The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Structural insights into the catalysis and regulation of E3 ubiquitin ligases
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
E3 ligases are part of the cellular ubiquitin system that controls selective degradation of proteins by the 26S proteasome and can modify proteins and regulate their cellular localization.
“E3 ligases are part of the cellular ubiquitin system that not only controls the selective degradation of proteins by the 26S proteasome, but can also modify proteins and regulate their cellular localization5.”
From RNF130 Regulates LDLR Availability and Plasma LDL Cholesterol Levels (2023) · cites this paper as [5]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Parkin is recruited selectively to impaired mitochondria and promotes their autophagy
Narendra, D., Tanaka, A., Suen, D.-F., & Youle, R. J. (2008) · The Journal of Cell Biology · doi:10.1083/jcb.200809125 · Cited by 4,026
RING Domain E3 Ubiquitin Ligases
Deshaies, R. J., & Joazeiro, C. A. P. (2009) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.78.101807.093809 · Cited by 2,679
Familial Parkinson disease gene product, parkin, is a ubiquitin-protein ligase
Shimura, H., Hattori, N., Kubo, S.-I., Mizuno, Y., Asakawa, S., Minoshima, S., Shimizu, N., Iwai, K., Chiba, T., Tanaka, K., et al. (2000) · Nature Genetics · doi:10.1038/77060 · Cited by 2,024
A multiubiquitin chain is confined to specific lysine in a targeted short-lived protein
Chau, V., Tobias, J. W., Bachmair, A., Marriott, D., Ecker, D. J., Gonda, D. K., & Varshavsky, A. (1989) · Science · doi:10.1126/science.2538923 · Cited by 1,535
Structure of the Cul1–Rbx1–Skp1–F boxSkp2 SCF ubiquitin ligase complex
Zheng, N., Schulman, B. A., Song, L., Miller, J. J., Jeffrey, P. D., Wang, P., Chu, C., Koepp, D. M., Elledge, S. J., Pagano, M., et al. (2002) · Nature · doi:10.1038/416703a · Cited by 1,507
The mitochondrial deubiquitinase USP30 opposes parkin-mediated mitophagy
Bingol, B., Tea, J. S., Phu, L., Reichelt, M., Bakalarski, C. E., Song, Q., Foreman, O., Kirkpatrick, D. S., & Sheng, M. (2014) · Nature · doi:10.1038/nature13418 · Cited by 855
Parkin is activated by PINK1-dependent phosphorylation of ubiquitin at Ser65
Kazlauskaite, A., Kondapalli, C., Gourlay, R., Campbell, D. G., Ritorto, M. S., Hofmann, K., Alessi, D. R., Knebel, A., Trost, M., & Muqit, M. M. K. (2014) · Biochemical Journal · doi:10.1042/bj20140334 · Cited by 806
Shiba-Fukushima, K., Imai, Y., Yoshida, S., Ishihama, Y., Kanao, T., Sato, S., & Hattori, N. (2012) · Scientific Reports · doi:10.1038/srep01002 · Cited by 577
Chemically ubiquitylated histone H2B stimulates hDot1L-mediated intranucleosomal methylation
McGinty, R. K., Kim, J., Chatterjee, C., Roeder, R. G., & Muir, T. W. (2008) · Nature · doi:10.1038/nature06906 · Cited by 563
Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis
Plechanovová, A., Jaffray, E. G., Tatham, M. H., Naismith, J. H., & Hay, R. T. (2012) · Nature · doi:10.1038/nature11376 · Cited by 521
HdmX stimulates Hdm2-mediated ubiquitination and degradation of p53
Linares, L. K., Hengstermann, A., Ciechanover, A., Müller, S., & Scheffner, M. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2030930100 · Cited by 361
Structure of an E3:E2∼Ub Complex Reveals an Allosteric Mechanism Shared among RING/U-box Ligases
Pruneda, J. N., Littlefield, P. J., Soss, S. E., Nordquist, K. A., Chazin, W. J., Brzovic, P. S., & Klevit, R. E. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.07.001 · Cited by 333
Mechanism of ubiquitin ligation and lysine prioritization by a HECT E3
Kamadurai, H. B., Qiu, Y., Deng, A., Harrison, J. S., MacDonald, C., Actis, M., Rodrigues, P., Miller, D. J., Souphron, J., Lewis, S. M., et al. (2013) · eLife · doi:10.7554/elife.00828 · Cited by 165
