Structural Insights into E1-Catalyzed Ubiquitin Activation and Transfer to Conjugating Enzymes

Cell

Volumn 134, Issue 2, 2008, Pages 268-278

  Lee, Imsang ^a   Schindelin, Hermann ^a,b  

^a STONY BROOK UNIVERSITY   (United States)

^b UNIVERSITY OF WÜRZBURG   (Germany)

Author keywords

PROTEINS

Indexed keywords

ADENOSINE PHOSPHATE; CYSTEINE; THIOESTER; UBIQUITIN;

ALPHA HELIX; ARTICLE; BINDING SITE; CATALYSIS; CONFORMATIONAL TRANSITION; CONJUGATE; CRYSTAL STRUCTURE; ELECTRICITY; ENZYME ACTIVATION; ENZYME ACTIVITY; ENZYME SPECIFICITY; MOLECULAR RECOGNITION; NONHUMAN; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN FUNCTION; PROTEIN STRUCTURE; YEAST;

EID: 47549111312     PISSN: 00928674     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cell.2008.05.046     Document Type: Article

References (37)

1. Bencsath K.P., Podgorski M.S., Pagala V.R., Slaughter C.A., and Schulman B.A. Identification of a multifunctional binding site on Ubc9p required for Smt3p conjugation. J. Biol. Chem. 277 (2002) 47938-47945
2. Bohnsack R.N., and Haas A.L. Conservation in the mechanism of Nedd8 activation by the human AppBp1-Uba3 heterodimer. J. Biol. Chem. 278 (2003) 26823-26830
3. Burch T.J., and Haas A.L. Site-directed mutagenesis of ubiquitin. Differential roles for arginine in the interaction with ubiquitin-activating enzyme. Biochemistry 33 (1994) 7300-7308
4. Davis I.W., Murray L.W., Richardson J.S., and Richardson D.C. MOLPROBITY: Structure validation and all-atom contact analysis for nucleic acids and their complexes. Nucleic Acids Res. 32 (2004) W615-W619
5. Duda D.M., Walden H., Sfondouris J., and Schulman B.A. Structural analysis of Escherichia coli ThiF. J. Mol. Biol. 349 (2005) 774-786
6. Haas A.L., and Rose I.A. The mechanism of ubiquitin activating enzyme. A kinetic and equilibrium analysis. J. Biol. Chem. 257 (1982) 10329-10337
7. Haas A.L., Warms J.V., Hershko A., and Rose I.A. Ubiquitin-activating enzyme. Mechanism and role in protein-ubiquitin conjugation. J. Biol. Chem. 257 (1982) 2543-2548
8. Haas A.L., Bright P.M., and Jackson V.E. Functional diversity among putative E2 isozymes in the mechanism of ubiquitin-histone ligation. J. Biol. Chem. 263 (1988) 13268-13275
9. Hamilton K.S., Ellison M.J., Barber K.R., Williams R.S., Huzil J.T., McKenna S., Ptak C., Glover M., and Shaw G.S. Structure of a conjugating enzyme-ubiquitin thiolester intermediate reveals a novel role for the ubiquitin tail. Structure 9 (2001) 897-904
10. Hershko A., and Ciechanover A. The ubiquitin system. Annu. Rev. Biochem. 67 (1998) 425-479
11. Hershko A., Heller H., Elias S., and Ciechanover A. Components of ubiquitin-protein ligase system. Resolution, affinity purification, and role in protein breakdown. J. Biol. Chem. 258 (1983) 8206-8214
12. Huang D.T., Miller D.W., Mathew R., Cassell R., Holton J.M., Roussel M.F., and Schulman B.A. A unique E1-E2 interaction required for optimal conjugation of the ubiquitin-like protein NEDD8. Nat. Struct. Mol. Biol. 11 (2004) 927-935
13. Huang D.T., Walden H., Duda D., and Schulman B.A. Ubiquitin-like protein activation. Oncogene 23 (2004) 1958-1971
14. Huang D.T., Paydar A., Zhuang M., Waddell M.B., Holton J.M., and Schulman B.A. Structural basis for recruitment of Ubc12 by an E2 binding domain in NEDD8's E1. Mol. Cell 17 (2005) 341-350
15. Huang D.T., Hunt H.W., Zhuang M., Ohi M.D., Holton J.M., and Schulman B.A. Basis for a ubiquitin-like protein thioester switch toggling E1-E2 affinity. Nature 445 (2007) 394-398
16. Huang D.T., Zhuang M., Ayrault O., and Schulman B.A. Identification of conjugation specificity determinants unmasks vestigial preference for ubiquitin within the NEDD8 E2. Nat. Struct. Mol. Biol. 15 (2008) 280-287
