Crystal structure of subunit VPS25 of the endosomal trafficking complex ESCRT-II
Tóm tắt
Down-regulation of plasma membrane receptors via the endocytic pathway involves their monoubiquitylation, transport to endosomal membranes and eventual sorting into multi vesicular bodies (MVB) destined for lysosomal degradation. Successive assemblies of E ndosomal S orting C omplexes R equired for T ransport (ESCRT-I, -II and III) largely mediate sorting of plasma membrane receptors at endosomal membranes, the formation of multivesicular bodies and their release into the endosomal lumen. In addition, the human ESCRT-II has been shown to form a complex with RNA polymerase II elongation factor ELL in order to exert transcriptional control activity. Here we report the crystal structure of Vps25 at 3.1 Å resolution. Vps25 crystallizes in a dimeric form and each monomer is composed of two winged helix domains arranged in tandem. Structural comparisons detect no conformational changes between unliganded Vps25 and Vps25 within the ESCRT-II complex composed of two Vps25 copies and one copy each of Vps22 and Vps36 [1, 2]. Our structural analyses present a framework for studying Vps25 interactions with ESCRT-I and ESCRT-III partners. Winged helix domain containing proteins have been implicated in nucleic acid binding and it remains to be determined whether Vps25 has a similar activity which might play a role in the proposed transcriptional control exerted by Vps25 and/or the whole ESCRT-II complex.
Tài liệu tham khảo
Hierro A, Sun J, Rusnak AS, Kim J, Prag G, Emr SD, Hurley JH: Structure of the ESCRT-II endosomal trafficking complex. Nature 2004, 431(7005):221–225. 10.1038/nature02914
Teo H, Perisic O, Gonzalez B, Williams RL: ESCRT-II, an Endosome-Associated Complex Required for Protein Sorting; Crystal Structure and Interactions with ESCRT-III and Membranes. Dev Cell 2004, 7(4):559–569. 10.1016/j.devcel.2004.09.003
Palade GE: A small particulate component of the cytoplasm. J Biophys Biochem Cytol 1955, 1(1):59–68.
Katzmann DJ, Odorizzi G, Emr SD: Receptor downregulation and multivesicular-body sorting. Nat Rev Mol Cell Biol 2002, 3(12):893–905. 10.1038/nrm973
Kleijmeer M, Ramm G, Schuurhuis D, Griffith J, Rescigno M, Ricciardi-Castagnoli P, Rudensky AY, Ossendorp F, Melief CJ, Stoorvogel W, Geuze HJ: Reorganization of multivesicular bodies regulates MHC class II antigen presentation by dendritic cells. J Cell Biol 2001, 155(1):53–63. 10.1083/jcb.200103071
Strack B, Calistri A, Craig S, Popova E, Gottlinger HG: AIP1/ALIX is a binding partner for HIV-1 p6 and EIAV p9 functioning in virus budding. Cell 2003, 114: 689–699. 10.1016/S0092-8674(03)00653-6
von Schwedler UK, Stuchell M, Muller B, Ward DM, Chung HY, Morita E, Wang HE, Davis T, He GP, Cimbora DM, Scott A, Krausslich HG, Kaplan J, Morham SG, Sundquist WI: The protein network of HIV budding. Cell 2003, 114(6):701–713. 10.1016/S0092-8674(03)00714-1
Babst M, Katzmann DJ, Estepa-Sabal EJ, Meerloo T, Emr SD: ESCRT-III: an endosome-associated heterooligomeric protein complex required for MVB sorting. Dev Cell 2002, 3(2):271–282. 10.1016/S1534-5807(02)00220-4
Babst M, Katzmann DJ, Snyder WB, Wendland B, Emr SD: Endosome-associated complex, ESCRT-II, recruits transport machinery for protein sorting at the multivesicular body. Dev Cell 2002, 3(2):283–289. 10.1016/S1534-5807(02)00219-8
Katzmann DJ, Babst M, Emr SD: Ubiquitin-dependent sorting into the multivesicular body pathway requires the function of a conserved endosomal protein sorting complex, ESCRT-I. Cell 2001, 106(2):145–155. 10.1016/S0092-8674(01)00434-2
Katzmann DJ, Stefan CJ, Babst M, Emr SD: Vps27 recruits ESCRT machinery to endosomes during MVB sorting. J Cell Biol 2003, 162(3):413–423. 10.1083/jcb.200302136
Odorizzi G, Babst M, Emr SD: Fab1p PtdIns(3)P 5-kinase function essential for protein sorting in the multivesicular body. Cell 1998, 95(6):847–858. 10.1016/S0092-8674(00)81707-9
Pornillos O, Alam SL, Rich RL, Myszka DG, Davis DR, Sundquist WI: Structure and functional interactions of the Tsg101 UEV domain. EMBO J 2002, 21(10):2397–2406. 10.1093/emboj/21.10.2397
Schmidt AE, Miller T, Schmidt SL, Shiekhattar R, Shilatifard A: Cloning and characterization of the EAP30 subunit of the ELL complex that confers derepression of transcription by RNA polymerase II. J Biol Chem 1999, 274(31):21981–21985. 10.1074/jbc.274.31.21981
Kamura T, Burian D, Khalili H, Schmidt SL, Sato S, Liu WJ, Conrad MN, Conaway RC, Conaway JW, Shilatifard A: Cloning and characterization of ELL-associated proteins EAP45 and EAP20. a role for yeast EAP-like proteins in regulation of gene expression by glucose. J Biol Chem 2001, 276(19):16528–16533. 10.1074/jbc.M010142200
Yeghiayan P, Tu J, Vallier LG, Carlson M: Molecular analysis of the SNF8 gene of Saccharomyces cerevisiae. Yeast 1995, 11(3):219–224.