El-Mahdy, M. A., Zhu, Q., Wang, Q.-E., Wani, G., Prætorius-Ibba, M., & Wani, A. A. (2006) · Journal of Biological Chemistry · doi:10.1074/jbc.m511834200 · Cited by 151
Structural Basis for the Versatile Interactions of Smad7 with Regulator WW Domains in TGF-β Pathways
Aragón, E., Goerner, N., Xi, Q., Gomes, T., Gao, S., Massagué, J., & Macias, M. J. (2012) · Structure · doi:10.1016/j.str.2012.07.014 · Cited by 99
Flagged first, then by citations
Research works printed but not linked: 145
- Hershko, A. & Ciechanover, A. The ubiquitin system. Annu. Rev. Biochem. 67, 425–479 (1998). · DOI · Paper page
- Dye, B. T. & Schulman, B. A. Structural mechanisms underlying posttranslational modification by ubiquitin-like proteins. Annu. Rev. Biophys. Biomol. Struct. 36, 131–150 (2007). · DOI
- Pickart, C. M. & Eddins, M. J. Ubiquitin: structures, functions, mechanisms. Biochim. Biophys. Acta 1695, 55–72 (2004). · DOI
- Komander, D. & Rape, M. The ubiquitin code. Annu. Rev. Biochem. 81, 203–229 (2012). · DOI · Paper page
- Finley, D. Recognition and processing of ubiquitin–protein conjugates by the proteasome. Annu. Rev. Biochem. 78, 477–513 (2009). · DOI · Paper page
- Haglund, K. & Dikic, I. The role of ubiquitylation in receptor endocytosis and endosomal sorting. J. Cell Sci. 125, 265–275 (2012). · DOI
- Chen, Z. J. & Sun, L. J. Nonproteolytic functions of ubiquitin in cell signaling. Mol. Cell 33, 275–286 (2009). · DOI
- Ulrich, H. D. & Walden, H. Ubiquitin signalling in DNA replication and repair. Nat. Rev. Mol. Cell Biol. 11, 479–489 (2010). · DOI
- Hoege, C., Pfander, B., Moldovan, G. L., Pyrowolakis, G. & Jentsch, S. RAD6-dependent DNA repair is linked to modification of PCNA by ubiquitin and SUMO. Nature 419, 135–141 (2002). · DOI
- Robzyk, K., Recht, J. & Osley, M. A. Rad6-dependent ubiquitination of histone H2B in yeast. Science 287, 501–504 (2000). · DOI
- Jin, J., Li, X., Gygi, S. P. & Harper, J. W. Dual E1 activation systems for ubiquitin differentially regulate E2 enzyme charging. Nature 447, 1135–1138 (2007). · DOI
- Ye, Y. & Rape, M. Building ubiquitin chains: E2 enzymes at work. Nat. Rev. Mol. Cell Biol. 10, 755–764 (2009). · DOI · Paper page
- Li, W. et al. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling. PLoS ONE 3, e1487 (2008). · DOI
- Levkowitz, G. et al. Ubiquitin ligase activity and tyrosine phosphorylation underlie suppression of growth factor signaling by c-Cbl/Sli-1. Mol. Cell 4, 1029–1040 (1999). · DOI
- Waterman, H. et al. A mutant EGF-receptor defective in ubiquitylation and endocytosis unveils a role for Grb2 in negative signaling. EMBO J. 21, 303–313 (2002). · DOI
- Mizushima, T. et al. Structural basis for the selection of glycosylated substrates by SCFFbs1 ubiquitin ligase. Proc. Natl Acad. Sci. USA 104, 5777–5781 (2007). · DOI
- Scrima, A. et al. Structural basis of UV DNA-damage recognition by the DDB1–DDB2 complex. Cell 135, 1213–1223 (2008). · DOI · Paper page
- Sugasawa, K. et al. UV-induced ubiquitylation of XPC protein mediated by UV-DDB–ubiquitin ligase complex. Cell 121, 387–400 (2005). · DOI · Paper page
- Zheng, N., Wang, P., Jeffrey, P. D. & Pavletich, N. P. Structure of a c-Cbl–UbcH7 complex: RING domain function in ubiquitin–protein ligases. Cell 102, 533–539 (2000). · DOI · Paper page
- Dominguez, C. et al. Structural model of the UbcH5B/CNOT4 complex revealed by combining NMR, mutagenesis, and docking approaches. Structure 12, 633–644 (2004). · DOI
- Buetow, L. et al. Activation of a primed RING E3-E2–ubiquitin complex by non-covalent ubiquitin. Mol. Cell 58, 297–310 (2015). · DOI
- 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). · DOI
