The crystal structure of human Atg4b, a processing and de-conjugating enzyme for autophagosome-forming modifiers

Journal of Molecular Biology

Volumn 355, Issue 4, 2006, Pages 612-618

  Kumanomidou, Taichi ^a   Mizushima, Tsunehiro ^a,b   Komatsu, Masaaki ^c,d   Suzuki, Atsuo ^a   Tanida, Isei ^d   Sou, Yu Shin ^d   Ueno, Takashi ^d   Kominami, Eiki ^d   Tanaka, Keiji ^c   Yamane, Takashi ^a  

^a NAGOYA UNIVERSITY   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c TOKYO METROPOLITAN INSTITUTE OF MEDICAL SCIENCE   (Japan)

^d JUNTENDO UNIVERSITY   (Japan)

Author keywords

Atg4b; Autophagy; Cysteine protease; Tertiary structure; Ubiquitin like modifier

Indexed keywords

CYSTEINE; CYSTEINE PROTEINASE; NITROGEN; PAPAIN; PHOSPHOLIPID; UBIQUITIN;

ARTICLE; CATALYSIS; CONJUGATION; CRYSTAL STRUCTURE; HUMAN; PHAGOSOME; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN LOCALIZATION; PROTEIN STRUCTURE; REACTION ANALYSIS; X RAY CRYSTALLOGRAPHY;

EID: 29144517659     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2005.11.018     Document Type: Article

References (29)

