The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8

Genes to Cells

Volumn 9, Issue 7, 2004, Pages 611-618

  Sugawara, Kenji ^a   Suzuki, Nobuo N ^a   Fujioka, Yuko ^a   Mizushima, Noboru ^b,c   Ohsumi, Yoshinori ^b   Inagaki, Fuyuhiko ^a  

^a HOKKAIDO UNIVERSITY   (Japan)

^b NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

^c JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

4 AMINOBUTYRIC ACID A RECEPTOR; ADENOSINE TRIPHOSPHATASE; MICROTUBULE ASSOCIATED PROTEIN; MICROTUBULE ASSOCIATED PROTEIN LIGHT CHAIN 3; NEDD8 PROTEIN; SACCHAROMYCES CEREVISIAE PROTEIN; UBIQUITIN; UNCLASSIFIED DRUG;

ALPHA HELIX; AMINO TERMINAL SEQUENCE; ANIMAL CELL; ARTICLE; CONJUGATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; ELECTRIC POTENTIAL; ENHANCER REGION; GENETIC CONSERVATION; GOLGI COMPLEX; HYDROPHOBICITY; MAMMAL; MOLECULAR RECOGNITION; MOLECULAR WEIGHT; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FOLDING; PROTEIN FUNCTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; PROTEIN TARGETING; R FACTOR; RAT; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS; SURFACE PROPERTY;

AMINO ACID SEQUENCE; ANIMALS; CRYSTALLOGRAPHY, X-RAY; MICROTUBULE-ASSOCIATED PROTEINS; MODELS, MOLECULAR; MOLECULAR SEQUENCE DATA; PROTEIN CONFORMATION; RATS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SEQUENCE HOMOLOGY, AMINO ACID;

MAMMALIA; SACCHAROMYCES; SACCHAROMYCES CEREVISIAE; STAPHYLOCOCCUS PHAGE 3A;

EID: 4344696843     PISSN: 13569597     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1356-9597.2004.00750.x     Document Type: Article

References (38)