Gajiwala KS, Burley SK: Winged helix proteins. Curr Opin Struct Biol 2000, 10(1):110–116. 10.1016/S0959-440X(99)00057-3
Zheng N, Fraenkel E, Pabo CO, Pavletich NP: Structural basis of DNA recognition by the heterodimeric cell cycle transcription factor E2F-DP. Genes Dev 1999, 13(6):666–674.
Holm L, Sander C: Dali: a network tool for protein structure comparison. Trends Biochem Sci 1995, 20(11):478–480. 10.1016/S0968-0004(00)89105-7
Bowers K, Lottridge J, Helliwell SB, Goldthwaite LM, Luzio JP, Stevens TH: Protein-protein interactions of ESCRT complexes in the yeast Saccharomyces cerevisiae. Traffic 2004, 5(3):194–210.
Howard TL, Stauffer DR, Degnin CR, Hollenberg SM: CHMP1 functions as a member of a newly defined family of vesicle trafficking proteins. J Cell Sci 2001, 114(Pt 13):2395–2404.
Katoh K, Shibata H, Hatta K, Maki M: CHMP4b is a major binding partner of the ALG-2-interacting protein Alix among the three CHMP4 isoforms. Arch Biochem Biophys 2004, 421(1):159–165. 10.1016/j.abb.2003.09.038
Xie W, Li L, Cohen SN: Cell cycle-dependent subcellular localization of the TSG101 protein and mitotic and nuclear abnormalities associated with TSG101 deficiency. Proc Natl Acad Sci U S A 1998, 95(4):1595–1600. 10.1073/pnas.95.4.1595
Burchett SA, Flanary P, Aston C, Jiang L, Young KH, Uetz P, Fields S, Dohlman HG: Regulation of stress response signaling by the N-terminal dishevelled/EGL-10/pleckstrin domain of Sst2, a regulator of G protein signaling in Saccharomyces cerevisiae. J Biol Chem 2002, 277(25):22156–22167. 10.1074/jbc.M202254200
Carlson M: Regulation of glucose utilization in yeast. Curr Opin Genet Dev 1998, 8(5):560–564. 10.1016/S0959-437X(98)80011-7
Alam SL, Sun J, Payne M, Welch BD, Blake BK, Davis DR, Meyer HH, Emr SD, Sundquist WI: Ubiquitin interactions of NZF zinc fingers. EMBO J 2004, 23(7):1411–1421. 10.1038/sj.emboj.7600114
4 CCPN: The CCP4 suite programs for protein crystallography. Acta Cryst 1994, D50: 760–763.
Sheldrick GM, Schneider TR: SHELXL: High-resolution refinement. Methods Enzymol 1997, 277: 319–343.
Terwilliger TC, Berendzen J: Automated MAD and MIR structure solution. Acta Crystallogr D Biol Crystallogr 1999, D55: 849–861. 10.1107/S0907444999000839
Terwilliger TC: Maximum likelihood density modification. Acta Crystallogr D Biol Crystallogr 2000, D56: 965–972. 10.1107/S0907444900005072
Jones TA, Zou J-Y, Cowan SW, Kjeldgaard M: Improved methods for building protein models in electron density maps and location of errors in these models. Acta Crystallogr D Biol Crystallogr 1991, A47: 110–119.
Brünger AT, Adams PD, Clore GM, DeLano WL, Gros P, Grosse-Kunstleve RW, Jiang J-S, Kuszewski J, Nilges M, Pannu NS, Read RJ, Rice LM, Simonson T, Warren GL: Crystallography & NMR system : a new software suite for macromolecular crystallography. Acta Crystallogr D Biol Crystallogr 1998, D54: 905–921. 10.1107/S0907444998003254
Laskowski RA, McArthur MW, Moss DS, Thornton JM: PROCHECK : a program to check the stereochemical quality of protein structures. J Appl Cryst 1993, 26: 283–291. 10.1107/S0021889892009944
Kraulis PJ: MOLSCRIPT: a program to produce detailed and schematic plots of protein structures. J Appl Cryst 1991, 24: 946–950. 10.1107/S0021889891004399
Merritt EA, Bacon DJ: Raster3D: photorealistic molecular graphics. Methods Enzymol 1997, 277: 505–524.
Gouet P, Courcell E, Stuart DI, Metoz F: ESPript: multiple sequence alignments in PostScript. Bioinformatics 1999, 15: 305–308. 10.1093/bioinformatics/15.4.305
Nicholls A, Sharp KA, Honig B: Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 1991, 11: 281–296.
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The CLustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997, 25: 4876–4882. 10.1093/nar/25.24.4876
Kabsch W, Sander C: Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers 1983, 22(12):2577–2637.
Kleywegt GJ, Jones TA: A super position. CCP4/ESF-EACBM Newsletter Prt Cryst 1994, 31: 9–14.