Structural basis for phosphorylation-triggered autophagic clearance of Salmonella

Biochemical Journal

Volumn 454, Issue 3, 2013, Pages 459-466

  Rogov, Vladimir V ^a,b   Suzuki, Hironori ^c   Fiskin, Evgenij ^a   Wild, Philipp ^a   Kniss, Andreas ^a   Rozenknop, Alexis ^a   Kato, Ryuichi ^c   Kawasaki, Masato ^c   McEwan, David G ^a   Löhr, Frank ^a   Güntert, Peter ^a   Dikic, Ivan ^a   Wakatsuki, Soichi ^c   Dötsch, Volker ^a  

^a GOETHE UNIVERSITY   (Germany)

^b INSTITUTE OF PROTEIN RESEARCH   (Russian Federation)

^c INSTITUTE OF MATERIALS STRUCTURE SCIENCE   (Japan)

Author keywords

Microtubule associated protein light chain 3 beta (LC3); NMR spectroscopy; Optineurin; Protein protein interaction; Selective autophagy; X ray crystallography

Indexed keywords

AMINO ACID; CARBON 13; DNA FRAGMENT; GLUTAMIC ACID; GLUTATHIONE TRANSFERASE; MICROTUBULE ASSOCIATED PROTEIN; MICROTUBULE ASSOCIATED PROTEIN LIGHT CHAIN 3BETA; NITROGEN 15; OPTINEURIN; PHENYLALANINE; SERINE; TRYPTOPHAN; UNCLASSIFIED DRUG;

AMINO ACID SUBSTITUTION; ARTICLE; AUTOPHAGY; ISOTHERMAL TITRATION CALORIMETRY; ISOTOPE LABELING; NONHUMAN; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; PROTEIN PHOSPHORYLATION; PROTEIN PROTEIN INTERACTION; SALMONELLA; SELECTIVE AUTOPHAGY; STRUCTURE ANALYSIS; X RAY CRYSTALLOGRAPHY;

AMINO ACID MOTIFS; AMINO ACID SUBSTITUTION; AUTOPHAGY; CRYSTALLOGRAPHY, X-RAY; HOST-PATHOGEN INTERACTIONS; HUMANS; HYDROGEN BONDING; MICROTUBULE-ASSOCIATED PROTEINS; MODELS, MOLECULAR; MUTAGENESIS, SITE-DIRECTED; NUCLEAR MAGNETIC RESONANCE, BIOMOLECULAR; PHOSPHORYLATION; PROTEIN BINDING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, SECONDARY; SALMONELLA; THERMODYNAMICS; TRANSCRIPTION FACTOR TFIIIA;

EID: 84883369848     PISSN: 02646021     EISSN: 14708728     Source Type: Journal    
DOI: 10.1042/BJ20121907     Document Type: Article

References (26)

