Biochemical and structural characterization of a novel ubiquitin-conjugating enzyme E2 from Agrocybe aegeria reveals Ube2w family-specific properties

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Qi, Chao ^a,b   Li, De Feng ^a   Feng, Lei ^a   Hou, Yanjie ^a   Sun, Hui ^c   Wang, Da Cheng ^a   Liu, Wei ^d  

^a INSTITUTE OF BIOPHYSICS   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c WUHAN UNIVERSITY   (China)

^d THIRD MILITARY MEDICAL UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

FUNGAL PROTEIN; PEPTIDE; RECOMBINANT PROTEIN; UBIQUITIN; UBIQUITIN CONJUGATING ENZYME;

AGROCYBE; AMINO ACID SEQUENCE; BIOSYNTHESIS; CHEMISTRY; DIMERIZATION; ENZYMOLOGY; GENETICS; HUMAN; HYDROGEN BOND; ISOLATION AND PURIFICATION; METABOLISM; MOLECULAR GENETICS; MUTAGENESIS; PROTEIN QUATERNARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; TANDEM MASS SPECTROMETRY; UBIQUITINATION; ULTRACENTRIFUGATION; X RAY CRYSTALLOGRAPHY;

AGROCYBE; AMINO ACID SEQUENCE; CRYSTALLOGRAPHY, X-RAY; DIMERIZATION; FUNGAL PROTEINS; HUMANS; HYDROGEN BONDING; MOLECULAR SEQUENCE DATA; MUTAGENESIS; PEPTIDES; PROTEIN STRUCTURE, QUATERNARY; PROTEIN STRUCTURE, TERTIARY; RECOMBINANT PROTEINS; SEQUENCE ALIGNMENT; TANDEM MASS SPECTROMETRY; UBIQUITIN; UBIQUITIN-CONJUGATING ENZYMES; UBIQUITINATION; ULTRACENTRIFUGATION;

EID: 84946779981     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep16056     Document Type: Article

References (44)