- Yin, Q. et al. E2 interaction and dimerization in the crystal structure of TRAF6. Nat. Struct. Mol. Biol. 16, 658–666 (2009). · DOI
- Plechanovova, A. et al. Mechanism of ubiquitylation by dimeric RING ligase RNF4. Nat. Struct. Mol. Biol. 18, 1052–1059 (2011). · DOI
- 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). · DOI
- 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). · DOI
- Badciong, J. C. & Haas, A. L. MdmX is a RING finger ubiquitin ligase capable of synergistically enhancing Mdm2 ubiquitination. J. Biol. Chem. 277, 49668–49675 (2002). · DOI
- Li, Z. et al. Structure of a Bmi-1-Ring1B polycomb group ubiquitin ligase complex. J. Biol. Chem. 281, 20643–20649 (2006). · DOI
- Micale, L., Chaignat, E., Fusco, C., Reymond, A. & Merla, G. The tripartite motif: structure and function. Adv. Exp. Med. Biol. 770, 11–25 (2012). · DOI
- Lydeard, J. R., Schulman, B. A. & Harper, J. W. Building and remodelling Cullin–RING E3 ubiquitin ligases. EMBO Rep. 14, 1050–1061 (2013). · DOI · Paper page
- Petroski, M. D. & Deshaies, R. J. Function and regulation of cullin–RING ubiquitin ligases. Nat. Rev. Mol. Cell Biol. 6, 9–20 (2005). · DOI · Paper page
- Chang, L. & Barford, D. Insights into the anaphase-promoting complex: a molecular machine that regulates mitosis. Curr. Opin. Struct. Biol. 29, 1–9 (2014). · DOI
- Ohi, M. D., Vander Kooi, C. W., Rosenberg, J. A., Chazin, W. J. & Gould, K. L. Structural insights into the U-box, a domain associated with multi-ubiquitination. Nat. Struct. Biol. 10, 250–255 (2003). · DOI
- Tu, D., Li, W., Ye, Y. & Brunger, A. T. Structure and function of the yeast U-box-containing ubiquitin ligase Ufd2p. Proc. Natl Acad. Sci. USA 104, 15599–15606 (2007). · DOI
- 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). · DOI
- 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). · DOI
- Rotin, D. & Kumar, S. Physiological functions of the HECT family of ubiquitin ligases. Nat. Rev. Mol. Cell Biol. 10, 398–409 (2009). · DOI
- Huang, L. et al. Structure of an E6AP-UbcH7 complex: insights into ubiquitination by the E2-E3 enzyme cascade. Science 286, 1321–1326 (1999). · DOI
- Verdecia, M. A. et al. Conformational flexibility underlies ubiquitin ligation mediated by the WWP1 HECT domain E3 ligase. Mol. Cell 11, 249–259 (2003). · DOI
- Smit, J. J. & Sixma, T. K. RBR E3-ligases at work. EMBO Rep. 15, 142–154 (2014). · DOI
- Spratt, D. E., Walden, H. & Shaw, G. S. RBR E3 ubiquitin ligases: new structures, new insights, new questions. Biochem. J. 458, 421–437 (2014). · DOI
- Imai, Y., Soda, M. & Takahashi, R. Parkin suppresses unfolded protein stress-induced cell death through its E3 ubiquitin-protein ligase activity. J. Biol. Chem. 275, 35661–35664 (2000). · DOI
- Zhang, Y. et al. Parkin functions as an E2-dependent ubiquitin-protein ligase and promotes the degradation of the synaptic vesicle-associated protein, CDCrel-1. Proc. Natl Acad. Sci. USA 97, 13354–13359 (2000). · DOI · Paper page
- Moynihan, T. P. et al. The ubiquitin-conjugating enzymes UbcH7 and UbcH8 interact with RING finger/IBR motif-containing domains of HHARI and H7-AP1. J. Biol. Chem. 274, 30963–30968 (1999). · DOI
- Wenzel, D. M., Lissounov, A., Brzovic, P. S. & Klevit, R. E. UBCH7 reactivity profile reveals parkin and HHARI to be RING/HECT hybrids. Nature 474, 105–108 (2011). · DOI
- Ozkan, E., Yu, H. & Deisenhofer, J. Mechanistic insight into the allosteric activation of a ubiquitin-conjugating enzyme by RING-type ubiquitin ligases. Proc. Natl Acad. Sci. USA 102, 18890–18895 (2005). · DOI
- Petroski, M. D. & Deshaies, R. J. Mechanism of lysine 48-linked ubiquitin-chain synthesis by the cullin-RING ubiquitin-ligase complex SCF-Cdc34. Cell 123, 1107–1120 (2005). · DOI
- 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). · DOI