1. Mizushima, N., Levine, B., Cuervo, A. M. and Klionsky, D. J. (2008) Autophagy fights disease through cellular self-digestion. Nature 451, 1069-1075
2. Novak, I., Kirkin, V., McEwan, D. G., Zhang, J., Wild, P., Rozenknop, A., Rogov, V., Löhr, F., Popovic, D., Occhipinti, A. et al. (2010) Nix is a selective autophagy receptor for mitochondrial clearance. EMBO Rep. 11, 45-51
3. Kirkin, V., McEwan, D. G., Novak, I. and Dikic, I. (2009) A role for ubiquitin in selective autophagy. Mol. Cell 34, 259-269
4. Kraft, C., Peter, M. and Hofmann, K. (2010) Selective autophagy: ubiquitin-mediated recognition and beyond. Nat. Cell Biol. 12, 836-841
5. Pankiv, S., Clausen, T. H., Lamark, T., Brech, A., Bruun, J. A., Outzen, H., Overvatn, A., Bjorkoy, G. and Johansen, T. (2007) p62/SQSTM1 binds directly to Atg8/LC3 to facilitate degradation of ubiquitinated protein aggregates by autophagy. J. Biol. Chem. 282, 24131-24145
6. Ichimura, Y., Kumanomidou, T., Sou, Y. S., Mizushima, T., Ezaki, J., Ueno, T., Kominami, E., Yamane, T., Tanaka, K. and Komatsu, M. (2008) Structural basis for sorting mechanism of p62 in selective autophagy. J. Biol. Chem. 283, 22847-22857
7. Noda, N. N., Kumeta, H., Nakatogawa, H., Satoo, K., Adachi, W., Ishii, J., Fujioka, Y., Ohsumi, Y. and Inagaki, F. (2008) Structural basis of target recognition by Atg8/LC3 during selective autophagy. Genes Cells 13, 1211-1218
8. Thielmann, Y., Weiergraber, O. H., Mohrluder, J. and Willbold, D. (2009) Structural framework of the GABARAP-calreticulin interface: implications for substrate binding to endoplasmic reticulum chaperones. FEBS J. 276, 1140-1152
9. Weiergraber, O. H., Stangler, T., Thielmann, Y., Mohrluder, J., Wiesehan, K. and Willbold, D. (2008) Ligand binding mode of GABAA receptor-associated protein. J. Mol. Biol. 381, 1320-1331
10. Rozenknop, A., Rogov, V. V., Rogova, N. Yu., Löhr, F., Güntert, P., Dikic, I. and Dötsch, V. (2011) Characterization of the interaction of GABARAPL-1 with the LIR motif of NBR1. J. Mol. Biol. 410, 477-487
11. von Muhlinen, N., Akutsu, M., Ravenhill, B. J., Foeglein, A., Bloor, S., Rutherford, T. J., Freund, S. M., Komander, D. and Randow, F. (2012) LC3C, bound selectively by a noncanonical LIR motif in NDP52, is required for antibacterial autophagy. Mol. Cell 48, 329-342
12. Wild, P., Farhan, H., McEwan, D. G., Wagner, S., Rogov, V. V., Brady, N., Richter, B., Korac, J., Waidmann, O., Choudhary, C. et al. (2011) Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science 333, 228-233
13. Alemu, E. A., Lamark, T., Torgersen, K. M., Birgisdottir, A. B., Larsen, K. B., Jain, A., Olsvik, H., Øvervatn, A., Kirkin, V. and Johansen, T. (2012) ATG8 family proteins act as scaffolds for assembly of the ULK complex: sequence requirements for LC3-interacting region (LIR) motifs. J. Biol. Chem. 283, 39275-39290
14. Rogov, V. V., Rozenknop, A., Rogova, N. Yu., Löhr, F., Tikole, S., Jaravine, V., Güntert, P., Dikic, I. and Dötsch, V. (2012) A universal tag for structural and functional studies of proteins. ChemBioChem. 13, 959-963
15. Hiraki, M., Kato, R., Nagai, M., Satoh, T., Hirano, S., Ihara, K., Kudo, N., Nagae, M., Kobayashi, M., Inoue, M. et al. (2006) Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses. Acta Crystallogr., Sect. D: Biol. Crystallogr, 62, 1058-1065
16. Löhr, F., Hänsel, R., Rogov, V. V. and Dötsch, V. (2007) Improved pulse sequences for sequence specific assignment of aromatic proton resonances in proteins. J. Biomol. NMR 37, 205-224
17. Iwahara, J., Wojciak, J. M. and Clubb, R. T. (2001) Improved NMR spectra of a protein-DNA complex through rational mutagenesis and the application of a sensitivity optimized isotope-filtered NOESY experiment. J. Biomol. NMR 19, 231-241
18. Igarashi, N., Matsugaki, N., Yamada, Y., Hiraki, M., Koyama, A., Hirano, K., Miyoshi, T. and Wakatsuki, S. (2007) BL-17A, a new protein micro-crystallography beam line of the Photon Factory. AIP Conf. Proc. 879, 812-815
19. Igarashi, N., Ikuta, K., Miyoshi, T, Matsugaki, N., Yamada, Y., Yousef, M. S. and Wakatsuki, S. (2008) X-ray beam stabilization at BL-17A, the protein microcrystallography beamline of the Photon Factory. J. Synch. Rad. 15, 292-295
20. Kawano, Y., Shimizu, N., Baba, S., Hasegawa, K., Makino, M., Mizuno, N., Hoshino, T., Ito, R., Wada, I., Hirata, K. et al. (2010) Present status of SPring-8 macromolecular crystallography beamlines. AIP Conf. Proc. 1234, 359-362
21. Leslie, A. G. W. and Powell, H. R. (2007) Processing diffraction data with Mosflm. Nato Sci. Ser. II Math. 245, 41-51
22. Potterton, E., Briggs, M., Turkenburg, M. and Dodson, E. (1994) A graphical user interface to the CCP4 program suite. Acta Crystallogr, Sect. D: Biol. Crystallogr. 50, 760-763
23. Vagin, A. and Teplyakov, A. (1997) MOLREP: an automated program for molecular replacement. J. Appl. Crystallogr. 30, 1022-1025
24. Murshudov, G. N., Vagin, A. A. and Dodson, E. J. (1997) Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr., Sect. D: Biol. Crystallogr. 53, 240-255
25. Emsley, P. and Cowtan, K. (2004) Coot: model-building tools for molecular graphics. Acta Crystallogr., Sect. D: Biol. Crystallogr. 60, 2126-2132
26. Zhu, Y., Massen, S., Terenzio, M., Lang, V., Chen-Lindner, S., Eils, R., Novak, I., Dikic, I., Hamacher-Brady, A. and Brady, N. R. (2013) Modulation of serines 17 and 24 in the LC3-interacting region of Bnip3 determines pro-survival mitophagy versus apoptosis. J. Biol. Chem. 288, 1099-1113