Cited by 523Ubiquitin and proteasome pathwaysEnzyme Structure and FunctionProtein Degradation and Inhibitors

The DOI matches its Crossref record; 41 of the 41 references it cites were found in a registry or an index.

Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis

Open access

Plechanovová, Anna, Jaffray, Ellis G., Tatham, Michael H., Naismith, James H., Hay, Ronald T.·2012·Nature

Open this paper in CoChat — free account

Abstract

Ubiquitin modification is mediated by a large family of specificity determining ubiquitin E3 ligases. To facilitate ubiquitin transfer, RING E3 ligases bind both substrate and a ubiquitin E2 conjugating enzyme linked to ubiquitin via a thioester bond, but the mechanism of transfer has remained elusive. Here we report the crystal structure of the dimeric RING domain of rat RNF4 in complex with E2 (UbcH5A) linked by an isopeptide bond to ubiquitin. While the E2 contacts a single protomer of the RING, ubiquitin is folded back onto the E2 by contacts from both RING protomers. The carboxy-terminal tail of ubiquitin is locked into an active site groove on the E2 by an intricate network of interactions, resulting in changes at the E2 active site. This arrangement is primed for catalysis as it can deprotonate the incoming substrate lysine residue and stabilize the consequent tetrahedral transition-state intermediate.

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

Crossref · 10.1038/nature11376

Cites

41 of 41 references verified0 citation errors · 0 not checkable

Statistics

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?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Features and development of Coot
Emsley, P., Lohkamp, B., Scott, W. G., & Cowtan, K. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910007493 · Cited by 29,915
Phaser crystallographic software
McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C., & Read, R. J. (2007) · Journal of Applied Crystallography · doi:10.1107/s0021889807021206 · Cited by 20,612
Refinement of Macromolecular Structures by the Maximum-Likelihood Method
Murshudov, G. N., Vagin, A. A., & Dodson, E. J. (1997) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444996012255 · Cited by 14,796
MolProbity : all-atom structure validation for macromolecular crystallography
Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S., & Richardson, D. C. (2010) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444909042073 · Cited by 14,115
Overview of the CCP 4 suite and current developments
Winn, M. D., Ballard, C. C., Cowtan, K. D., Dodson, E. J., Emsley, P., Evans, P. R., Keegan, R. M., Krissinel, E. B., Leslie, A. G. W., McCoy, A., et al. (2011) · Acta Crystallographica Section D Biological Crystallography · doi:10.1107/s0907444910045749 · Cited by 12,353
Inference of Macromolecular Assemblies from Crystalline State
Krissinel, E., & Henrick, K. (2007) · Journal of Molecular Biology · doi:10.1016/j.jmb.2007.05.022 · Cited by 10,007
Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment
Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,520
In-gel digestion for mass spectrometric characterization of proteins and proteomes
Shevchenko, A., Tomas, H., Havli, J., Olsen, J. V., & Mann, M. (2006) · Nature Protocols · doi:10.1038/nprot.2006.468 · Cited by 4,947
Structure of ubiquitin refined at 1.8 A resolution.
Vijay-Kumar, S., Bugg, C., & Cook, W. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90679-6 · Cited by 1,636
RNF4 is a poly-SUMO-specific E3 ubiquitin ligase required for arsenic-induced PML degradation
Tatham, M. H., Geoffroy, M., Shen, L., Plechanovová, A., Hattersley, N., Jaffray, E., Palvimo, J. J., & Hay, R. T. (2008) · Nature Cell Biology · doi:10.1038/ncb1716 · Cited by 837
Self-citation