17. Johnson E.S., Schwienhorst I., Dohmen R.J., and Blobel G. The ubiquitin-like protein Smt3p is activated for conjugation to other proteins by an Aos1p/Uba2p heterodimer. EMBO J. 16 (1997) 5509-5519
18. 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 (1991) 110-119
19. Lake M.W., Wuebbens M.M., Rajagopalan K.V., and Schindelin H. Mechanism of ubiquitin activation revealed by the structure of a bacterial MoeB-MoaD complex. Nature 414 (2001) 325-329
20. Lehmann C., Begley T.P., and Ealick S.E. Structure of the Escherichia coli ThiS-ThiF complex, a key component of the sulfur transfer system in thiamin biosynthesis. Biochemistry 45 (2006) 11-19
21. Lois L.M., and Lima C.D. Structures of the SUMO E1 provide mechanistic insights into SUMO activation and E2 recruitment to E1. EMBO J. 24 (2005) 439-451
22. McKenna S., Spyracopoulos L., Moraes T., Pastushok L., Ptak C., Xiao W., and Ellison M.J. Noncovalent interaction between ubiquitin and the human DNA repair protein Mms2 is required for Ubc13-mediated polyubiquitination. J. Biol. Chem. 276 (2001) 40120-40126
23. Merkley N., and Shaw G.S. Solution structure of the flexible class II ubiquitin-conjugating enzyme Ubc1 provides insights for polyubiquitin chain assembly. J. Biol. Chem. 279 (2004) 47139-47147
24. Moraes T.F., Edwards R.A., McKenna S., Pastushok L., Xiao W., Glover J.N., and Ellison M.J. Crystal structure of the human ubiquitin conjugating enzyme complex, hMms2-hUbc13. Nat. Struct. Biol. 8 (2001) 669-673
25. Otwinowski Z., and Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276 (1997) 307-326
26. 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
27. Pitluk Z.W., McDonough M., Sangan P., and Gonda D.K. Novel CDC34 (UBC3) ubiquitin-conjugating enzyme mutants obtained by charge-to-alanine scanning mutagenesis. Mol. Cell. Biol. 15 (1995) 1210-1219
28. Ramachandran G.N., and Sasisekharan V. Conformation of polypeptides and proteins. Adv. Protein Chem. 23 (1968) 283-438
29. Sloper-Mould K.E., Jemc J.C., Pickart C.M., and Hicke L. Distinct functional surface regions on ubiquitin. J. Biol. Chem. 276 (2001) 30483-30489
30. Sullivan M.L., and Vierstra R.D. Cloning of a 16-kDa ubiquitin carrier protein from wheat and Arabidopsis thaliana. Identification of functional domains by in vitro mutagenesis. J. Biol. Chem. 266 (1991) 23878-23885
31. Szczepanowski R.H., Filipek R., and Bochtler M. Crystal structure of a fragment of mouse ubiquitin-activating enzyme. J. Biol. Chem. 280 (2005) 22006-22011
32. VanDemark A.P., Hofmann R.M., Tsui C., Pickart C.M., and Wolberger C. Molecular insights into polyubiquitin chain assembly: Crystal structure of the Mms2/Ubc13 heterodimer. Cell 105 (2001) 711-720
33. Verdecia M.A., Joazeiro C.A., Wells N.J., Ferrer J.L., Bowman M.E., Hunter T., and Noel J.P. Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase. Mol. Cell 11 (2003) 249-259
34. Walden H., Podgorski M.S., Huang D.T., Miller D.W., Howard R.J., Minor Jr. D.L., Holton J.M., and Schulman B.A. The structure of the APPBP1-UBA3-NEDD8-ATP complex reveals the basis for selective ubiquitin-like protein activation by an E1. Mol. Cell 12 (2003) 1427-1437
35. Walden H., Podgorski M.S., and Schulman B.A. Insights into the ubiquitin transfer cascade from the structure of the activating enzyme for NEDD8. Nature 422 (2003) 330-334
36. Wang J., Hu W., Cai S., Lee B., Song J., and Chen Y. The intrinsic affinity between E2 and the Cys domain of E1 in ubiquitin-like modifications. Mol. Cell 27 (2007) 228-237
37. Whitby F.G., Xia G., Pickart C.M., and Hill C.P. Crystal structure of the human ubiquitin-like protein NEDD8 and interactions with ubiquitin pathway enzymes. J. Biol. Chem. 273 (1998) 34983-34991