- Benirschke, R. C. et al. Molecular basis for the association of human E4B U box ubiquitin ligase with E2-conjugating enzymes UbcH5c and Ubc4. Structure 18, 955–965 (2010). · DOI
- Dou, H., Buetow, L., Sibbet, G. J., Cameron, K. & Huang, D. T. BIRC7–E2 ubiquitin conjugate structure reveals the mechanism of ubiquitin transfer by a RING dimer. Nat. Struct. Mol. Biol. 19, 876–883 (2012). References 55 and 56 provide the first crystal structures of dimeric RING E3 bound to E2∼ubiquitin in a primed conformation. · DOI · Paper page
- 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). · DOI
- Soss, S. E., Klevit, R. E. & Chazin, W. J. Activation of UbcH5c∼Ub is the result of a shift in interdomain motions of the conjugate bound to U-box E3 ligase E4B. Biochemistry 52, 2991–2999 (2013). · DOI
- Page, R. C., Pruneda, J. N., Amick, J., Klevit, R. E. & Misra, S. Structural insights into the conformation and oligomerization of E2∼ubiquitin conjugates. Biochemistry 51, 4175–4187 (2012). · DOI
- Dou, H., Buetow, L., Sibbet, G. J., Cameron, K. & Huang, D. T. Essentiality of a non-RING element in priming donor ubiquitin for catalysis by a monomeric E3. Nat. Struct. Mol. Biol. 20, 982–986 (2013). · DOI
- Branigan, E., Plechanovova, A., Jaffray, E. G., Naismith, J. H. & Hay, R. T. Structural basis for the RING-catalyzed synthesis of K63-linked ubiquitin chains. Nat. Struct. Mol. Biol. 22, 597–602 (2015). · DOI
- Reverter, D. & Lima, C. D. Insights into E3 ligase activity revealed by a SUMO–RanGAP1–Ubc9–Nup358 complex. Nature 435, 687–692 (2005). · DOI
- Scott, D. C. et al. Structure of a RING E3 trapped in action reveals ligation mechanism for the ubiquitin-like protein NEDD8. Cell 157, 1671–1684 (2014). Presents a crystal structure of a RING E3-E2∼ubiquitin like protein–substrate complex, revealing the mechanism of substrate ligation. · DOI · Paper page
- Koliopoulos, M. G., Esposito, D., Christodoulou, E., Taylor, I. A. & Rittinger, K. Functional role of TRIM E3 ligase oligomerization and regulation of catalytic activity. EMBO J. 35, 1204–1218 (2016). · DOI
- 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). · DOI
- Berndsen, C. E., Wiener, R., Yu, I. W., Ringel, A. E. & Wolberger, C. A conserved asparagine has a structural role in ubiquitin-conjugating enzymes. Nat. Chem. Biol. 9, 154–156 (2013). · DOI
- Yunus, A. A. & Lima, C. D. Lysine activation and functional analysis of E2-mediated conjugation in the SUMO pathway. Nat. Struct. Mol. Biol. 13, 491–499 (2006). · DOI
- Wright, J. D., Mace, P. D. & Day, C. L. Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity. Nat. Struct. Mol. Biol. 23, 45–52 (2016). · DOI
- Das, R. et al. Allosteric activation of E2-RING finger-mediated ubiquitylation by a structurally defined specific E2-binding region of gp78. Mol. Cell 34, 674–685 (2009). · DOI
- Metzger, M. B. et al. A structurally unique E2-binding domain activates ubiquitination by the ERAD E2, Ubc7p, through multiple mechanisms. Mol. Cell 50, 516–527 (2013). · DOI
- Hibbert, R. G., Huang, A., Boelens, R. & Sixma, T. K. E3 ligase Rad18 promotes monoubiquitination rather than ubiquitin chain formation by E2 enzyme Rad6. Proc. Natl Acad. Sci. USA 108, 5590–5595 (2011). · DOI
- Li, S. et al. Insights into ubiquitination from the unique clamp-like binding of the RING E3 AO7 to the E2 UbcH5B. J. Biol. Chem. 290, 30225–30239 (2015). · DOI
- Das, R. et al. Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine. EMBO J. 32, 2504–2516 (2013). · DOI
- 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). · DOI
- 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). · DOI
- Ranaweera, R. S. & Yang, X. Auto-ubiquitination of Mdm2 enhances its substrate ubiquitin ligase activity. J. Biol. Chem. 288, 18939–18946 (2013). · DOI