Flagged first, then by citations

Show all 41 references

Sorted by citations

Items 101–200 of 523

Mechanism of B-box 2 domain-mediated higher-order assembly of the retroviral restriction factor TRIM5α
Wagner, J. M., Roganowicz, M., Skorupka, K. A., Alam, S. L., Christensen, D. E., Doss, G., Wan, Y., Frank, G. A., Ganser‐Pornillos, B. K., Sundquist, W. I., et al. (2016) · eLife · doi:10.7554/elife.16309 · Cited by 100
SUMO-SIM interactions: From structure to biological functions
Lascorz, J., Codina-Fabra, J., Reverter, D., & Torres‐Rosell, J. (2021) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2021.11.007 · Cited by 100
Ubc13: the Lys63 ubiquitin chain building machine
Hodge, C. D., Spyracopoulos, L., & Glover, J. N. M. (2016) · Oncotarget · doi:10.18632/oncotarget.10948 · Cited by 99
Live and let die: insights into pseudoenzyme mechanisms from structure
Murphy, J. M., Mace, P. D., & Eyers, P. A. (2017) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2017.07.004 · Cited by 94
Structural complexity in the KCTD family of Cullin3-dependent E3 ubiquitin ligases
Pinkas, D. M., Sanvitale, C., Bufton, J. C., Sorrell, F. J., Solcan, N., Chalk, R., Doutch, J., & Bullock, A. N. (2017) · Biochemical Journal · doi:10.1042/bcj20170527 · Cited by 93
A Bifunctional Role for the UHRF1 UBL Domain in the Control of Hemi-methylated DNA-Dependent Histone Ubiquitylation
DaRosa, P. A., Harrison, J. S., Zelter, A., Davis, T. N., Brzović, P. S., Kuhlman, B. A., & Klevit, R. E. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.09.029 · Cited by 92
Interconversion between Anticipatory and Active GID E3 Ubiquitin Ligase Conformations via Metabolically Driven Substrate Receptor Assembly
Qiao, S., Langlois, C., Chrustowicz, J., Sherpa, D., Karayel, Ö., Hansen, F. M., Beier, V., von Gronau, S., Bollschweiler, D., Schäfer, T., et al. (2019) · Molecular Cell · doi:10.1016/j.molcel.2019.10.009 · Cited by 93
E2 enzyme inhibition by stabilization of a low-affinity interface with ubiquitin
Huang, H., Ceccarelli, D. F. J., Orlicky, S. M., St‐Cyr, D. J., Ziemba, A. J., Garg, P., Plamondon, S., Auer, M., Sidhu, S. S., Marinier, A., et al. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1412 · Cited by 94
Changes in PUB22 Ubiquitination Modes Triggered by MITOGEN-ACTIVATED PROTEIN KINASE3 Dampen the Immune Response
Furlan, G., Nakagami, H., Eschen‐Lippold, L., Jiang, X., Majovsky, P., Kowarschik, K., Hoehenwarter, W., Lee, J., & Trujillo, M. (2017) · The Plant Cell · doi:10.1105/tpc.16.00654 · Cited by 94
The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A
(2024) · doi:10.1038/s41594-023-01196-0 · Cited by 92
The nucleosome acidic patch plays a critical role in RNF168-dependent ubiquitination of histone H2A
Mattiroli, F., Uckelmann, M., Sahtoe, D. D., van Dijk, W. J., & Sixma, T. K. (2014) · Nature Communications · doi:10.1038/ncomms4291 · Cited by 90
Allosteric regulation of E2:E3 interactions promote a processive ubiquitination machine
Das, R., Liang, Y., Mariano, J. M., Li, J., Huang, T., King, A., Tarasov, S. G., Weissman, A. M., Ji, X., & Byrd, R. A. (2013) · The EMBO Journal · doi:10.1038/emboj.2013.174 · Cited by 92
A non‐canonical scaffold‐type E3 ligase complex mediates protein UFMylation
Peter, J. J., Magnussen, H., DaRosa, P. A., Millrine, D., Matthews, S. P., Lamoliatte, F., Sundaramoorthy, R., Kopito, R. R., & Kulathu, Y. (2022) · The EMBO Journal · doi:10.15252/embj.2022111015 · Cited by 83
