Mechanism of ubiquitylation by dimeric RING ligase RNF4 (original) (raw)

• Dye, B.T. & Schulman, B.A. Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu. Rev. Biophys. Biomol. Struct. 36, 131–150 (2007).
  Article CAS PubMed Google Scholar
• Pickart, C.M. & Eddins, M.J. Ubiquitin: structures, functions, mechanisms. Biochim. Biophys. Acta 1695, 55–72 (2004).
  Article CAS PubMed Google Scholar
• Deshaies, R.J. & Joazeiro, C.A. RING domain E3 ubiquitin ligases. Annu. Rev. Biochem. 78, 399–434 (2009).
  Article CAS PubMed Google Scholar
• Hay, R.T. SUMO: a history of modification. Mol. Cell 18, 1–12 (2005).
  Article CAS PubMed Google Scholar
• Perry, J.J., Tainer, J.A. & Boddy, M.N. A SIM-ultaneous role for SUMO and ubiquitin. Trends Biochem. Sci. 33, 201–208 (2008).
  Article CAS PubMed Google Scholar
• Kosoy, A., Calonge, T.M., Outwin, E.A. & O'Connell, M.J. Fission yeast Rnf4 homologs are required for DNA repair. J. Biol. Chem. 282, 20388–20394 (2007).
  Article CAS PubMed Google Scholar
• Prudden, J. et al. SUMO-targeted ubiquitin ligases in genome stability. EMBO J. 26, 4089–4101 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Sun, H., Leverson, J.D. & Hunter, T. Conserved function of RNF4 family proteins in eukaryotes: targeting a ubiquitin ligase to SUMOylated proteins. EMBO J. 26, 4102–4112 (2007).
  Article CAS PubMed PubMed Central Google Scholar
• Uzunova, K. et al. Ubiquitin-dependent proteolytic control of SUMO conjugates. J. Biol. Chem. 282, 34167–34175 (2007).
  Article CAS PubMed Google Scholar
• Xie, Y. et al. The yeast Hex3.Slx8 heterodimer is a ubiquitin ligase stimulated by substrate sumoylation. J. Biol. Chem. 282, 34176–34184 (2007).
  Article CAS PubMed Google Scholar
• Häkli, M., Lorick, K.L., Weissman, A.M., Janne, O.A. & Palvimo, J.J. Transcriptional coregulator SNURF (RNF4) possesses ubiquitin E3 ligase activity. FEBS Lett. 560, 56–62 (2004).
  Article PubMed Google Scholar
• Lallemand-Breitenbach, V. et al. Arsenic degrades PML or PML-RARα through a SUMO-triggered RNF4/ubiquitin-mediated pathway. Nat. Cell Biol. 10, 547–555 (2008).
  Article CAS PubMed Google Scholar
• Tatham, M.H. et al. RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation. Nat. Cell Biol. 10, 538–546 (2008).
  Article CAS PubMed Google Scholar
• Song, J., Durrin, L.K., Wilkinson, T.A., Krontiris, T.G. & Chen, Y. Identification of a SUMO-binding motif that recognizes SUMO-modified proteins. Proc. Natl. Acad. Sci. USA 101, 14373–14378 (2004).
  Article CAS PubMed PubMed Central Google Scholar
• Hecker, C.M., Rabiller, M., Haglund, K., Bayer, P. & Dikic, I. Specification of SUMO1- and SUMO2-interacting motifs. J. Biol. Chem. 281, 16117–16127 (2006).
  Article CAS PubMed Google Scholar
• Song, J., Zhang, Z., Hu, W. & Chen, Y. Small ubiquitin-like modifier (SUMO) recognition of a SUMO binding motif: a reversal of the bound orientation. J. Biol. Chem. 280, 40122–40129 (2005).
  Article CAS PubMed Google Scholar
• Liew, C.W., Sun, H., Hunter, T. & Day, C.L. RING domain dimerization is essential for RNF4 function. Biochem. J. 431, 23–29 (2010).
  Article CAS PubMed Google Scholar
• Mace, P.D. et al. Structures of the cIAP2 RING domain reveal conformational changes associated with ubiquitin-conjugating enzyme (E2) recruitment. J. Biol. Chem. 283, 31633–31640 (2008).
