Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase

Molecular Cell

Volumn 11, Issue 1, 2003, Pages 249-259

  Verdecia, Mark A ^b   Joazeiro, Claudio A P ^a,d   Wells, Nicholas J ^a,e   Ferrer, Jean Luc ^c   Bowman, Marianne E ^f   Hunter, Tony ^a   Noel, Joseph P ^f  

^a SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c INSTITUT DE BIOLOGIE STRUCTURALE   (France)

^d Genomics Inst of the N R F (GNF)   (United States)

^e IMPERIAL COLLEGE LONDON   (United Kingdom)

^f NONE

Author keywords

[No Author keywords available]

Indexed keywords

LIGASE; UBIQUITIN;

ARTICLE; CATALYSIS; CONFORMATION; CRYSTAL STRUCTURE; MOLECULAR RECOGNITION; PROTEIN DEGRADATION;

EID: 0037249354     PISSN: 10972765     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1097-2765(02)00774-8     Document Type: Article

References (53)

1. Abrahams J.P., Leslie A.G.W. Methods used in the structure determination of bovine mitochondrial F1 ATPase. Acta Crystallogr. D. 52:1996;30-42.
2. Amundsen C., Anger S., Antler R., Baily J., Barish E., Bayer D., Bennett K., Bennett S., Buck D., Collins A.et al. X-POV-Team POV-Ray. persistence of vision ray tracer http://www.povray.org:1997.
3. Beaudenon S.L., Huacani M.R., Wang G., McDonell D.P., Huibregtse J.M. Rsp5 ubiquitin-protein ligase mediates DNA damage-induced degradation of the large subunit of RNA polymerase II in Saccharomyces cerevisiae. Mol. Cell. Biol. 19:1999;6972-6979.
4. Boname J.M., Stevenson P.G. MHC class I ubiquitylation by a viral PHD/LAP finger protein. Immunity. 15:2001;627-636.
5. Brunger A.T., Adams P.D., Clore G.M., DeLano W.L., Gros P., Grosse-Kunstleve R.W., Jiang J.S., Kuszewski J., Nilges M., Pannu N.S.et al. Crystallography & NMR system. a new software suite for macromolecular structure determination Acta Crystallogr. D. 54:1998;905-921.
6. Conkright M.D., Wani M.A., Lingrel J.B. Lung Krüppel-like factor contains an autoinhibitory domain that regulates its transcriptional activation by binding WWP1, an E3 ubiquitin ligase. J. Biol. Chem. 276:2001;29299-29306.
7. Coscoy L., Sanchez D.J., Ganem D. A novel class of herpesvirus-encoded membrane-bound E3 ubiquitin ligases regulates endocytosis of proteins involved in immune recognition. J. Cell Biol. 155:2001;1265-1273.
8. de La Fortelle E., Bricogne G. Maximum likelihood heavy-atom parameter refinement for multiple isomorphous replacement and multiwavelength anomalous diffraction methods. Methods Enzymol. 276:1997;472-494.
9. Deshaies R.J. SCF and Cullins/Ring H2-based ubiquitin ligases. Annu. Rev. Cell Dev. Biol. 15:1999;435-467.
10. Doublié S. Preparation of selenomethionyl proteins for phase determination. Methods Enzymol. 276:1997;523-530.
11. Fang D., Elly C., Gao B., Fang N., Altman Y., Joazeiro C., Hunter T., Copeland N., Jenkins N., Liu Y.C. Dysregulation of T lymphocyte function in itchy mice. a role for Itch in TH2 differentiation Nat. Immunol. 3:2002;281-287.
12. Ferrin T.E., Huang C.C., Jarvis L.E., Langridge R. The MIDAS display system. J. Mol. Graph. 6:1988;13-27.
13. Flasza M., Gorman P., Roylance R., Canfield A.E., Baron M. Alternative splicing determines the domain structure of WWP1, a Nedd4 family protein. Biochem. Biophys. Res. Commun. 290:2002;431-437.
14. Gmachl M., Gieffers C., Podtelejnikov A.V., Mann M., Peters J.M. The RING-H2 finger protein APC11 and the E2 enzyme UBC4 are sufficient to ubiquitinate substrates of the anaphase-promoting complex. Proc. Natl. Acad. Sci. USA. 97:2000;8973-8978.