GID E3 ligase supramolecular chelate assembly configures multipronged ubiquitin targeting of an oligomeric metabolic enzyme
Sherpa, D., Chrustowicz, J., Qiao, S., Langlois, C., Hehl, L. A., Gottemukkala, K. V., Hansen, F. M., Karayel, Ö., von Gronau, S., Prabu, J. R., et al. (2021) · Molecular Cell · doi:10.1016/j.molcel.2021.03.025 · Cited by 85
Regulating the Regulators: Recent Revelations in the Control of E3 Ubiquitin Ligases
Vittal, V., Stewart, M. D., Brzović, P. S., & Klevit, R. E. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.r115.675165 · Cited by 88
Structure of the nutrient-sensing hub GATOR2
Valenstein, M. L., Rogala, K. B., Lalgudi, P. V., Brignole, E. J., Gu, X., Saxton, R. A., Chantranupong, L., Kolibius, J., Quast, J.-P., & Sabatini, D. M. (2022) · Nature · doi:10.1038/s41586-022-04939-z · Cited by 94
SUMO Chain-Induced Dimerization Activates RNF4
Rojas‐Fernández, A., Plechanovová, A., Hattersley, N., Jaffray, E., Tatham, M. H., & Hay, R. T. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.02.031 · Cited by 90
Self-citation
RING Dimerization Links Higher-Order Assembly of TRIM5α to Synthesis of K63-Linked Polyubiquitin
Yudina, Z., Roa, A., Johnson, R., Biris, N., Vieira, D. A. D. S. A., Tsiperson, V., Reszka, N., Taylor, A. B., Hart, P. J., Demeler, B., et al. (2015) · Cell Reports · doi:10.1016/j.celrep.2015.06.072 · Cited by 84
Ubiquitin‐Activated Interaction Traps (UBAITs) identify E3 ligase binding partners
O’Connor, H. F., Lyon, N., Leung, J. W. C., Agarwal, P., Swaim, C. D., Miller, K. M., & Huibregtse, J. M. (2015) · EMBO Reports · doi:10.15252/embr.201540620 · Cited by 86
The logic of protein post‐translational modifications (PTMs): Chemistry, mechanisms and evolution of protein regulation through covalent attachments
Suskiewicz, M. J. (2024) · BioEssays · doi:10.1002/bies.202300178 · Cited by 91
Intrinsic disorder drives N-terminal ubiquitination by Ube2w
Vittal, V., Shi, L., Wenzel, D. M., Scaglione, K. M., Duncan, E. D., Basrur, V., Elenitoba‐Johnson, K. S. J., Baker, D. A., Paulson, H. L., Brzović, P. S., et al. (2014) · Nature Chemical Biology · doi:10.1038/nchembio.1700 · Cited by 82
Mechanism and disease association of E2-conjugating enzymes: lessons from UBE2T and UBE2L3
Alpi, A. F., Chaugule, V. K., & Walden, H. (2016) · Biochemical Journal · doi:10.1042/bcj20160028 · Cited by 81
PEX5 translocation into and out of peroxisomes drives matrix protein import
Skowyra, M. L., & Rapoport, T. A. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.07.004 · Cited by 81
Mechanism of degrader-targeted protein ubiquitinability
Crowe, C., Nakasone, M. A., Chandler, S., Craigon, C., Sathe, G. J., Tatham, M. H., Makukhin, N., Hay, R. T., & Ciulli, A. (2024) · Science Advances · doi:10.1126/sciadv.ado6492 · Cited by 90
Self-citation
Molecular mechanisms in SUMO conjugation
Varejão, N., Lascorz, J., Li, Y., & Reverter, D. (2019) · Biochemical Society Transactions · doi:10.1042/bst20190357 · Cited by 81
Structural basis for RING-Cys-Relay E3 ligase activity and its role in axon integrity
Mabbitt, P. D., Loreto, A., Déry, M.-A. C., Fletcher, A. J., Stanley, M., Pao, K., Wood, N. T., Coleman, M. P., & Virdee, S. (2020) · Nature Chemical Biology · doi:10.1038/s41589-020-0598-6 · Cited by 80
