Structure of the human ATG12~ATG5 conjugate required for LC3 lipidation in autophagy (original) (raw)
Mizushima, N. & Komatsu, M. Autophagy: renovation of cells and tissues. Cell147, 728–741 (2011). ArticleCAS Google Scholar
Levine, B., Mizushima, N. & Virgin, H.W. Autophagy in immunity and inflammation. Nature469, 323–335 (2011). ArticleCAS Google Scholar
Yang, Z. & Klionsky, D.J. Eaten alive: a history of macroautophagy. Nat. Cell Biol.12, 814–822 (2010). ArticleCAS Google Scholar
Rubinsztein, D.C., Marino, G. & Kroemer, G. Autophagy and aging. Cell146, 682–695 (2011). ArticleCAS Google Scholar
Yamamoto, A. & Simonsen, A. The elimination of accumulated and aggregated proteins: a role for aggrephagy in neurodegeneration. Neurobiol. Dis.43, 17–28 (2011). ArticleCAS Google Scholar
Youle, R.J. & Narendra, D.P. Mechanisms of mitophagy. Nat. Rev. Mol. Cell Biol.12, 9–14 (2011). ArticleCAS Google Scholar
Bernales, S., McDonald, K.L. & Walter, P. Autophagy counterbalances endoplasmic reticulum expansion during the unfolded protein response. PLoS Biol.4, e423 (2006). Article Google Scholar
Xie, Z. & Klionsky, D.J. Autophagosome formation: core machinery and adaptations. Nat. Cell Biol.9, 1102–1109 (2007). ArticleCAS Google Scholar
Mizushima, N., Yoshimori, T. & Ohsumi, Y. The role of Atg proteins in autophagosome formation. Annu. Rev. Cell Dev. Biol.27, 107–132 (2011). ArticleCAS Google Scholar
Ohsumi, Y. Molecular dissection of autophagy: two ubiquitin-like systems. Nat. Rev. Mol. Cell Biol.2, 211–216 (2001). ArticleCAS Google Scholar
Geng, J. & Klionsky, D.J. The Atg8 and Atg12 ubiquitin-like conjugation systems in macroautophagy. ′Protein modifications: beyond the usual suspects′ review series. EMBO Rep.9, 859–864 (2008). ArticleCAS Google Scholar
Ichimura, Y. et al. A ubiquitin-like system mediates protein lipidation. Nature408, 488–492 (2000). ArticleCAS Google Scholar
Mizushima, N. et al. Dissection of autophagosome formation using Apg5-deficient mouse embryonic stem cells. J. Cell Biol.152, 657–668 (2001). ArticleCAS Google Scholar
Kraft, C., Peter, M. & Hofmann, K. Selective autophagy: ubiquitin-mediated recognition and beyond. Nat. Cell Biol.12, 836–841 (2010). ArticleCAS Google Scholar
Lynch-Day, M.A. & Klionsky, D.J. The Cvt pathway as a model for selective autophagy. FEBS Lett.584, 1359–1366 (2010). ArticleCAS Google Scholar
Mizushima, N. et al. A protein conjugation system essential for autophagy. Nature395, 395–398 (1998). ArticleCAS Google Scholar
Matsushita, M. et al. Structure of Atg5.Atg16, a complex essential for autophagy. J. Biol. Chem.282, 6763–6772 (2007). ArticleCAS Google Scholar
Schulman, B.A. & Harper, J.W. Ubiquitin-like protein activation by E1 enzymes: the apex for downstream signalling pathways. Nat. Rev. Mol. Cell Biol.10, 319–331 (2009). ArticleCAS Google Scholar
Hanada, T. et al. The Atg12–Atg5 conjugate has a novel E3-like activity for protein lipidation in autophagy. J. Biol. Chem.282, 37298–37302 (2007). ArticleCAS Google Scholar
Uetz, P. et al. A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae. Nature403, 623–627 (2000). ArticleCAS Google Scholar
Tanida, I., Tanida-Miyake, E., Komatsu, M., Ueno, T. & Kominami, E. Human Apg3p/Aut1p homologue is an authentic E2 enzyme for multiple substrates, GATE-16, GABARAP, and MAP-LC3, and facilitates the conjugation of hApg12p to hApg5p. J. Biol. Chem.277, 13739–13744 (2002). ArticleCAS Google Scholar
Fujita, N. et al. The Atg16L complex specifies the site of LC3 lipidation for membrane biogenesis in autophagy. Mol. Biol. Cell19, 2092–2100 (2008). ArticleCAS Google Scholar
Mizushima, N., Noda, T. & Ohsumi, Y. Apg16p is required for the function of the Apg12p–Apg5p conjugate in the yeast autophagy pathway. EMBO J.18, 3888–3896 (1999). ArticleCAS Google Scholar
Fujioka, Y., Noda, N.N., Nakatogawa, H., Ohsumi, Y. & Inagaki, F. Dimeric coiled-coil structure of Saccharomyces cerevisiae Atg16 and its functional significance in autophagy. J. Biol. Chem.285, 1508–1515 (2010). ArticleCAS Google Scholar
