Modulation of K11-linkage formation by variable loop residues within UbcH5A

Journal of Molecular Biology

Volumn 408, Issue 3, 2011, Pages 420-431

  Bosanac, Ivan ^a   Phu, Lilian ^a   Pan, Borlan ^a   Zilberleyb, Inna ^a   Maurer, Brigitte ^a   Dixit, Vishva M ^a   Hymowitz, Sarah G ^a   Kirkpatrick, Donald S ^a  

^a GENENTECH INC   (United States)

Author keywords

anaphase promoting complex; APC; polyUb; polyubiquitin; Ub; ubiquitin; wild type; WT

Indexed keywords

CYSTEINE; LYSINE; LYSINE 11; POLYUBIQUITIN; PROTEIN; UBCH5A; UBIQUITIN; UBIQUITIN CONJUGATING ENZYME; UBIQUITIN CONJUGATING ENZYME E1; UBIQUITIN CONJUGATING ENZYME E2; UBIQUITIN CONJUGATING ENZYME E3; UNCLASSIFIED DRUG;

ARTICLE; BIOCHEMISTRY; CELLULAR PARAMETERS; CRYSTAL STRUCTURE; HUMAN; IN VITRO STUDY; LINKAGE ANALYSIS; MASS SPECTROMETRY; MUTAGENESIS; PRIORITY JOURNAL; PROTEIN SYNTHESIS; PROTEOMICS; UBIQUITINATION;

EID: 79953846027     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.jmb.2011.03.011     Document Type: Article

References (35)