Evolution and Functions of Plant U-Box Proteins: From Protein Quality Control to Signaling
Trenner, J., Monaghan, J., Saeed, B., Quint, M., Shabek, N., & Trujillo, M. (2022) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-102720-012310 · Cited by 79
A Structurally Unique E2-Binding Domain Activates Ubiquitination by the ERAD E2, Ubc7p, through Multiple Mechanisms
Metzger, M. B., Liang, Y., Das, R., Mariano, J. M., Li, S., Li, J., Kostova, Z., Byrd, R. A., Ji, X., & Weissman, A. M. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.04.004 · Cited by 77
Structure of the Human FANCL RING-Ube2T Complex Reveals Determinants of Cognate E3-E2 Selection
Hodson, C., Purkiss, A. G., Miles, J. A., & Walden, H. (2014) · Structure · doi:10.1016/j.str.2013.12.004 · Cited by 83
Advancing targeted protein degradation for metabolic diseases therapy
Zhou, Q., Xiao, H., Yang, F., Wang, Y., Li, P., & Zheng, Z. (2022) · Pharmacological Research · doi:10.1016/j.phrs.2022.106627 · Cited by 77
A General Strategy for Discovery of Inhibitors and Activators of RING and U-box E3 Ligases with Ubiquitin Variants
Gabrielsen, M., Buetow, L., Nakasone, M. A., Ahmed, S. F., Sibbet, G. J., Smith, B. O., Zhang, W., Sidhu, S. S., & Huang, D. T. C. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.09.027 · Cited by 74
Ubc9 Sumoylation Controls SUMO Chain Formation and Meiotic Synapsis in Saccharomyces cerevisiae
Klug, H., Xaver, M., Chaugule, V. K., Koidl, S., Mittler, G., Klein, F., & Pichler, A. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.03.027 · Cited by 75
Covalent Inhibition of Ubc13 Affects Ubiquitin Signaling and Reveals Active Site Elements Important for Targeting
Hodge, C. D., Edwards, R. A., Markin, C. J., McDonald, D., Pulvino, M. J., Huen, M. S. Y., Zhao, J., Spyracopoulos, L., Hendzel, M. J., & Glover, J. N. M. (2015) · ACS Chemical Biology · doi:10.1021/acschembio.5b00222 · Cited by 76
Non-lysine ubiquitylation: Doing things differently
Kelsall, I. R. (2022) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2022.1008175 · Cited by 78
Ubiquitin Chain Elongation Requires E3-Dependent Tracking of the Emerging Conjugate
Kelly, A., Wickliffe, K. E., Song, L., Fedrigo, I., & Rapé, M. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.09.010 · Cited by 73
Does it take two to tango? RING domain self-association and activity in TRIM E3 ubiquitin ligases
Fiorentini, F., Esposito, D., & Rittinger, K. (2020) · Biochemical Society Transactions · doi:10.1042/bst20200383 · Cited by 74
Structural analysis of MDM2 RING separates degradation from regulation of p53 transcription activity
Nomura, K., Klejnot, M., Kowalczyk, D., Hock, A. K., Sibbet, G. J., Vousden, K. H., & Huang, D. T. C. (2017) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3414 · Cited by 72
Structural basis for the recognition and degradation of host TRIM proteins by Salmonella effector SopA
Fiškin, E., Bhogaraju, S., Herhaus, L., Kalayil, S., Hahn, M., & Đikić, I. (2017) · Nature Communications · doi:10.1038/ncomms14004 · Cited by 74
How to Inactivate Human Ubiquitin E3 Ligases by Mutation
Garcia-Barcena, C., Osinalde, N., Ramírez, J., & Mayor, U. (2020) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2020.00039 · Cited by 79
Specificity of the anaphase-promoting complex: A single-molecule study
Lu, Y., Wang, W., & Kirschner, M. W. (2015) · Science · doi:10.1126/science.1248737 · Cited by 72
