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. 1997 Jun 15;16(12):3396–3404. doi: 10.1093/emboj/16.12.3396

Structure of the PH domain and Btk motif from Bruton's tyrosine kinase: molecular explanations for X-linked agammaglobulinaemia.

M Hyvönen 1, M Saraste 1
PMCID: PMC1169965  PMID: 9218782

Abstract

Bruton's tyrosine kinase (Btk) is an enzyme which is involved in maturation of B cells. It is a target for mutations causing X-linked agammaglobulinaemia (XLA) in man. We have determined the structure of the N-terminal part of Btk by X-ray crystallography at 1.6 A resolution. This part of the kinase contains a pleckstrin homology (PH) domain and a Btk motif. The structure of the PH domain is similar to those published previously: a seven-stranded bent beta-sheet with a C-terminal alpha-helix. Individual point mutations within the Btk PH domain which cause XLA can be classified as either structural or functional in the light of the three-dimensional structure and biochemical data. All functional mutations cluster into the positively charged end of the molecule around the predicted binding site for phosphatidylinositol lipids. It is likely that these mutations inactivate the Btk pathway in cell signalling by reducing its affinity for inositol phosphates, which causes a failure in translocation of the kinase to the cell membrane. A small number of signalling proteins contain a Btk motif that always follows a PH domain in the sequence. This small module has a novel fold which is held together by a zinc ion bound by three conserved cysteines and a histidine. The Btk motif packs against the second half of the beta-sheet of the PH domain, forming a close contact with it. Our structure opens up new ways to study the role of the PH domain and Btk motif in the cellular function of Btk and the molecular basis of its dysfunction in XLA patients.