- Kamadurai, H. B. et al. Insights into ubiquitin transfer cascades from a structure of a UbcH5B∼ubiquitin-HECTNEDD4L complex. Mol. Cell 36, 1095–1102 (2009). The first crystal structure of a HECT E3 bound to E2∼ubiquitin. · DOI
- Nuber, U. & Scheffner, M. Identification of determinants in E2 ubiquitin-conjugating enzymes required for HECT E3 ubiquitin–protein ligase interaction. J. Biol. Chem. 274, 7576–7582 (1999). · DOI
- Ogunjimi, A. A. et al. Regulation of Smurf2 ubiquitin ligase activity by anchoring the E2 to the HECT domain. Mol. Cell 19, 297–308 (2005). · DOI
- Maspero, E. et al. Structure of a ubiquitin-loaded HECT ligase reveals the molecular basis for catalytic priming. Nat. Struct. Mol. Biol. 20, 696–701 (2013). The first crystal structure of a primed HECT E3∼ubiquitin complex. · DOI
- Salvat, C., Wang, G., Dastur, A., Lyon, N. & Huibregtse, J. M. The -4 phenylalanine is required for substrate ubiquitination catalyzed by HECT ubiquitin ligases. J. Biol. Chem. 279, 18935–18943 (2004). · DOI
- Ronchi, V. P., Klein, J. M. & Haas, A. L. E6AP/UBE3A ubiquitin ligase harbors two E2∼ubiquitin binding sites. J. Biol. Chem. 288, 10349–10360 (2013). · DOI
- French, M. E., Kretzmann, B. R. & Hicke, L. Regulation of the RSP5 ubiquitin ligase by an intrinsic ubiquitin-binding site. J. Biol. Chem. 284, 12071–12079 (2009). · DOI
- Maspero, E. et al. Structure of the HECT:ubiquitin complex and its role in ubiquitin chain elongation. EMBO Rep. 12, 342–349 (2011). · DOI
- Kim, H. C., Steffen, A. M., Oldham, M. L., Chen, J. & Huibregtse, J. M. Structure and function of a HECT domain ubiquitin-binding site. EMBO Rep. 12, 334–341 (2011). · DOI
- Stieglitz, B. et al. Structural basis for ligase-specific conjugation of linear ubiquitin chains by HOIP. Nature 503, 422–426 (2013). The first crystal structure of a RBR RING2 bound to donor and acceptor ubiquitin. · DOI
- Spratt, D. E. et al. A molecular explanation for the recessive nature of parkin-linked Parkinson's disease. Nat. Commun. 4, 1983 (2013). · DOI
- Beasley, S. A., Hristova, V. A. & Shaw, G. S. Structure of the Parkin in-between-ring domain provides insights for E3-ligase dysfunction in autosomal recessive Parkinson's disease. Proc. Natl Acad. Sci. USA 104, 3095–3100 (2007). · DOI
- Spratt, D. E., Mercier, P. & Shaw, G. S. Structure of the HHARI catalytic domain shows glimpses of a HECT E3 ligase. PLoS ONE 8, e74047 (2013). · DOI
- Lechtenberg, B. C. et al. Structure of a HOIP/E2∼ubiquitin complex reveals RBR E3 ligase mechanism and regulation. Nature 529, 546–550 (2016). The first crystal structure of a RBR domain bound to E2∼ubiquitin. · DOI
- Duda, D. M. et al. Structure of HHARI, a RING-IBR-RING ubiquitin ligase: autoinhibition of an Ariadne-family E3 and insights into ligation mechanism. Structure 21, 1030–1041 (2013). · DOI · Paper page
- Riley, B. E. et al. Structure and function of Parkin E3 ubiquitin ligase reveals aspects of RING and HECT ligases. Nat. Commun. 4, 1982 (2013). · DOI
- Wauer, T. & Komander, D. Structure of the human Parkin ligase domain in an autoinhibited state. EMBO J. 32, 2099–2112 (2013). · DOI · Paper page
- Trempe, J. F. et al. Structure of parkin reveals mechanisms for ubiquitin ligase activation. Science 340, 1451–1455 (2013). The first crystal structure of full-length PARKIN in an autoinhibited conformation. · DOI · Paper page
- Kumar, A. et al. Disruption of the autoinhibited state primes the E3 ligase parkin for activation and catalysis. EMBO J. 34, 2506–2521 (2015). · DOI
- Stieglitz, B., Morris-Davies, A. C., Koliopoulos, M. G., Christodoulou, E. & Rittinger, K. LUBAC synthesizes linear ubiquitin chains via a thioester intermediate. EMBO Rep. 13, 840–846 (2012). · DOI
