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The phox homology (PX) domain of human phosphoinositide-3-kinase-C2-gamma

PDB Code 2WWE Target Class Phosphoinosotide dependent signalling Target PIK3C2G Alias n/a Disease Area/Function cancer Date Deposited Oct 22 2009 Authors Roos, A.K., Tresaugues, L., Arrowsmith, C.H., Berglund, H., Bountra, C., Collins, R., Edwards, A.M., Flodin, S., Flores, A., Graslund, S., Hammarstrom, M., Johansson, A., Johansson, I., Kallas, A., Karlberg, T., Kotyenova, T., Kotzch, A., Kraulis, P., Markova, N., Moche, M., Nielsen, T.K., Nyman, T., Persson, C., Schuler, H., Schutz, P., Siponen, M.I., Svensson, L., Thorsell, A.G., van den Berg, S., Wahlberg, E., Weigelt, J., Welin, M., Wisniewska, M., Nordlund, P., Structural Genomics Consortium (SGC)

About this structure

PIK3C2G (Phosphoinositide 3-Kinase-C2-gamma) belongs to the class II family of phosphoinositide 3-kinases (PI3Ks) that use preferentially phosphatidylinositol or phosphatidylinositol-4-phosphate as substrates [1,2]. There are three class II PI3K isoforms, and a structural feature that distinguishes this subfamily from other PI3Ks is a C-terminal extension containing a C2 domain and a PX (phox homology) domain. PX domains are found in more than 100 eukaryotic proteins and several act as specific phosphoinositide binding modules with varying lipid-binding specificity [3]. The class II family PI3Ks are often localized to membrane structures and are activated by RTKs, cytokine receptors and integrins [1]. Amplification of the PIK3C2G gene in ovarian cancer cell line indicates that it is a putative oncogene [4]. Moreover SNPs of the PIK3C2G gene has been associated with type II diabetes [5]. However no clear cellular role for this PIK3 family has been defined, partly due to the lack of specific inhibitors.

We have solved the PX domain of PIK3C2G to a resolution of 1.25 Å and deposited the coordinates and structure factors in the protein data bank with the code 2WWE. The structure was solved by molecular replacement using an ensemble of the PX domains 2AR5, 2IWL, 1O7K, 2V6V as the search model. Comparisons to these other PX domains show that the overall fold is very similar despite low sequence homology (24% seq. identity). Main differences are seen in the loop regions connecting the secondary structural elements. Superpositioning the p40phox PX-domain (1H6H.pdb [6]), which has a molecule of phosphatidylinositol 3-phosphate in its ligand binding pocket onto our structure shows that the residues lining the pocket are not conserved. In 1H6H several arginines and a lysine are involved in ligand binding, whereas in the PIK3C2G PX domain the equivalent residues are either negatively charged or hydrophobic, suggesting that this PX domain has a different mode of binding its substrate. Arg 1275 is situated in a favourable position for binding the phosphate moiety of a molecule of phosphatidylinositol-4-phosphate. The membrane interaction loop of PIK3C2G PX is the area of the structure with least ordered density implying higher flexibility in this region. It should also be noted that crystal packing interactions may influence this part of the structure.

References

  1. Falasca M, Maffucci T. (2007). Role of class II phosphoinositide 3-kinase in cell signalling. Biochem Soc Trans. 35(Pt 2):211-4. PubMed 17371240
  2. Rozycka M, Lu YJ, Brown RA, Lau MR, Shipley JM, Fry MJ. (1998). cDNA cloning of a third human C2-domain-containing class II phosphoinositide 3-kinase, PI3K-C2gamma, and chromosomal assignment of this gene (PIK3C2G) to 12p12. Genomics. 54(3):569-74. PubMed 9878262
  3. Ellson CD, Andrews S, Stephens LR, Hawkins PT. (2002). The PX domain: a new phosphoinositide-binding module. J Cell Sci. 115(Pt 6):1099-105. PubMed 11884510
  4. Lambros MB, Fiegler H, Jones A, Gorman P, Roylance RR, Carter NP, Tomlinson IP. (2005). Analysis of ovarian cancer cell lines using array-based comparative genomic hybridization. J Pathol. 205(1):29-40. PubMed 15586366
  5. Daimon M, Sato H, Oizumi T, Toriyama S, Saito T, Karasawa S, Jimbu Y, Wada K, Kameda W, Susa S, Yamaguchi H, Emi M, Muramatsu M, Kubota I, Kawata S, Kato T. (2008). Association of the PIK3C2G gene polymorphisms with type 2 DM in a Japanese population. Biochem Biophys Res Commun. 365(3):466-71. PubMed 17991425
  6. Bravo J, Karathanassis D, Pacold CM, Pacold ME, Ellson CD, Anderson KE, Butler PJ, Lavenir I, Perisic O, Hawkins PT, Stephens L, Williams RL. (2001). The crystal structure of the PX domain from p40(phox) bound to phosphatidylinositol 3-phosphate. Mol. Cell 8(4):829-39. PubMed 11684018