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Selected References

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  1. Bolen J. B. Protein tyrosine kinases in the initiation of antigen receptor signaling. Curr Opin Immunol. 1995 Jun;7(3):306–311. doi: 10.1016/0952-7915(95)80103-0. [DOI] [PubMed] [Google Scholar]
  2. Brinkmann U., Mattes R. E., Buckel P. High-level expression of recombinant genes in Escherichia coli is dependent on the availability of the dnaY gene product. Gene. 1989 Dec 21;85(1):109–114. doi: 10.1016/0378-1119(89)90470-8. [DOI] [PubMed] [Google Scholar]
  3. Cullen P. J., Hsuan J. J., Truong O., Letcher A. J., Jackson T. R., Dawson A. P., Irvine R. F. Identification of a specific Ins(1,3,4,5)P4-binding protein as a member of the GAP1 family. Nature. 1995 Aug 10;376(6540):527–530. doi: 10.1038/376527a0. [DOI] [PubMed] [Google Scholar]
  4. Divecha N., Irvine R. F. Phospholipid signaling. Cell. 1995 Jan 27;80(2):269–278. doi: 10.1016/0092-8674(95)90409-3. [DOI] [PubMed] [Google Scholar]
  5. Ferguson K. M., Lemmon M. A., Schlessinger J., Sigler P. B. Crystal structure at 2.2 A resolution of the pleckstrin homology domain from human dynamin. Cell. 1994 Oct 21;79(2):199–209. doi: 10.1016/0092-8674(94)90190-2. [DOI] [PubMed] [Google Scholar]
  6. Ferguson K. M., Lemmon M. A., Schlessinger J., Sigler P. B. Structure of the high affinity complex of inositol trisphosphate with a phospholipase C pleckstrin homology domain. Cell. 1995 Dec 15;83(6):1037–1046. doi: 10.1016/0092-8674(95)90219-8. [DOI] [PubMed] [Google Scholar]
  7. Fukuda M., Kojima T., Kabayama H., Mikoshiba K. Mutation of the pleckstrin homology domain of Bruton's tyrosine kinase in immunodeficiency impaired inositol 1,3,4,5-tetrakisphosphate binding capacity. J Biol Chem. 1996 Nov 29;271(48):30303–30306. doi: 10.1074/jbc.271.48.30303. [DOI] [PubMed] [Google Scholar]
  8. Fukuda M., Mikoshiba K. Structure-function relationships of the mouse Gap1m. Determination of the inositol 1,3,4,5-tetrakisphosphate-binding domain. J Biol Chem. 1996 Aug 2;271(31):18838–18842. doi: 10.1074/jbc.271.31.18838. [DOI] [PubMed] [Google Scholar]
  9. Gibson T. J., Hyvönen M., Musacchio A., Saraste M., Birney E. PH domain: the first anniversary. Trends Biochem Sci. 1994 Sep;19(9):349–353. doi: 10.1016/0968-0004(94)90108-2. [DOI] [PubMed] [Google Scholar]
  10. Gill S. C., von Hippel P. H. Calculation of protein extinction coefficients from amino acid sequence data. Anal Biochem. 1989 Nov 1;182(2):319–326. doi: 10.1016/0003-2697(89)90602-7. [DOI] [PubMed] [Google Scholar]
  11. Harlan J. E., Hajduk P. J., Yoon H. S., Fesik S. W. Pleckstrin homology domains bind to phosphatidylinositol-4,5-bisphosphate. Nature. 1994 Sep 8;371(6493):168–170. doi: 10.1038/371168a0. [DOI] [PubMed] [Google Scholar]
  12. Holm L., Sander C. Protein structure comparison by alignment of distance matrices. J Mol Biol. 1993 Sep 5;233(1):123–138. doi: 10.1006/jmbi.1993.1489. [DOI] [PubMed] [Google Scholar]
  13. Laemmli U. K. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature. 1970 Aug 15;227(5259):680–685. doi: 10.1038/227680a0. [DOI] [PubMed] [Google Scholar]
  14. Leitges M., Schmedt C., Guinamard R., Davoust J., Schaal S., Stabel S., Tarakhovsky A. Immunodeficiency in protein kinase cbeta-deficient mice. Science. 1996 Aug 9;273(5276):788–791. doi: 10.1126/science.273.5276.788. [DOI] [PubMed] [Google Scholar]
  15. Lemmon M. A., Ferguson K. M., O'Brien R., Sigler P. B., Schlessinger J. Specific and high-affinity binding of inositol phosphates to an isolated pleckstrin homology domain. Proc Natl Acad Sci U S A. 1995 Nov 7;92(23):10472–10476. doi: 10.1073/pnas.92.23.10472. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Li T., Tsukada S., Satterthwaite A., Havlik M. H., Park H., Takatsu K., Witte O. N. Activation of Bruton's tyrosine kinase (BTK) by a point mutation in its pleckstrin homology (PH) domain. Immunity. 1995 May;2(5):451–460. doi: 10.1016/1074-7613(95)90026-8. [DOI] [PubMed] [Google Scholar]
  17. Merritt E. A., Murphy M. E. Raster3D Version 2.0. A program for photorealistic molecular graphics. Acta Crystallogr D Biol Crystallogr. 1994 Nov 1;50(Pt 6):869–873. doi: 10.1107/S0907444994006396. [DOI] [PubMed] [Google Scholar]
  18. Musacchio A., Gibson T., Rice P., Thompson J., Saraste M. The PH domain: a common piece in the structural patchwork of signalling proteins. Trends Biochem Sci. 1993 Sep;18(9):343–348. doi: 10.1016/0968-0004(93)90071-t. [DOI] [PubMed] [Google Scholar]