1. S. Jentsch, and G. Pyrowolakis Ubiquitin and its kin: how close are the family ties? Trends Cell Biol. 10 2000 335 342
2. C.M. Pickart, and M.J. Eddins Ubiquitin: structures, functions, mechanisms Biochim. Biophys. Acta 1695 2004 55 72
3. R.L. Welchman, C. Gordon, and R.J. Mayer Ubiquitin and ubiquitin-like proteins as multifunctional signals Nature Rev. Mol. Cell Biol. 6 2005 599 609
4. D. Finley, B. Bartel, and A. Varshavsky The tails of ubiquitin precursors are ribosomal proteins whose fusion to ubiquitin facilitates ribosome biogenesis Nature 338 1989 394 401
5. O. Wiborg, M.S. Pedersen, A. Wind, L.E. Berglund, K.A. Marcker, and J. Vuust The human ubiquitin multigene family: some genes contain multiple directly repeated ubiquitin coding sequences EMBO J. 4 1985 755 759
6. D.C. Schwartz, and M. Hochstrasser A superfamily of protein tags: ubiquitin, SUMO and related modifiers Trends Biochem. Sci. 28 2003 321 328
7. J.H. Kim, K.C. Park, S.S. Chung, O. Bang, and C.H. Chung Deubiquitinating enzymes as cellular regulators J. Biochem. (Tokyo) 134 2003 9 18
8. Y. Kabeya, N. Mizushima, A. Yamamoto, S. Oshitani-Okamoto, Y. Ohsumi, and T. Yoshimori LC3, GABARA and GATE16 localize to autophagosomal membrane depending on form-II formation J. Cell Sci. 117 2004 2805 2812
9. I. Tanida, Y.S. Sou, J. Ezaki, N. Minematsu-Ikeguchi, T. Ueno, and E. Kominami HsAtg4B/HsApg4B/autophagin-1 cleaves the carboxyl termini of three human Atg8 homologues and delipidates microtubule-associated protein light chain 3- and GABAA receptor-associated protein-phospholipid conjugates J. Biol. Chem. 279 2004 36268 36276
10. Y. Ichimura, T. Kirisako, T. Takao, Y. Satomi, Y. Shimonishi, and N. Ishihara A ubiquitin-like system mediates protein lipidation Nature 408 2000 488 492
11. D.J. Klionsky The molecular machinery of autophagy: unanswered questions J. Cell Sci 118 2005 7 18
12. Y. Ohsumi Molecular dissection of autophagy: two ubiquitin-like systems Nature Rev. Mol. Cell Biol. 2 2001 211 216
13. N. Mizushima, Y. Ohsumi, and T. Yoshimori Autophagosome formation in mammalian cells Cell Struct. Funct. 27 2002 421 429
14. Y. Kabeya, N. Mizushima, T. Ueno, A. Yamamoto, T. Kirisako, and T. Noda LC3, a mammalian homologue of yeast Apg8p, is localized in autophagosome membranes after processing EMBO J. 19 2000 5720 5728
15. L. Holm, and C. Sander Protein structure comparison by alignment of distance matrices J. Mol. Biol. 233 1993 123 138
16. K. Wenig, L. Chatwell, U. von Pawel-Rammingen, L. Bjorck, R. Huber, and P. Sondermann Structure of the streptococcal endopeptidase IdeS, a cysteine proteinase with strict specificity for IgG Proc. Natl Acad. Sci. USA 101 2004 17371 17376
17. T. Kirisako, Y. Ichimura, H. Okada, Y. Kabeya, N. Mizushima, and T. Yoshimori 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 2000 263 276
18. S.C. Johnston, C.N. Larsen, W.J. Cook, K.D. Wilkinson, and C.P. Hill Crystal structure of a deubiquitinating enzyme (human UCH-L3) at 1.8 Å resolution EMBO J. 16 1997 3787 3796
19. E. Schroder, C. Phillips, E. Garman, K. Harlos, and C. Crawford X-ray crystallographic structure of a papain-leupeptin complex FEBS Letters 315 1993 38 42
20. A. Yamamoto, K. Tomoo, K. Matsugi, T. Hara, Y. In, and M. Murata Structural basis for development of cathepsin B-specific noncovalent-type inhibitor: crystal structure of cathepsin B-E64c complex Biochim. Biophys. Acta 1597 2002 244 251
21. M. Hu, P. Li, M. Li, W. Li, T. Yao, and J.W. Wu Crystal structure of a UBP-family deubiquitinating enzyme in isolation and in complex with ubiquitin aldehyde Cell 111 2002 1041 1054
22. K. Sugawara, N.N. Suzuki, Y. Fujioka, N. Mizushima, Y. Ohsumi, and F. Inagaki The crystal structure of microtubule-associated protein light chain 3, a mammalian homologue of Saccharomyces cerevisiae Atg8 Genes Cells 9 2004 611 618
23. V.N. Bavro, M. Sola, A. Bracher, M. Kneussel, H. Betz, and W. Weissenhorn Crystal structure of the GABA(A)-receptor-associated protein, GABARAP EMBO Rep. 3 2002 183 189
24. L.N. Shen, H. Liu, C. Dong, D. Xirodimas, J.H. Naismith, and R.T. Hay Structural basis of NEDD8 ubiquitin discrimination by the deNEDDylating enzyme NEDP1 EMBO J. 24 2005 1341 1351
25. M.T. Stubbs, B. Laber, W. Bode, R. Huber, R. Jerala, B. Lenarcic, and V. Turk The refined 2.4 Å X-ray crystal structure of recombinant human stefin B in complex with the cysteine proteinase papain: a novel type of proteinase inhibitor interaction EMBO J. 9 1990 1939 1947
26. T.R. Schneider, and G.M. Sheldrick Substructure solution with SHELXD Acta Crystallog. sect. D 58 2002 1772 1779
27. A. Perrakis, R. Morris, and V.S. Lamzin Automated protein model building combined with iterative structure refinement Nature Struct. Biol. 6 1999 458 463
28. D.E. McRee XtalView/Xfit-A versatile program for manipulating atomic coordinates and electron density J. Struct. Biol. 125 1999 156 165
29. G.N. Murshudov, A.A. Vagin, A. Lebedev, K.S. Wilson, and E.J. Dodson Efficient anisotropic refinement of macromolecular structures using FFT Acta Crystallog. sect. D 55 1999 247 255