  Article CAS PubMed Google Scholar
• Linke, K. et al. Structure of the MDM2/MDMX RING domain heterodimer reveals dimerization is required for their ubiquitylation in trans. Cell Death Differ. 15, 841–848 (2008).
  Article CAS PubMed Google Scholar
• Vander Kooi, C.W. et al. The Prp19 U-box crystal structure suggests a common dimeric architecture for a class of oligomeric E3 ubiquitin ligases. Biochemistry 45, 121–130 (2006).
  Article CAS PubMed Google Scholar
• Yin, Q. et al. E2 interaction and dimerization in the crystal structure of TRAF6. Nat. Struct. Mol. Biol. 16, 658–666 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Wu, P.Y. et al. A conserved catalytic residue in the ubiquitin-conjugating enzyme family. EMBO J. 22, 5241–5250 (2003).
  Article CAS PubMed PubMed Central Google Scholar
• Sakata, E. et al. Crystal structure of UbcH5b~ubiquitin intermediate: insight into the formation of the self-assembled E2~Ub conjugates. Structure 18, 138–147 (2010).
  Article CAS PubMed Google Scholar
• Dikic, I., Wakatsuki, S. & Walters, K.J. Ubiquitin-binding domains—from structures to functions. Nat. Rev. Mol. Cell Biol. 10, 659–671 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Lee, S. et al. Structural basis for ubiquitin recognition and autoubiquitination by Rabex-5. Nat. Struct. Mol. Biol. 13, 264–271 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Penengo, L. et al. Crystal structure of the ubiquitin binding domains of rabex-5 reveals two modes of interaction with ubiquitin. Cell 124, 1183–1195 (2006).
  Article CAS PubMed Google Scholar
• Rahighi, S. et al. Specific recognition of linear ubiquitin chains by NEMO is important for NF-κB activation. Cell 136, 1098–1109 (2009).
  Article CAS PubMed Google Scholar
• Mastrandrea, L.D., Kasperek, E.M., Niles, E.G. & Pickart, C.M. Core domain mutation (S86Y) selectively inactivates polyubiquitin chain synthesis catalyzed by E2–25K. Biochemistry 37, 9784–9792 (1998).
  Article CAS PubMed Google Scholar
• Brzovic, P.S., Lissounov, A., Christensen, D.E., Hoyt, D.W. & Klevit, R.E.A. UbcH5/ubiquitin noncovalent complex is required for processive BRCA1-directed ubiquitination. Mol. Cell 21, 873–880 (2006).
  Article CAS PubMed Google Scholar
• Christensen, D.E., Brzovic, P.S. & Klevit, R.E. E2-BRCA1 RING interactions dictate synthesis of mono- or specific polyubiquitin chain linkages. Nat. Struct. Mol. Biol. 14, 941–948 (2007).
  Article CAS PubMed Google Scholar
• Kleiger, G., Saha, A., Lewis, S., Kuhlman, B. & Deshaies, R.J. Rapid E2–E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell 139, 957–968 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Pierce, N.W., Kleiger, G., Shan, S.O. & Deshaies, R.J. Detection of sequential polyubiquitylation on a millisecond timescale. Nature 462, 615–619 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Brzovic, P.S., Rajagopal, P., Hoyt, D.W., King, M.C. & Klevit, R.E. Structure of a BRCA1-BARD1 heterodimeric RING-RING complex. Nat. Struct. Biol. 8, 833–837 (2001).
  Article CAS PubMed Google Scholar
• Buchwald, G. et al. Structure and E3-ligase activity of the Ring-Ring complex of Polycomb proteins Bmi1 and Ring1b. EMBO J. 25, 2465–2474 (2006).
  Article CAS PubMed PubMed Central Google Scholar
• Xu, Z. et al. Interactions between the quality control ubiquitin ligase CHIP and ubiquitin conjugating enzymes. BMC Struct. Biol. 8, 26 (2008).
  Article PubMed PubMed Central Google Scholar
• Zhang, M. et al. Chaperoned ubiquitylation—crystal structures of the CHIP U box E3 ubiquitin ligase and a CHIP-Ubc13-Uev1a complex. Mol. Cell 20, 525–538 (2005).