- Smit, J. J. et al. The E3 ligase HOIP specifies linear ubiquitin chain assembly through its RING-IBR-RING domain and the unique LDD extension. EMBO J. 31, 3833–3844 (2012). · DOI
- 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). · DOI · Paper page
- Rodrigo-Brenni, M. C. & Morgan, D. O. Sequential E2s drive polyubiquitin chain assembly on APC targets. Cell 130, 127–139 (2007). · DOI
- Jin, L., Williamson, A., Banerjee, S., Philipp, I. & Rape, M. Mechanism of ubiquitin-chain formation by the human anaphase-promoting complex. Cell 133, 653–665 (2008). · DOI
- McGinty, R. K., Henrici, R. C. & Tan, S. Crystal structure of the PRC1 ubiquitylation module bound to the nucleosome. Nature 514, 591–596 (2014). Reports a crystal structure showing how RNF2-BMI1 monoubiquitylates histone. · DOI
- Chang, L., Zhang, Z., Yang, J., McLaughlin, S. H. & Barford, D. Atomic structure of the APC/C and its mechanism of protein ubiquitination. Nature 522, 450–454 (2015). The first atomic structure of APC/C, revealing the mechanism of ubiquitylation. · DOI
- Brown, N. G. et al. RING E3 mechanism for ubiquitin ligation to a disordered substrate visualized for human anaphase-promoting complex. Proc. Natl Acad. Sci. USA 112, 5272–5279 (2015). · DOI
- McNatt, M. W., McKittrick, I., West, M. & Odorizzi, G. Direct binding to Rsp5 mediates ubiquitin-independent sorting of Sna3 via the multivesicular body pathway. Mol. Biol. Cell 18, 697–706 (2007). · DOI
- Oestreich, A. J. et al. Characterization of multiple multivesicular body sorting determinants within Sna3: a role for the ubiquitin ligase Rsp5. Mol. Biol. Cell 18, 707–720 (2007). · DOI
- Stawiecka-Mirota, M. et al. Targeting of Sna3p to the endosomal pathway depends on its interaction with Rsp5p and multivesicular body sorting on its ubiquitylation. Traffic 8, 1280–1296 (2007). · DOI
- Watson, H. & Bonifacino, J. S. Direct binding to Rsp5p regulates ubiquitination-independent vacuolar transport of Sna3p. Mol. Biol. Cell 18, 1781–1789 (2007). · DOI
- Wang, H. et al. Role of histone H2A ubiquitination in Polycomb silencing. Nature 431, 873–878 (2004). · DOI
- Dou, H. et al. Structural basis for autoinhibition and phosphorylation-dependent activation of c-Cbl. Nat. Struct. Mol. Biol. 19, 184–192 (2012). · DOI
- Kobashigawa, Y. et al. Autoinhibition and phosphorylation-induced activation mechanisms of human cancer and autoimmune disease-related E3 protein Cbl-b. Proc. Natl Acad. Sci. USA 108, 20579–20584 (2011). · DOI
- Duda, D. M. et al. Structural insights into NEDD8 activation of cullin-RING ligases: conformational control of conjugation. Cell 134, 995–1006 (2008). · DOI · Paper page
- Calabrese, M. F. et al. A RING E3-substrate complex poised for ubiquitin-like protein transfer: structural insights into cullin-RING ligases. Nat. Struct. Mol. Biol. 18, 947–949 (2011). · DOI
- Chang, L., Zhang, Z., Yang, J., McLaughlin, S. H. & Barford, D. Molecular architecture and mechanism of the anaphase-promoting complex. Nature 513, 388–393 (2014). · DOI
- Merbl, Y. & Kirschner, M. W. Large-scale detection of ubiquitination substrates using cell extracts and protein microarrays. Proc. Natl Acad. Sci. USA 106, 2543–2548 (2009). · DOI
- Ordureau, A. et al. Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol. Cell 56, 360–375 (2014). · DOI
- Eddins, M. J., Carlile, C. M., Gomez, K. M., Pickart, C. M. & Wolberger, C. Mms2–Ubc13 covalently bound to ubiquitin reveals the structural basis of linkage-specific polyubiquitin chain formation. Nat. Struct. Mol. Biol. 13, 915–920 (2006). · DOI
- Brown, N. G. et al. Mechanism of polyubiquitination by human anaphase-promoting complex: RING repurposing for ubiquitin chain assembly. Mol. Cell 56, 246–260 (2014). · DOI
- Kelly, A., Wickliffe, K. E., Song, L., Fedrigo, I. & Rape, M. Ubiquitin chain elongation requires E3-dependent tracking of the emerging conjugate. Mol. Cell 56, 232–245 (2014). · DOI
