genes Dev. 2008;22:1325–1330. doi: 10.1101/gad.469408. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Moser M., Legate K.R., Zent R., Fässler R. The tail of integrins, talin, and kindlins. Science. 2009;324:895–899. doi: 10.1126/science.1163865. [DOI] [PubMed] [Google Scholar]
  17. Moser M., Nieswandt B., Ussar S., Pozgajova M., Fässler R. Kindlin-3 is essential for integrin activation and platelet aggregation. Nat Med. 2008;14:325–330. doi: 10.1038/nm1722. [DOI] [PubMed] [Google Scholar]
  18. Otwinowski Z., Minor W. Processing of x-ray diffraction data collected in oscillation mode. Methods Enzymol. 1997;276:307–326. doi: 10.1016/S0076-6879(97)76066-X. [DOI] [PubMed] [Google Scholar]
  19. Perera H.D., Ma Y.Q., Yang J., Hirbawi J., Plow E.F., Qin J. Membrane binding of the N-terminal ubiquitin-like domain of kindlin-2 is crucial for its regulation of integrin activation. Structure. 2011;19:1664–1671. doi: 10.1016/j.str.2011.08.012. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Plow E.F., Qin J., Byzova T. Kindling the flame of integrin activation and function with kindlins. Curr Opin Hematol. 2009;16:323–328. doi: 10.1097/MOH.0b013e32832ea389. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Qin J., Vinogradova O., Plow E.F. Integrin bidirectional signaling: a molecular view. PLoS Biol. 2004;2:e169. doi: 10.1371/journal.pbio.0020169. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Qu H., Tu Y., Shi X., Larjava H., Saleem M.A., Shattil S.J., Fukuda K., Qin J., Kretzler M., Wu C. Kindlin-2 regulates podocyte adhesion and fibronectin matrix deposition through interactions with phosphoinositides and integrins. J Cell Sci. 2011;124:879–891. doi: 10.1242/jcs.076976. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Rogalski T.M., Mullen G.P., Gilbert M.M., Williams B.D., Moerman D.G. 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. 2000;150:253–264. doi: 10.1083/jcb.150.1.253. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Shi X., Ma Y.Q., Tu Y., Chen K., Wu S., Fukuda K., Qin J., Plow E.F., Wu C. The MIG-2/integrin interaction strengthens cell-matrix adhesion and modulates cell motility. J Biol Chem. 2007;282:20455–20466. doi: 10.1074/jbc.M611680200. [DOI] [PubMed] [Google Scholar]
  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., et al. 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. 2003;73:174–187. doi: 10.1086/376609. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Vinogradova O., Velyvis A., Velyviene A., Hu B., Haas T., Plow E., Qin J. A structural mechanism of integrin alpha(IIb)beta(3) “inside-out” activation as regulated by its cytoplasmic face. Cell. 2002;110:587–597. doi: 10.1016/S0092-8674(02)00906-6. [DOI] [PubMed] [Google Scholar]
  27. Zhang Y., Wang H. Integrin signalling and function in immune cells. Immunology. 2012;135:268–275. doi: 10.1111/j.1365-2567.2011.03549.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

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