  19. Nicholls A., Sharp K. A., Honig B. Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins. 1991;11(4):281–296. doi: 10.1002/prot.340110407. [DOI] [PubMed] [Google Scholar]
  20. Park H., Wahl M. I., Afar D. E., Turck C. W., Rawlings D. J., Tam C., Scharenberg A. M., Kinet J. P., Witte O. N. Regulation of Btk function by a major autophosphorylation site within the SH3 domain. Immunity. 1996 May;4(5):515–525. doi: 10.1016/s1074-7613(00)80417-3. [DOI] [PubMed] [Google Scholar]
  21. Paterson H. F., Savopoulos J. W., Perisic O., Cheung R., Ellis M. V., Williams R. L., Katan M. Phospholipase C delta 1 requires a pleckstrin homology domain for interaction with the plasma membrane. Biochem J. 1995 Dec 15;312(Pt 3):661–666. doi: 10.1042/bj3120661. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Peränen J., Rikkonen M., Hyvönen M., Käriäinen L. T7 vectors with modified T7lac promoter for expression of proteins in Escherichia coli. Anal Biochem. 1996 May 1;236(2):371–373. doi: 10.1006/abio.1996.0187. [DOI] [PubMed] [Google Scholar]
  23. Rawlings D. J., Saffran D. C., Tsukada S., Largaespada D. A., Grimaldi J. C., Cohen L., Mohr R. N., Bazan J. F., Howard M., Copeland N. G. Mutation of unique region of Bruton's tyrosine kinase in immunodeficient XID mice. Science. 1993 Jul 16;261(5119):358–361. doi: 10.1126/science.8332901. [DOI] [PubMed] [Google Scholar]
  24. Rawlings D. J., Scharenberg A. M., Park H., Wahl M. I., Lin S., Kato R. M., Fluckiger A. C., Witte O. N., Kinet J. P. Activation of BTK by a phosphorylation mechanism initiated by SRC family kinases. Science. 1996 Feb 9;271(5250):822–825. doi: 10.1126/science.271.5250.822. [DOI] [PubMed] [Google Scholar]
  25. Rebecchi M., Peterson A., McLaughlin S. Phosphoinositide-specific phospholipase C-delta 1 binds with high affinity to phospholipid vesicles containing phosphatidylinositol 4,5-bisphosphate. Biochemistry. 1992 Dec 29;31(51):12742–12747. doi: 10.1021/bi00166a005. [DOI] [PubMed] [Google Scholar]
  26. Sali A., Blundell T. L. Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 1993 Dec 5;234(3):779–815. doi: 10.1006/jmbi.1993.1626. [DOI] [PubMed] [Google Scholar]
  27. Salim K., Bottomley M. J., Querfurth E., Zvelebil M. J., Gout I., Scaife R., Margolis R. L., Gigg R., Smith C. I., Driscoll P. C. Distinct specificity in the recognition of phosphoinositides by the pleckstrin homology domains of dynamin and Bruton's tyrosine kinase. EMBO J. 1996 Nov 15;15(22):6241–6250. [PMC free article] [PubMed] [Google Scholar]
  28. Thomas J. D., Sideras P., Smith C. I., Vorechovský I., Chapman V., Paul W. E. Colocalization of X-linked agammaglobulinemia and X-linked immunodeficiency genes. Science. 1993 Jul 16;261(5119):355–358. doi: 10.1126/science.8332900. [DOI] [PubMed] [Google Scholar]
  29. Tsukada S., Simon M. I., Witte O. N., Katz A. Binding of beta gamma subunits of heterotrimeric G proteins to the PH domain of Bruton tyrosine kinase. Proc Natl Acad Sci U S A. 1994 Nov 8;91(23):11256–11260. doi: 10.1073/pnas.91.23.11256. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Vihinen M., Iwata T., Kinnon C., Kwan S. P., Ochs H. D., Vorechovský I., Smith C. I. BTKbase, mutation database for X-linked agammaglobulinemia (XLA). Nucleic Acids Res. 1996 Jan 1;24(1):160–165. doi: 10.1093/nar/24.1.160. [DOI] [PMC free article] [PubMed] [Google Scholar]
  31. Vihinen M., Nilsson L., Smith C. I. Tec homology (TH) adjacent to the PH domain. FEBS Lett. 1994 Aug 22;350(2-3):263–265. doi: 10.1016/0014-5793(94)00783-7. [DOI] [PubMed] [Google Scholar]
  32. Vihinen M., Zvelebil M. J., Zhu Q., Brooimans R. A., Ochs H. D., Zegers B. J., Nilsson L., Waterfield M. D., Smith C. I. Structural basis for pleckstrin homology domain mutations in X-linked agammaglobulinemia. Biochemistry. 1995 Feb 7;34(5):1475–1481. doi: 10.1021/bi00005a002. [DOI] [PubMed] [Google Scholar]
  33. Yoon H. S., Hajduk P. J., Petros A. M., Olejniczak E. T., Meadows R. P., Fesik S. W. Solution structure of a pleckstrin-homology domain. Nature. 1994 Jun 23;369(6482):672–675. doi: 10.1038/369672a0. [DOI] [PubMed] [Google Scholar]
  34. de Weers M., Brouns G. S., Hinshelwood S., Kinnon C., Schuurman R. K., Hendriks R. W., Borst J. B-cell antigen receptor stimulation activates the human Bruton's tyrosine kinase, which is deficient in X-linked agammaglobulinemia. J Biol Chem. 1994 Sep 30;269(39):23857–23860. [PubMed] [Google Scholar]

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