- Peters, J. M. The anaphase promoting complex/cyclosome: a machine designed to destroy. Nat. Rev. Mol. Cell Biol. 7, 644–656 (2006). · DOI · Paper page
- Frye, J. J. et al. Electron microscopy structure of human APC/CCDH1–EMI1 reveals multimodal mechanism of E3 ligase shutdown. Nat. Struct. Mol. Biol. 20, 827–835 (2013). · DOI
- Wang, W. & Kirschner, M. W. Emi1 preferentially inhibits ubiquitin chain elongation by the anaphase-promoting complex. Nat. Cell Biol. 15, 797–806 (2013). · DOI
- Fulda, S. & Vucic, D. Targeting IAP proteins for therapeutic intervention in cancer. Nat. Rev. Drug Discov. 11, 109–124 (2012). · DOI · Paper page
- Dueber, E. C. et al. Antagonists induce a conformational change in cIAP1 that promotes autoubiquitination. Science 334, 376–380 (2011). · DOI
- Lopez, J. et al. CARD-mediated autoinhibition of cIAP1's E3 ligase activity suppresses cell proliferation and migration. Mol. Cell 42, 569–583 (2011). · DOI
- Phillips, A. H. et al. Internal motions prime cIAP1 for rapid activation. Nat. Struct. Mol. Biol. 21, 1068–1074 (2014). · DOI
- Feltham, R. et al. Smac mimetics activate the E3 ligase activity of cIAP1 protein by promoting RING domain dimerization. J. Biol. Chem. 286, 17015–17028 (2011). · DOI
- Mund, T. & Pelham, H. R. Control of the activity of WW-HECT domain E3 ubiquitin ligases by NDFIP proteins. EMBO Rep. 10, 501–507 (2009). · DOI
- Riling, C. et al. Itch WW domains inhibit its E3 ubiquitin ligase activity by blocking E2-E3 ligase trans-thiolation. J. Biol. Chem. 290, 23875–23887 (2015). · DOI
- Gallagher, E., Gao, M., Liu, Y. C. & Karin, M. Activation of the E3 ubiquitin ligase Itch through a phosphorylation-induced conformational change. Proc. Natl Acad. Sci. USA 103, 1717–1722 (2006). · DOI · Paper page
- Wan, L. et al. Cdh1 regulates osteoblast function through an APC/C-independent modulation of Smurf1. Mol. Cell 44, 721–733 (2011). · DOI
- Wang, J. et al. Calcium activates Nedd4 E3 ubiquitin ligases by releasing the C2 domain-mediated auto-inhibition. J. Biol. Chem. 285, 12279–12288 (2010). · DOI
- Wiesner, S. et al. Autoinhibition of the HECT-type ubiquitin ligase Smurf2 through its C2 domain. Cell 130, 651–662 (2007). · DOI
- Mari, S. et al. Structural and functional framework for the autoinhibition of Nedd4-family ubiquitin ligases. Structure 22, 1639–1649 (2014). · DOI
- Chaugule, V. K. et al. Autoregulation of Parkin activity through its ubiquitin-like domain. EMBO J. 30, 2853–2867 (2011). · DOI · Paper page
- Kondapalli, C. et al. PINK1 is activated by mitochondrial membrane potential depolarization and stimulates Parkin E3 ligase activity by phosphorylating Serine 65. Open Biol. 2, 120080 (2012). · DOI · Paper page
- Shiba-Fukushima, K., Inoshita, T., Hattori, N. & Imai, Y. PINK1-mediated phosphorylation of Parkin boosts Parkin activity in Drosophila. PLoS Genet. 10, e1004391 (2014). · DOI
- Koyano, F. et al. Ubiquitin is phosphorylated by PINK1 to activate parkin. Nature 510, 162–166 (2014). · DOI · Paper page
- Kane, L. A. et al. PINK1 phosphorylates ubiquitin to activate Parkin E3 ubiquitin ligase activity. J. Cell Biol. 205, 143–153 (2014). · DOI · Paper page
- Ordureau, A. et al. Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy. Proc. Natl Acad. Sci. USA 112, 6637–6642 (2015). · DOI · Paper page
- Kazlauskaite, A. et al. Binding to serine 65-phosphorylated ubiquitin primes Parkin for optimal PINK1-dependent phosphorylation and activation. EMBO Rep. 16, 939–954 (2015). · DOI
- Sarraf, S. A. et al. Landscape of the PARKIN-dependent ubiquitylome in response to mitochondrial depolarization. Nature 496, 372–376 (2013). · DOI · Paper page