1. Pickart C.M. Mechanisms underlying ubiquitination Annu. Rev. Biochem. 70 2001 503 533 (Pubitemid 32663902)
2. Ikeda F., and Dikic I. Atypical ubiquitin chains: new molecular signals. 'Protein Modifications: Beyond the Usual Suspects' Review Series EMBO Rep. 9 2008 536 542 (Pubitemid 351772916)
3. Pickart C.M., and Fushman D. Polyubiquitin chains: polymeric protein signals Curr. Opin. Chem. Biol. 8 2004 610 616 (Pubitemid 39535722)
4. Kim H.T., Kim K.P., Lledias F., Kisselev A.F., Scaglione K.M., and Skowyra D. Certain pairs of ubiquitin-conjugating enzymes (E2s) and ubiquitin-protein ligases (E3s) synthesize nondegradable forked ubiquitin chains containing all possible isopeptide linkages J. Biol. Chem. 282 2007 17375 17386 (Pubitemid 47100279)
5. Crosas B., Hanna J., Kirkpatrick D.S., Zhang D.P., Tone Y., and Hathaway N.A. Ubiquitin chains are remodeled at the proteasome by opposing ubiquitin ligase and deubiquitinating activities Cell 127 2006 1401 1413 (Pubitemid 44960408)
6. Kim H.C., and Huibregtse J.M. Polyubiquitination by HECT E3s and the determinants of chain type specificity Mol. Cell. Biol. 29 2009 3307 3318
7. Ye Y., and Rape M. Building ubiquitin chains: E2 enzymes at work Nat. Rev. Mol. Cell. Biol. 10 2009 755 764
8. Rodrigo-Brenni M.C., Foster S.A., and Morgan D.O. Catalysis of lysine 48-specific ubiquitin chain assembly by residues in E2 and ubiquitin Mol. Cell 39 2010 548 559
9. Petroski M.D., and Deshaies R.J. Mechanism of lysine 48-linked ubiquitin-chain synthesis by the Cullin-RING ubiquitin-ligase complex SCF-Cdc34 Cell 123 2005 1107 1120 (Pubitemid 41785424)
10. Sadowski, M., Suryadinata, R., Lai, X., Heierhorst, J. & Sarcevic, B. Molecular basis for lysine specificity in the yeast ubiquitin-conjugating enzyme Cdc34. Mol. Cell. Biol. 30, 2316-2329.
11. Eddins M.J., Carlile C.M., Gomez K.M., Pickart C.M., and Wolberger C. Mms2-Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation Nat. Struct. Mol. Biol. 13 2006 915 920 (Pubitemid 44527374)
12. Brzovic P.S., and Klevit R.E. Ubiquitin transfer from the E2 perspective: why is UbcH5 so promiscuous? Cell Cycle 5 2006 2867 2873 (Pubitemid 44953937)
13. Kirkpatrick D.S., Hathaway N.A., Hanna J., Elsasser S., Rush J., and Finley D. Quantitative analysis of in vitro ubiquitinated cyclin B1 reveals complex chain topology Nat. Cell Biol. 8 2006 700 710
14. Rodrigo-Brenni M.C., and Morgan D.O. Sequential E2s drive polyubiquitin chain assembly on APC targets Cell 130 2007 127 139 (Pubitemid 47031321)
15. Brzovic P.S., Lissounov A., Christensen D.E., Hoyt D.W., and Klevit R.E. A UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination Mol. Cell 21 2006 873 880 (Pubitemid 43376136)
16. Sakata E., Satoh T., Yamamoto S., Yamaguchi Y., Yagi-Utsumi M., and Kurimoto E. Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates Structure 18 2010 138 147
17. Blankenship J.W., Varfolomeev E., Goncharov T., Fedorova A.V., Kirkpatrick D.S., and Izrael-Tomasevic A. Ubiquitin binding modulates IAP antagonist-stimulated proteasomal degradation of c-IAP1 and c-IAP2 Biochem. J. 417 2009 149 160
18. Newton K., Matsumoto M.L., Wertz I.E., Kirkpatrick D.S., Lill J.R., and Tan J. Ubiquitin chain editing revealed by polyubiquitin linkage-specific antibodies Cell 134 2008 668 678
19. Ben-Saadon R., Zaaroor D., Ziv T., and Ciechanover A. The polycomb protein Ring1B generates self atypical mixed ubiquitin chains required for its in vitro histone H2A ligase activity Mol. Cell 24 2006 701 711 (Pubitemid 44839211)
20. Bosanac I., Wertz I.E., Pan B., Yu C., Kusam S., and Lam C. Ubiquitin binding to A20 ZnF4 is required for modulation of NF-κB signaling Mol. Cell 40 2010 548 557
21. Capili A.D., and Lima C.D. Structure and analysis of a complex between SUMO and Ubc9 illustrates features of a conserved E2-Ubl interaction J. Mol. Biol. 369 2007 608 618 (Pubitemid 46709931)
22. Duda D.M., van Waardenburg R.C., Borg L.A., McGarity S., Nourse A., and Waddell M.B. Structure of a SUMO-binding-motif mimic bound to Smt3p-Ubc9p: conservation of a non-covalent ubiquitin-like protein-E2 complex as a platform for selective interactions within a SUMO pathway J. Mol. Biol. 369 2007 619 630 (Pubitemid 46709932)
23. Knipscheer P., van Dijk W.J., Olsen J.V., Mann M., and Sixma T.K. Noncovalent interaction between Ubc9 and SUMO promotes SUMO chain formation EMBO J. 26 2007 2797 2807 (Pubitemid 46884280)
24. Jin L., Williamson A., Banerjee S., Philipp I., and Rape M. Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex Cell 133 2008 653 665 (Pubitemid 351636306)
25. Reverter D., and Lima C.D. Insights into E3 ligase activity revealed by a SUMO-RanGAP1-Ubc9-Nup358 complex Nature 435 2005 687 692 (Pubitemid 40825514)
26. Yunus A.A., and Lima C.D. Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway Nat. Struct. Mol. Biol. 13 2006 491 499 (Pubitemid 43848903)
27. Phu L., Izrael-Tomasevic A., Matsumoto M.L., Bustos D., Dynek J.N., and Fedorova A.V. Improved quantitative mass spectrometry methods for characterizing complex ubiquitin signals Mol. Cell. Proteomics 2010
28. Bennett E.J., Shaler T.A., Woodman B., Ryu K.Y., Zaitseva T.S., and Becker C.H. Global changes to the ubiquitin system in Huntington's disease Nature 448 2007 704 708 (Pubitemid 47236860)
29. Peng J., Schwartz D., Elias J.E., Thoreen C.C., Cheng D., and Marsischky G. A proteomics approach to understanding protein ubiquitination Nat. Biotechnol. 21 2003 921 926 (Pubitemid 36936199)
30. Xu P., Duong D.M., Seyfried N.T., Cheng D., Xie Y., and Robert J. Quantitative proteomics reveals the function of unconventional ubiquitin chains in proteasomal degradation Cell 137 2009 133 145
31. Hoeller D., Hecker C.M., Wagner S., Rogov V., Dotsch V., and Dikic I. E3-independent monoubiquitination of ubiquitin-binding proteins Mol. Cell 26 2007 891 898 (Pubitemid 46921003)
32. Kirisako T., Kamei K., Murata S., Kato M., Fukumoto H., and Kanie M. A ubiquitin ligase complex assembles linear polyubiquitin chains EMBO J. 25 2006 4877 4887 (Pubitemid 44607032)
33. Eldridge A.G., Loktev A.V., Hansen D.V., Verschuren E.W., Reimann J.D., and Jackson P.K. The evi5 oncogene regulates cyclin accumulation by stabilizing the anaphase-promoting complex inhibitor emi1 Cell 124 2006 367 380 (Pubitemid 43121984)
34. Emsley P., and Cowtan K. Coot: Model-building tools for molecular graphics Acta Crystallogr. D Biol. Crystallogr. 60 2004 2126 2132 (Pubitemid 41742764)
35. Winn M.D., Isupov M.N., and Murshudov G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr D Biol. Crystallogr. 57 2001 122 133 (Pubitemid 32062682)