1. Baba, M., Takeshige, K., Baba, N. & Ohsumi, Y. (1994) Ultrastructural analysis of the autophagic process in yeast: detection of autophagosomes and their characterization. J. Cell Biol. 124, 903-913.
2. Bavro, V.N., Sola, M., Bracher, A., Kneussel, M., Betz, H. & Weissenhorn, W. (2002) Crystal structure of the GABA (A) - receptor-associated protein, GABARAP. EMBO Rep. 3, 183-189.
3. Brünger, A.T., Adams, P.D., Clore, G.M., et al. (1998) Crystallography & NMR system: a new software suite for macromolecular structure determination. Acta Crystallogr. D Biol. Crystallogr. 54, 905-921.
4. Cambillau, C. & Roussel, A. (1997) Turbo-Frodo, Version OpenGL. 1. Marseille: Universite Aix-Marseille II.
5. Coyle, J.E., Qamar, S., Rajashankar, K.R. & Nikolov, D.B. (2002) Structure of GABARAP in two conformations: implications for GABA (A) receptor localization and tubulin binding. Neuron 33, 63-74.
6. Hemelaar, J., Lelyveld, V.S., Kessler, B.M. & Ploegh, H.L. (2003) A single protease, Apg4B, is specific for the autophagy-related ubiquitin-like proteins GATE-16, MAP1-LC3, GABARAP, and Apg8L. J. Biol. Chem. 278, 51841-51850.
7. Holm, L. & Sander, C. (1996) Mapping the protein universe. Science 273, 595-603.
8. Ichimura, Y., Kirisako, T., Takao, T., et al. (2000) A ubiquitin-like system mediates protein lipidation. Nature 408, 489-493.
9. Kabeya, Y., Mizushima, N., Ueno, T., et al. (2000) LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing. EMBO J. 19, 5720-5728.
10. Kabeya, Y., Mizushima, N., Yamamoto, A., Oshitani-Okamoto, S., Ohsumi, Y. & Yoshimori, T. (2004) LC3, GABARAP and GATE16 localize to autophagosome membrane depending on form-II formation. J. Cell Sci. 117, 2805-2812.
11. Kirisako, T., Ichimura, Y., Okada, H., et al. (2000) The reversible modification regulates the membrane-binding state of Apg8/Aut7 essential for autophagy and the cytoplasm to vacuole targeting pathway. J. Cell Biol. 151, 263-275.
12. Klionsky, D.J. & Ohsumi, Y. (1999) Vacuolar import of proteins and organelles from the cytoplasm. Annu. Rev. Cell Dev. Biol. 15, 1-32.
13. Knight, D., Harris, R., McAlister, M.S., et al. (2002) The X-ray crystal structure and putative ligand-derived peptide binding properties of gamma-aminobutyric acid receptor type A receptor-associated protein. J. Biol. Chem. 277, 5556-5561.
14. Kraulis, P.J. (1991) MOLSCRIPT: a program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24, 946-950.
15. Legesse-Miller, A., Sagiv, Y., Porat, A. & Elazar, Z. (1998) Isolation and characterization of a novel low molecular weight protein involved in intra-Golgi traffic. J. Biol. Chem. 273, 3105-3109.
16. Mann, S.S. & Hammarback, J.A. (1994) Molecular characterization of light chain 3. A micrombule binding subunit of MAP1A and MAP1B. J. Biol. Chem. 269, 11492-11497.
17. Merritt, E.A. & Bacon, D.J. (1997) Raster3D: photorealistic molecular graphics. Meth. Enzymol. 277, 505-524.
18. Mortimore, G.E. & Poso, A.R. (1987) Intracellular protein catabolism and its control during nutrient deprivation and supply. Annu. Rev. Nutr. 7, 539-564.
19. Nassar, N., Horn, G., Herrmann, C., Scherer, A., McCormick, F. & Wittinghofer, A. (1995) The 2.2 Å crystal structure of the Ras-binding domain of the serine/threonine kinase c-Raf1 in complex with Rap1A and a GTP analogue. Nature 375, 554-560.
20. Nicholls, A., Sharp, K. & Honig, B. (1991) Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11, 281-296.
21. Ohsumi, Y. (2001) Molecular dissection of autophagy: two ubiquitin-like systems. Nature Rev. Mol. Cell Biol. 2, 211-216.
22. Otwinowski, Z. & Minor, W. (1997) Processing of X-ray diffraction data collected in oscillation mode. Meth. Enzymol. 276, 307-326.
23. Paz, Y., Elazar, Z. & Fass, D. (2000) Structure of GATE-16, membrane transport modulator and mammalian ortholog of autophagocytosis factor Aut7p. J. Biol. Chem. 275, 25445-25450.
24. Ponting, C.P., Ito, T., Moscat, J., Diaz-Meco, M.T., Inagaki, F. & Sumimoto, H. (2002) OPR, PC and AID: all in the PB1 family. Trends Biochem. Sci. 27, 10.
25. Sagiv, Y., Legesse-Miller, A., Porat, A. & Elazar, Z. (2000) GATE-16, a membrane transport modulator, interacts with NSF and the Golgi v-SNARE GOS-28. EMBO J. 19, 1494-1504.
26. Scherz-Shouval, R., Sagiv, Y., Shorer, H. & Elazar, Z. (2003) The COOH terminus of GATE-16, an intra-Golgi transport modulator, is cleaved by the human cysteine protease HsApg4A. J. Biol. Chem. 278, 14053-14058.
27. Stangler, T., Mayr, L.M. & Willbold, D. (2002) Solution structure of human GABA (A) receptor-associated protein GABARAP: implications for biological function and its regulation. J. Biol. Chem. 19, 13363-13366.
28. Sugawara, K., Suzuki, N.N., Fujioka, Y., Mizushima, N., Ohsumi, Y. & Inagaki, F. (2003) Crystallization and preliminary X-ray analysis of LC3-I. Acta Crystallogr. Sect. D Biol. Crystallogr. 59, 1464-1465.
29. Tanida, I., Komatsu, M., Ueno, T. & Kominami, E. (2003) GATE-16 and GABARAP are authentic modifiers mediated by Apg7 and Apg3. Biochem. Biophys. Res. Commun. 300, 637-644.
30. Tanida, I., Tanida-Miyake, E., Komatsu, M., Ueno, T. & Kominami, E. (2002) 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.
31. Tanida, I., Tanida-Miyake, E., Ueno, T. & Kominami, E. (2001) The human homolog of Saccharomyces cerevisiae Apg7p is a Protein-activating enzyme for multiple substrates including human Apg12p, GATE-16, GABARAP and MAP-LC3. J. Biol. Chem. 276, 1701-1706.
32. Terasawa, H., Noda, Y, Ito, T., et al. (2001) Structure and ligand recognition of the PB1 domain: a novel protein module binding to the PC motif EMBO J. 20, 3947-3956.
33. Thumm, M., Egner, R., Koch, B., et al. (1994) Isolation of autophagocytosis mutants of Saccharomyces cerevisiae. FEBS Lett. 349, 275-280.
34. Tsukada, M. & Ohsumi, Y. (1993) Isolation and characterization of autophagy-defective mutants of Saccharomyces cerevisiae. FEBS Lett. 333, 169-174.
35. Vijay-Kumar, S., Bugg, C.E., Wilkinson, K.D., Vierstra, R.D., Hatfield, P.M. & Cook, W.J. (1987) Structure of ubiquitin refined at 1.8 Å resolution. J. Biol. Chem. 262, 6396-6399.
36. Walden, H., Podgorski, M.S., Huang, D.T., et al. (2003) The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Mol. Cell 12, 1427-1437.
37. Wang, H., Bedford, F.K., Brandon, N.J., Moss, S.J. & Olsen, R.W. (1999) GABA (A) - receptor-associated protein links GABA (A) receptors and the cytoskeleton. Nature 397, 69-72.
38. Yoshinaga, S., Kohjima, M., Ogura, K., et al. (2003) The PB1 domain and the PC motif-containing region are structurally similar protein binding modules. EMBO J. 22, 4888-4897.