- Sauve, V. et al. A Ubl/ubiquitin switch in the activation of Parkin. EMBO J. 34, 2492–2505 (2015). · DOI
- Wauer, T., Simicek, M., Schubert, A. & Komander, D. Mechanism of phospho-ubiquitin-induced PARKIN activation. Nature 524, 370–374 (2015). Reports a crystal structure showing how phospho-ubiquitin activates PARKIN. · DOI
- Kulathu, Y. & Komander, D. Atypical ubiquitylation — the unexplored world of polyubiquitin beyond Lys48 and Lys63 linkages. Nat. Rev. Mol. Cell Biol. 13, 508–523 (2012). · DOI · Paper page
- Rosner, D., Schneider, T., Schneider, D., Scheffner, M. & Marx, A. Click chemistry for targeted protein ubiquitylation and ubiquitin chain formation. Nat. Protoc. 10, 1594–1611 (2015). · DOI
- Eger, S. et al. Generation of a mono-ubiquitinated PCNA mimic by click chemistry. Chembiochem 12, 2807–2812 (2011). · DOI
- Chen, J., Ai, Y., Wang, J., Haracska, L. & Zhuang, Z. Chemically ubiquitylated PCNA as a probe for eukaryotic translesion DNA synthesis. Nat. Chem. Biol. 6, 270–272 (2010). · DOI
- Sommer, S., Weikart, N. D., Brockmeyer, A., Janning, P. & Mootz, H. D. Expanded click conjugation of recombinant proteins with ubiquitin-like modifiers reveals altered substrate preference of SUMO2-modified Ubc9. Angew. Chem. Int. Ed. Engl. 50, 9888–9892 (2011). · DOI
- Oualid, F. E., Hameed, D. S., Atmioui, D. E., Hilkmann, H. & Ovaa, H. Synthesis of atypical diubiquitin chains. Methods Mol. Biol. 832, 597–609 (2012). · DOI
- Popovic, D., Vucic, D. & Dikic, I. Ubiquitination in disease pathogenesis and treatment. Nat. Med. 20, 1242–1253 (2014). · DOI
- Husnjak, K. & Dikic, I. Ubiquitin-binding proteins: decoders of ubiquitin-mediated cellular functions. Annu. Rev. Biochem. 81, 291–322 (2012). · DOI
Cited by
Sorted by citations
Targeting transcription factors in cancer — from undruggable to reality
Bushweller, J. H. (2019) · Nature Reviews Cancer · doi:10.1038/s41568-019-0196-7 · Cited by 919
Mechanisms and functions of ribosome-associated protein quality control
Joazeiro, C. A. P. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-019-0118-2 · Cited by 456
Zhong, Q., Xiao, X., Qiu, Y., Xu, Z., Chen, C., Chong, B., Zhao, X., Hai, S., Li, S., An, Z., et al. (2023) · MedComm · doi:10.1002/mco2.261 · Cited by 442
Human skeletal muscle possesses an epigenetic memory of hypertrophy
Seaborne, R. A., Strauss, J., Cocks, M., Shepherd, S., O’Brien, T. D., van Someren, K. A., Bell, P. G., Murgatroyd, C., Morton, J. P., Stewart, C. E., et al. (2018) · Scientific Reports · doi:10.1038/s41598-018-20287-3 · Cited by 334
Structural bases of IMiD selectivity that emerges by 5-hydroxythalidomide
Furihata, H., Yamanaka, S., Honda, T., Miyauchi, Y., Asano, A., Shibata, N., Tanokura, M., Sawasaki, T., & Miyakawa, T. (2020) · Nature Communications · doi:10.1038/s41467-020-18488-4 · Cited by 89
O’Connor, H. F., & Huibregtse, J. M. (2017) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-017-2529-6 · Cited by 42
Structural Basis for Recruitment of DAPK1 to the KLHL20 E3 Ligase
Chen, Z., Picaud, S., Filippakopoulos, P., D'Angiolella, V., & Bullock, A. N. (2019) · Structure · doi:10.1016/j.str.2019.06.005 · Cited by 37
RNF130 Regulates LDLR Availability and Plasma LDL Cholesterol Levels
Clifford, B. L., Jarrett, K. E., Cheng, J., Cheng, A., Seldin, M., Morand, P., Lee, R., Chen, M., Baldan, A., de Aguiar Vallim, T. Q., et al. (2023) · Circulation Research · doi:10.1161/circresaha.122.321938 · Cited by 20
Metadata
- Authors
- Buetow, L., & Huang, D. T.
- Venue
- Nature Reviews Molecular Cell Biology
- Published
- 2016-08-03
- Volume
- 17
- Issue
- 10
- Pages
- 626-642
- ISSN
- 1471-0072
- 1471-0080
- PMC
- PMC6211636
- Cited by
- 679
- References
- 15
- Language
- en
- Licence
- www.springer.com/tdm (tdm)
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review