The crystal structure of PPIL1 bound to cyclosporine a suggests a binding mode for a linear epitope of the SKIP protein

PLoS ONE

Volumn 5, Issue 4, 2010, Pages

  Stegmann, Christian M ^a,b   Lührmann, Reinhard ^a   Wahl, Markus C ^a,b  

^a MAX PLANCK INSTITUTE FOR BIOPHYSICAL CHEMISTRY   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING PROTEIN; CADMIUM; CYCLOPHILIN; CYCLOSPORIN A; PEPTIDYLPROLYL ISOMERASE LIKE 1 PROTEIN; SKI INTERACTING PROTEIN; UNCLASSIFIED DRUG; CYCLOSPORIN; EPITOPE; IMMUNOSUPPRESSIVE AGENT; PEPTIDYLPROLYL ISOMERASE; PPIL1 PROTEIN, HUMAN; SIGNAL TRANSDUCING ADAPTOR PROTEIN; SKIP PROTEIN, HUMAN;

ARTICLE; BINDING KINETICS; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENZYME STRUCTURE; HYDROGEN BOND; HYDROPHOBICITY; MOLECULAR MODEL; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; SPLICEOSOME; BINDING SITE; CHEMISTRY; HUMAN; METABOLISM; PROTEIN BINDING; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY;

ADAPTOR PROTEINS, SIGNAL TRANSDUCING; BINDING SITES; CADMIUM; CRYSTALLOGRAPHY, X-RAY; CYCLOSPORINE; EPITOPES; HUMANS; IMMUNOSUPPRESSIVE AGENTS; PEPTIDYLPROLYL ISOMERASE; PROTEIN BINDING; PROTEIN CONFORMATION;

EID: 77956326875     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0010013     Document Type: Article

References (26)

1. Xu C, Zhang J, Huang X, Sun J, Xu Y, et al. (2006) Solution structure of human peptidyl prolyl isomerase-like protein 1 and insights into its interaction with SKIP. J Biol Chem 281: 15900-15908.
2. Fanghanel J, Fischer G (2004) Insights into the catalytic mechanism of peptidyl prolyl cis/trans isomerases. Front Biosci 9: 3453-3478.
3. Gothel SF, Marahiel MA (1999) Peptidyl-prolyl cis-trans isomerases, a superfamily of ubiquitous folding catalysts. Cell Mol Life Sci 55: 423-436.
4. Thai V, Renesto P, Fowler CA, Brown DJ, Davis T, et al. (2008) Structural, biochemical, and in vivo characterization of the first virally encoded cyclophilin from the Mimivirus. J Mol Biol 378: 71-86.
5. Wahl MC, Will CL, Luhrmann R (2009) The spliceosome: design principles of a dynamic RNP machine. Cell 136: 701-718.
6. Mesa A, Somarelli JA, Herrera RJ (2008) Spliceosomal immunophilins. FEBS Lett 582: 2345-2351.
7. Bessonov S, Anokhina M, Will CL, Urlaub H, Luhrmann R (2008) Isolation of an active step I spliceosome and composition of its RNP core. Nature 452: 846-850.
8. Albers M, Diment A, Muraru M, Russell CS, Beggs JD (2003) Identification and characterization of Prp45p and Prp46p, essential pre-mRNA splicing factors. RNA 9: 138-150.
9. Folk P, Puta F, Skruzny M (2004) Transcriptional coregulator SNW/SKIP: the concealed tie of dissimilar pathways. Cell Mol Life Sci 61: 629-640.
10. Bres V, Gomes N, Pickle L, Jones KA (2005) A human splicing factor, SKIP, associates with P-TEFb and enhances transcription elongation by HIV-1 Tat. Genes Dev 19: 1211-1226.
11. Obama K, Kato T, Hasegawa S, Satoh S, Nakamura Y, et al. (2006) Overexpression of peptidyl-prolyl isomerase-like 1 is associated with the growth of colon cancer cells. Clin Cancer Res 12: 70-76.
12. Reidt U, Wahl MC, Fasshauer D, Horowitz DS, Luhrmann R, et al. (2003) Crystal structure of a complex between human spliceosomal cyclophilin H and a U4/U6 snRNP-60K peptide. J Mol Biol 331: 45-56.
13. Skruzny M, Ambrozkova M, Fukova I, Martinkova K, Blahuskova A, et al. (2001) Cyclophilins of a novel subfamily interact with SNW/SKIP coregulator in Dictyostelium discoideum and Schizosaccharomyces pombe. Biochim Biophys Acta 1521: 146-151.
14. Kallen J, Spitzfaden C, Zurini MG, Wider G, Widmer H, et al. (1991) Structure of human cyclophilin and its binding site for cyclosporin A determined by X-ray crystallography and NMR spectroscopy. Nature 353: 276-279.
15. Mikol V, Kallen J, Pflugl G, Walkinshaw MD (1993) X-ray structure of a monomeric cyclophilin A-cyclosporin A crystal complex at 2.1 A resolution. J Mol Biol 234: 1119-1130.
16. Rees DC, Lewis M, Lipscomb WN (1983) Refined crystal structure of carboxypeptidase A at 1.54 A resolution. J Mol Biol 168: 367-387
17. Dominguez C, Boelens R, Bonvin AM (2003) HADDOCK: a protein-protein docking approach based on biochemical or biophysical information. J Am Chem Soc 125: 1731-1737.
18. Wang X, Zhang S, Zhang J, Huang X, Xu C, et al. (2009) A large intrinsically disordered region in SKIP and its disorder-order transition induced by PPIL1 binding revealed by NMR. J Biol Chem 285: 4951-4963.
19. Rydzanicz R, Zhao XS, Johnson PE (2005) Assembly PCR oligo maker: a tool for designing oligodeoxynucleotides for constructing long DNA molecules for RNA production. Nucleic Acids Res 33: W521-525.
20. Studier FW (2005) Protein production by auto-induction in high density shaking cultures. Protein Expr Purif 41: 207-234.
21. Stegmann CM, Seeliger D, Sheldrick GM, de Groot BL, Wahl MC (2009) The thermodynamic influence of trapped water molecules on a protein-ligand interaction. Angew Chem Int Ed Engl 48: 5207-5210.
22. Kabsch W (1993) Automatic processing of rotation diffraction data from crystals of initially unknown symmetry and cell constants. J Appl Cryst 26: 795-800.
23. Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64: 112-122.
24. Adams PD, Gopal K, Grosse-Kunstleve RW, Hung L-W, Ioerger TR, et al. (2004) Recent developments in the PHENIX software for automated crystallographic structure determination. Journal of Synchrotron Radiation 11: 53-55.
25. Maupetit J, Derreumaux P, Tuffery P (2009) PEP-FOLD: an online resource for de novo peptide structure prediction. Nucleic Acids Res 37: W498-503.
26. Lovell SC, Davis IW, Arendall WB, 3rd, de Bakker PI, Word JM, et al. (2003) Structure validation by Calpha geometry: phi,psi and Cbeta deviation. Proteins 50: 437-450.