  Article CAS PubMed Google Scholar
• Kamadurai, H.B. et al. Insights into ubiquitin transfer cascades from a structure of a UbcH5B~ubiquitin-HECT(NEDD4L) complex. Mol. Cell 36, 1095–1102 (2009).
  Article CAS PubMed PubMed Central Google Scholar
• Levin, I. et al. Identification of an unconventional E3 binding surface on the UbcH5~Ub conjugate recognized by a pathogenic bacterial E3 ligase. Proc. Natl. Acad. Sci. USA 107, 2848–2853 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Pruneda, J.N., Stoll, K.E., Bolton, L.J., Brzovic, P.S. & Klevit, R.E. Ubiquitin in motion: structural studies of the ubiquitin-conjugating enzyme~ubiquitin conjugate. Biochemistry 50, 1624–1633 (2011).
  Article CAS PubMed Google Scholar
• Wickliffe, K.E., Lorenz, S., Wemmer, D.E., Kuriyan, J. & Rape, M. The mechanism of linkage-specific ubiquitin chain elongation by a single-subunit E2. Cell 144, 769–781 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Saha, A., Lewis, S., Kleiger, G., Kuhlman, B. & Deshaies, R.J. Essential role for ubiquitin-ubiquitin-conjugating enzyme interaction in ubiquitin discharge from Cdc34 to substrate. Mol. Cell 42, 75–83 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Martin, S.F., Tatham, M.H., Hay, R.T. & Samuel, I.D. Quantitative analysis of multi-protein interactions using FRET: application to the SUMO pathway. Protein Sci. 17, 777–784 (2008).
  Article CAS PubMed PubMed Central Google Scholar
• Martin, S.F., Hattersley, N., Samuel, I.D., Hay, R.T. & Tatham, M.H. A fluorescence-resonance-energy-transfer-based protease activity assay and its use to monitor paralog-specific small ubiquitin-like modifier processing. Anal. Biochem. 363, 83–90 (2007).
  Article CAS PubMed Google Scholar
• Otwinowski, Z. & Minor, W. Processing of X-ray diffraction data collected in oscillation mode. Methods Enzymol. 276, 307–326 (1997).
  Article CAS PubMed Google Scholar
• Sheldrick, G.M. A short history of SHELX. Acta Crystallogr. A 64, 112–122 (2008).
  Article CAS PubMed Google Scholar
• Morris, R.J., Perrakis, A. & Lamzin, V.S. ARP/wARP and automatic interpretation of protein electron density maps. Methods Enzymol. 374, 229–244 (2003).
  Article CAS PubMed Google Scholar
• Murshudov, G.N., Vagin, A.A. & Dodson, E.J. Refinement of macromolecular structures by the maximum-likelihood method. Acta Crystallogr. D Biol. Crystallogr. 53, 240–255 (1997).
  Article CAS PubMed Google Scholar
• Winn, M.D. et al. Overview of the CCP4 suite and current developments. Acta Crystallogr. D Biol. Crystallogr. 67, 235–242 (2011).
  Article CAS PubMed PubMed Central Google Scholar
• Emsley, P., Lohkamp, B., Scott, W.G. & Cowtan, K. Features and development of Coot. Acta Crystallogr. D Biol. Crystallogr. 66, 486–501 (2010).
  Article CAS PubMed PubMed Central Google Scholar
• Winn, M.D., Isupov, M.N. & Murshudov, G.N. Use of TLS parameters to model anisotropic displacements in macromolecular refinement. Acta Crystallogr. D Biol. Crystallogr. 57, 122–133 (2001).
  Article CAS PubMed Google Scholar
• Davis, I.W. et al. MolProbity: all-atom contacts and structure validation for proteins and nucleic acids. Nucleic Acids Res. 35, W375–83 (2007).
  Article PubMed PubMed Central Google Scholar
• Krissinel, E. & Henrick, K. Inference of macromolecular assemblies from crystalline state. J. Mol. Biol. 372, 774–797 (2007).
  Article CAS PubMed Google Scholar