15. Hamilton K.S., Ellison M.J., Barber K.R., Williams R.S., Huzil J.T., McKenna S., Ptak C., Glover M., Shaw G.S. Structure of a conjugating enzyme-ubiquitin thioester intermediate reveals a novel role for the ubiquitin tail. Structure. 9:2001;897-904.
16. Hatakeyama S., Yada M., Matsumoto M., Ishida N., Nakayama K.-I. U box proteins as a new family of ubiquitin-protein ligases. J. Biol. Chem. 276:2001;33111-33120.
17. Hendrickson W.A. Determination of macromolecular structures from anomalous diffraction of synchrotron radiation. Science. 254:1991;51-58.
18. Huang L., Kinnucan E., Wang G., Beaudenon S., Howley P.M., Huibregtse J.M., Pavletich N.P. Structure of an E6AP-UbcH7 complex. insights into ubiquitylation by the E2-E3 enzyme cascade Science. 286:1999;1321-1326.
19. Huang K., Johnson K.D., Petcherski A.G., Vandergon T., Mosser E.A., Copeland N.G., Jenkins N.A., Kimble J., Bresnick E.H. A HECT domain ubiquitin ligase closely related to the mammalian protein WWP1 is essential for Caenorhabditis elegans embryogenesis. Gene. 252:2000;137-145.
20. Huibregtse J.M., Scheffner M., Beaudenon S., Howley P.M. A family of proteins structurally and functionally related to the E6-AP ubiquitin-protein ligase. Proc. Natl. Acad. Sci. USA. 92:1995;2563-2567.
21. Jiang Y.-H., Lev-Lehman E., Bressler J., Tsai T.-F., Beaudet A.L. Genetics of Angelman syndrome. Am. J. Hum. Genet. 65:1999;1-6.
22. Jiang J., Ballinger C.A., Wu Y., Dai Q., Cyr D.M., Hohfeld J., Patterson C. CHIP is a U-box-dependent E3 ubiquitin ligase. identification of Hsc70 as a target for ubiquitylation J. Biol. Chem. 276:2001;42938-42944.
23. Joazeiro C.A.P., Weissman A.M. RING finger proteins. mediators of ubiquitin ligase activity Cell. 102:2000;549-552.
24. Joazeiro C.A.P., Wing S.S., Huang H.-K., Leverson J.D., Hunter T., Liu Y.-C. The tyrosine kinase negative regulator c-Cbl as a RING-type, E2-dependent ubiquitin-protein ligase. Science. 286:1999;223-225.
25. Jones A.T., Zou J.-Y., Cowan S., 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.
26. Kavsak P., Rasmussen R.K., Causing C.G., Bonni S., Zhu H., Thomsen G.H., Wrana J.L. Smad7 binds to Smurf2 to form an E3 ubiquitin ligase that targets the TGFβ receptor for degradation. Mol. Cell. 6:2000;1365-1375.
27. Koegl M., Hoppe T., Schlenker S., Ulrich H.D., Mayer T.U., Jentsch S. A novel ubiquitylation factor, E4, is involved in multiubiquitin chain assembly. Cell. 96:1999;635-644.
28. Kraulis P.J. MOLSCRIPT. A program to produce both detailed and schematic plots of protein structures. J. Appl. Crystallogr. 24:1991;946-950.
29. Kumar S., Kao W.H., Howley P.M. Physical interaction between E2 and Hect E3 enzymes determines functional cooperativity. J. Biol. Chem. 272:1997;13548-13554.
30. Laskowski R.A., MacArthur M.W., Moss D.S., Thornton J.M. Procheck. a program to check the stereochemical quality of protein structures J. Appl. Crystallogr. 26:1993;283-291.
31. Leverson J.D., Joaziero C.A.P., Page A.M., Huang H.-K., Hieter P., Hunter T. The APC11 RING-H2 finger mediates E2-dependent ubiquitylation. Mol. Biol. Cell. 11:2000;2315-2325.
32. Lu Z., Xu S., Joazeiro C., Cobb M.H., Hunter T. The PHD domain of Mekk1 acts as an E3 ubiquitin ligase and mediates ubiquitylation and degradation of ERK1/2. Mol. Cell. 9:2002;945-956.