1. Geng, F., Wenzel, S. and Tansey, W. P. Ubiquitin and proteasomes in transcription. Annu Rev Biochem 81, 177-201 (2012).
2. Haglund, K. and Dikic, I. The role of ubiquitylation in receptor endocytosis and endosomal sorting. J Cell Sci 125, 265-275 (2012).
3. Mocciaro, A. and Rape, M. Emerging regulatory mechanisms in ubiquitin-dependent cell cycle control. J Cell Sci 125, 255-263 (2012).
4. Shang, F. and Taylor, A. Role of the ubiquitin-proteasome in protein quality control and signaling: implication in the pathogenesis of eye diseases. Prog Mol Biol Transl 109, 347-396 (2012).
5. Glickman, M. H. and Ciechanover, A. The ubiquitin-proteasome proteolytic pathway: destruction for the sake of construction. Physiol Rev 82, 373-428 (2002).
6. McDowell, G. S., Kucerova, R. and Philpott, A. Non-canonical ubiquitylation of the proneural protein Ngn2 occurs in both Xenopus embryos and mammalian cells. Biochem Bioph Res Co 400, 655-660 (2010).
7. Trausch-Azar, J., Leone, T. C., Kelly, D. P. and Schwartz, A. L. Ubiquitin proteasome-dependent degradation of the transcriptional coactivator PGC-1{alpha} via the N-terminal pathway. J Biol Chem 285, 40192-40200 (2010).
8. Scaglione, K. M. et al. The ubiquitin-conjugating enzyme (E2) Ube2w ubiquitinates the N terminus of substrates. J Biol Chem 288, 18784-18788 (2013).
9. Tatham, M. H., Plechanovova, A., Jaffray, E. G., Salmen, H. and Hay, R. T. Ube2W conjugates ubiquitin to alpha-amino groups of protein N-termini. Biochem J 453, 137-145 (2013).
10. Vittal, V. et al. Intrinsic disorder drives N-terminal ubiquitination by Ube2w. Nat Chem Biol 11, 83-89 (2015).
11. Burroughs, A. M., Jaffee, M., Iyer, L. M. and Aravind, L. Anatomy of the E2 ligase fold: implications for enzymology and evolution of ubiquitin/Ub-like protein conjugation. J Struct Biol 162, 205-218 (2008).
12. Michelle, C., Vourch, P., Mignon, L. and Andres, C. R. What was the set of ubiquitin and ubiquitin-like conjugating enzymes in the eukaryote common ancestor? J Mol Evol 68, 616-628 (2009).
13. Winn, P. J., Religa, T. L., Battey, J. N., Banerjee, A. and Wade, R. C. Determinants of functionality in the ubiquitin conjugating enzyme family. Structure 12, 1563-1574 (2004).
14. Van Wijk, S. J. and Timmers, H. T. The family of ubiquitin-conjugating enzymes (E2s): deciding between life and death of proteins. FASEB J 24, 981-993 (2010).
15. Wenzel, D. M., Stoll, K. E. and Klevit, R. E. E2s: structurally economical and functionally replete. Biochem J 433, 31-42 (2011).
16. Ye, Y. and Rape, M. Building ubiquitin chains: E2 enzymes at work. Nat Rev Mol Cell Bio 10, 755-764 (2009).
17. Borchers, A. T., Keen, C. L. and Gershwin, M. E. Mushrooms, tumors, and immunity: an update. Exp Biol Med 229, 393-406 (2004).
18. Borchers, A. T., Stern, J. S., Hackman, R. M., Keen, C. L. and Gershwin, M. E. Mushrooms, tumors, and immunity. P Soc Exp Biol Med 221, 281-293 (1999).
19. Feng, L., Sun, H., Zhang, Y., Li, D. F. and Wang, D. C. Structural insights into the recognition mechanism between an antitumor galectin AAL and the Thomsen-Friedenreich antigen. FASEB J 24, 3861-3868 (2010).
20. Yang, N. et al. Structural basis for the tumor cell apoptosis-inducing activity of an antitumor lectin from the edible mushroom Agrocybe aegerita. J Mol Biol 387, 694-705 (2009).
21. Li, N. et al. Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development. Sci China Life Sci 57, 1162-1171 (2014).
22. Zhang, G., Wang, T. and He, Q. How to discover new proteins-translatome profiling. Sci China Life Sci 57, 358-360 (2014).
23. Scaglione, K. M. et al. Ube2w and ataxin-3 coordinately regulate the ubiquitin ligase CHIP. Mol Cell 43, 599-612 (2011).
24. Zhang, Y. et al. UBE2W interacts with FANCL and regulates the monoubiquitination of Fanconi anemia protein FANCD2. Mol Cells 31, 113-122 (2011).
25. Vittal, V., Wenzel, D. M., Brzovic, P. S. and Klevit, R. E. Biochemical and structural characterization of the ubiquitin-conjugating enzyme UBE2W reveals the formation of a noncovalent homodimer. Cell Biochem Biophys 67, 103-110 (2013).
26. Wu, P. Y. et al. A conserved catalytic residue in the ubiquitin-conjugating enzyme family. EMBO J 22, 5241-5250 (2003).
27. Sheng, Y. et al. A human ubiquitin conjugating enzyme (E2)-HECT E3 ligase structure-function screen. Mol Cell Proteomics 11, 329-341 (2012).
28. Orengo, C. A. et al. CATH-a hierarchic classification of protein domain structures. Structure 5, 1093-1108 (1997).
29. Holm, L. and Rosenstrom, P. Dali server: conservation mapping in 3D. Nucleic Acids Res 38, W545-549 (2010).
30. Li, W., Tu, D., Brunger, A. T. and Ye, Y. A ubiquitin ligase transfers preformed polyubiquitin chains from a conjugating enzyme to a substrate. Nature 446, 333-337 (2007).
31. Ravid, T. and Hochstrasser, M. Autoregulation of an E2 enzyme by ubiquitin-chain assembly on its catalytic residue. Nat Cell Biol 9, 422-427 (2007).
32. Battye, T. G., Kontogiannis, L., Johnson, O., Powell, H. R. and Leslie, A. G. iMOSFLM: a new graphical interface for diffractionimage processing with MOSFLM. Acta Crystallogr D 67, 271-281 (2011).
33. Winn, M. D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr D 67, 235-242 (2011).
34. Li, D. F., Feng, L., Hou, Y. J. and Liu, W. The expression, purification and crystallization of a ubiquitin-conjugating enzyme E2 from Agrocybe aegerita underscore the impact of His-tag location on recombinant protein properties. Acta Crystallogr F 69, 153-157 (2013).
35. McCoy, A. J. et al. Phaser crystallographic software. J Appl Crystallogr 40, 658-674 (2007).
36. Navaza, J. AMoRe: an automated package for molecular replacement. Acta Crystallogr A 50, 157-163 (1994).
37. Jones, T. A., Zou, J. Y., Cowan, S. W. and Kjeldgaard, M. Improved methods for building protein models in electron density maps and the location of errors in these models. Acta Crystallogr A 47(Pt 2), 110-119 (1991).
38. Brunger, A. T. et al. Crystallography and NMR system: A new software suite for macromolecular structure determination. Acta Crystallogr D 54, 905-921 (1998).
39. Afonine, P. V. et al. Towards automated crystallographic structure refinement with phenix.refine. Acta Crystallogr D 68, 352-367 (2012).
40. Headd, J. J. et al. Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution. Acta Crystallogr D 68, 381-390 (2012).
41. Gille, C. and Frommel, C. STRAP: editor for STRuctural Alignments of Proteins. Bioinformatics 17, 377-378 (2001).
42. Schrodinger, LLC. The PyMOL Molecular Graphics System, Version 1.3r1 (2010).
43. Schuck, P., Perugini, M. A., Gonzales, N. R., Howlett, G. J. and Schubert, D. Size-distribution analysis of proteins by analytical ultracentrifugation: strategies and application to model systems. Biophys J 82, 1096-1111 (2002).
44. Laue, T. M., Shah, B. D., Ridgeway, T. M and Pelletier, S. L. In Analytical Ultracentrifugation in Biochemistry and Polymer Science (eds Harding, S. E. et al.) 90-125 (Royal Society of Chemistry, 1992).