Kuma, A., Mizushima, N., Ishihara, N. & Ohsumi, Y. Formation of the approximately 350-kDa Apg12–Apg5.Apg16 multimeric complex, mediated by Apg16 oligomerization, is essential for autophagy in yeast. J. Biol. Chem.277, 18619–18625 (2002). ArticleCAS Google Scholar
Baba, D. et al. Crystal structure of thymine DNA glycosylase conjugated to SUMO-1. Nature435, 979–982 (2005). ArticleCAS Google Scholar
Duda, D.M. et al. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell134, 995–1006 (2008). ArticleCAS Google Scholar
Armstrong, A.A., Mohideen, F. & Lima, C.D. Recognition of SUMO-modified PCNA requires tandem receptor motifs in Srs2. Nature483, 59–63 (2012). ArticleCAS Google Scholar
Mizushima, N., Yoshimori, T. & Levine, B. Methods in mammalian autophagy research. Cell140, 313–326 (2010). ArticleCAS Google Scholar
Suzuki, N.N., Yoshimoto, K., Fujioka, Y., Ohsumi, Y. & Inagaki, F. The crystal structure of plant ATG12 and its biological implication in autophagy. Autophagy1, 119–126 (2005). ArticleCAS Google Scholar
Winget, J.M. & Mayor, T. The diversity of ubiquitin recognition: hot spots and varied specificity. Mol. Cell38, 627–635 (2010). ArticleCAS Google Scholar
Hanada, T. & Ohsumi, Y. Structure-function relationship of Atg12, a ubiquitin-like modifier essential for autophagy. Autophagy1, 110–118 (2005). ArticleCAS Google Scholar
Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol.372, 774–797 (2007). ArticleCAS Google Scholar
Hosokawa, N., Hara, Y. & Mizushima, N. Generation of cell lines with tetracycline-regulated autophagy and a role for autophagy in controlling cell size. FEBS Lett.580, 2623–2629 (2006). ArticleCAS Google Scholar
Radoshevich, L. et al. ATG12 conjugation to ATG3 regulates mitochondrial homeostasis and cell death. Cell142, 590–600 (2010). ArticleCAS Google Scholar
Ichimura, Y. et al. In vivo and in vitro reconstitution of atg8 conjugation essential for autophagy. J. Biol. Chem.279, 40584–40592 (2004). ArticleCAS Google Scholar
Oh-oka, K., Nakatogawa, H. & Ohsumi, Y. Physiological pH and acidic phospholipids contribute to substrate specificity in lipidation of Atg8. J. Biol. Chem.283, 21847–21852 (2008). ArticleCAS Google Scholar
Nair, U. et al. SNARE proteins are required for macroautophagy. Cell146, 290–302 (2011). ArticleCAS Google Scholar
Deshaies, R.J. & Joazeiro, C.A. RING domain E3 ubiquitin ligases. Annu. Rev. Biochem.78, 399–434 (2009). ArticleCAS Google Scholar
Reverter, D. & Lima, C.D. Insights into E3 ligase activity revealed by a SUMO–RanGAP1–Ubc9–Nup358 complex. Nature435, 687–692 (2005). ArticleCAS Google Scholar
Dou, H., Buetow, L., Sibbet, G.J., Cameron, K. & Huang, D.T. BIRC7–E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer. Nat. Struct. Mol. Biol.19, 876–883 (2012). ArticleCAS Google Scholar
Plechanovová, A., Jaffray, E.G., Tatham, M.H., Naismith, J.H. & Hay, R.T. Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis. Nature489, 115–120 (2012). Article Google Scholar
Pruneda, J.N. et al. Structure of an E3:E2~Ub complex reveals an allosteric mechanism shared among RING/U-box ligases. Mol. Cell47, 933–942 (2012). ArticleCAS Google Scholar
Ashkenazy, H., Erez, E., Martz, E., Pupko, T. & Ben-Tal, N. ConSurf 2010: calculating evolutionary conservation in sequence and structure of proteins and nucleic acids. Nucleic Acids Res.38, W529–W33 (2010). ArticleCAS Google Scholar
Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol.276, 307–326 (1997). ArticleCAS Google Scholar
Adams, P.D. et al. PHENIX: a comprehensive Python-based system for macromolecular structure solution. Acta Crystallogr. D Biol. Crystallogr.66, 213–221 (2010). ArticleCAS Google Scholar
Emsley, P. & Cowtan, K. Coot: model-building tools for molecular graphics. Acta Crystallogr. D Biol. Crystallogr.60, 2126–2132 (2004). Article Google Scholar
Chen, V.B. et al. MolProbity: all-atom structure validation for macromolecular crystallography. Acta Crystallogr. D Biol. Crystallogr.66, 12–21 (2010). ArticleCAS Google Scholar
Kitamura, T. et al. Retrovirus-mediated gene transfer and expression cloning: powerful tools in functional genomics. Exp. Hematol.31, 1007–1014 (2003). ArticleCAS Google Scholar