33. McRee D.E. A visual protein crystallographic software system for X11/Xview. J. Mol. Graph. 10:1992;44-46.
34. Mitsui A., Sharp P.A. Ubiquitylation of RNA polymerase II large subunit signaled by phosphorylation of carboxy-terminal domain. Proc. Natl. Acad. Sci. USA. 96:1999;6054-6059.
35. Moreas T.F., Edwards R.A., Mckenna S., Pastushok L., Xiao W., Glover J.N.M., Ellison M.J. Crystal structure of the human ubiquitin conjugating enzyme comples, hMms2-hUbc13. Nat. Struct. Biol. 8:2001;669-673.
36. Mosser E.A., Kasanov J.D., Forsberg E.C., Kay B.K., Ney P.A., Bresnick E.H. Physical and functional interactions between the transactivation domain of the hematopoietic transcription factor NF-E2 and WW domains. Biochemistry. 37:1998;13686-13695.
37. Nefsky B., Beach D. Pub1 acts as an E6-AP-like protein ubiquitin ligase in the degradation of cdc25. EMBO J. 15:1996;1301-1312.
38. Otwinowski, Z. (1991). Daresbury Study Weekend proceedings.
39. Otwinowski Z., Minor W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276:1997;307-326.
40. Perry W.L., Hustad C.M., Swing D.A., O'Sullivan T.N., Jenkins N.A., Copeland N.G. The itchy locus encodes a novel ubiquitin protein ligase that is disrupted in a18H mice. Nat. Genet. 18:1998;143-146.
41. Piotrowski J., Beal R., Hoffman L., Wilkinson K.D., Cohen R.E., Pickart C.M. Inhibition of the 26 S proteosome by polyubiquitin chains synthesized to have defined lengths. J. Biol. Chem. 272:1997;23712-23721.
42. Pirozzi G., McConnell S.J., Uveges A.J., Carter J.M., Sparks A.B., Kay B.K., Fowlkes D.M. Identification of novel human WW domain-containing proteins by cloning of ligand targets. J. Biol. Chem. 272:1997;14611-14616.
43. Qiu L., Joazeiro C., Fang N., Wang H.-Y., Elly C., Altman Y., Fang D., Hunter T., Liu Y.-C. Recognition and ubiquitylation of Notch by Itch, a Hect-type E3 ubiquitin ligase. J. Biol. Chem. 275:2000;35734-35737.
44. Rotin D. WW (WWP) domains. from structure to function Curr. Top. Microbiol. Immunol. 228:1998;115-133.
45. Schwarz S.E., Rosa J.L., Scheffner M. Characterization of human hect domain family members and their interaction with UbcH5 and UbcH7. J. Biol. Chem. 273:1998;12148-12154.
46. Skowyra D., Koepp D.M., Kamura T., Conrad M.N., Conaway R.C., Conaway J.W., Elledge S.J., Harper J.W. Reconstitution of G1 cyclin ubiquitylation with complexes containing SCFGrr1 and Rbx1. Science. 284:1999;662-665.
47. Sudol M., Hunter T. NeW wrinkles for an old domain. Cell. 103:2000;1001-1004.
48. Terwilliger T.C., Berendzen J. Automated MAD and MIR structure solution. Acta Crystallogr. D. 55:1992;849-861.
49. Traweger A., Fang D., Liu Y.-C., Stelzhammer W., Krizbai I.A., Fresser F., Bauer H.-C., Bauer H. The tight junction-specific protein occludin is a functional target of the E3 ubiquitin-protein ligase itch. J. Biol. Chem. 277:2002;10201-10208.
50. VanDemark A.P., Hofmann R.M., Tsui C., Pickart C.M., Wolberger C. Molecular insights into polyubiquitin chain assembly. crystal structure of the Mms2/Ubc13 heterodimer Cell. 105:2001;711-720.
51. Weissman A.M. Themes and variations on ubiquitylation. Nat. Rev. Mol. Cell Biol. 2:2001;169-178.
52. Xie Y., Varshavsky A. The E2-E3 interaction in the N-end rule pathway. the RING-H2 finger of E3 is required for the synthesis of multiubiquitin chain EMBO J. 23:1999;6832-6844.
53. You J., Pickart C.M. A HECT domain E3 enzyme assembles novel polyubiquitin chains. J. Biol. Chem. 276:2001;19871-19878.