E2~Ub conjugates regulate the kinase activity of Shigella effector OspG during pathogenesis
Pruneda, J. N., Smith, F. D., Daurie, A., Swaney, D. L., Villén, J., Scott, J. D., Stadnyk, A. W., Trong, I. L., Stenkamp, R. E., Klevit, R. E., et al. (2014) · The EMBO Journal · doi:10.1002/embj.201386386 · Cited by 72
Structural dynamics of the E6AP/UBE3A-E6-p53 enzyme-substrate complex
Sailer, C., Offensperger, F., Julier, A., Kammer, K.-M., Walker‐Gray, R., Gold, M. G., Scheffner, M., & Stengel, F. (2018) · Nature Communications · doi:10.1038/s41467-018-06953-0 · Cited by 79
Secondary ubiquitin-RING docking enhances Arkadia and Ark2C E3 ligase activity
Wright, J. D., Mace, P. D., & Day, C. L. (2015) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.3142 · Cited by 70
Acetylation, Phosphorylation, Ubiquitination (Oh My!): Following Post-Translational Modifications on the Ubiquitin Road
Lacoursiere, R. E., Hadi, D., & Shaw, G. S. (2022) · Biomolecules · doi:10.3390/biom12030467 · Cited by 74
Targeting HECT ‐type E3 ligases – insights from catalysis, regulation and inhibitors
Fajner, V., Maspero, E., & Polo, S. (2017) · FEBS Letters · doi:10.1002/1873-3468.12775 · Cited by 70
The unifying catalytic mechanism of the RING-between-RING E3 ubiquitin ligase family
Wang, X. S., Cotton, T. R., Trevelyan, S. J., Richardson, L. W., Lee, W. T., Silke, J., & Lechtenberg, B. C. (2023) · Nature Communications · doi:10.1038/s41467-023-35871-z · Cited by 69
The UFM1 E3 ligase recognizes and releases 60S ribosomes from ER translocons
Makhlouf, L., Peter, J. J., Magnussen, H., Thakur, R., Millrine, D., Minshull, T. C., Harrison, G., Varghese, J., Lamoliatte, F., Foglizzo, M., et al. (2024) · Nature · doi:10.1038/s41586-024-07093-w · Cited by 68
A conserved asparagine has a structural role in ubiquitin-conjugating enzymes
Berndsen, C., Wiener, R., Yu, I., Ringel, A. E., & Wolberger, C. (2013) · Nature Chemical Biology · doi:10.1038/nchembio.1159 · Cited by 67
CUL5-ARIH2 E3-E3 ubiquitin ligase structure reveals cullin-specific NEDD8 activation
Kostrhon, S., Prabu, J. R., Baek, K., Horn‐Ghetko, D., von Gronau, S., Klügel, M., Basquin, J., Alpi, A. F., & Schulman, B. A. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00858-8 · Cited by 63
Kaposi's Sarcoma-Associated Herpesvirus K-Rta Exhibits SUMO-Targeting Ubiquitin Ligase (STUbL) Like Activity and Is Essential for Viral Reactivation
Izumiya, Y., Kobayashi, K., Kim, K. Y., Pochampalli, M. R., Izumiya, C., Shevchenko, B., Wang, D.-H., Huerta, S. B., Martinez, A. D., Campbell, M., et al. (2013) · PLoS Pathogens · doi:10.1371/journal.ppat.1003506 · Cited by 65
SUMO-Targeted Ubiquitin Ligases and Their Functions in Maintaining Genome Stability
Chang, Y., Oram, M. K., & Bielinsky, A. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms22105391 · Cited by 64
Antibody RING-Mediated Destruction of Endogenous Proteins
Ibrahim, A. F. M., Shen, L., Tatham, M. H., Dickerson, D. R., Prescott, A. R., Abidi, N., Xirodimas, D. P., & Hay, R. T. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.04.032 · Cited by 64
Self-citation
Ubiquitin transfer by a RING E3 ligase occurs from a closed E2~ubiquitin conformation
Branigan, E., Penedo, J. C., & Hay, R. T. (2020) · Nature Communications · doi:10.1038/s41467-020-16666-y · Cited by 65
Self-citation
Synergistic recruitment of UbcH7~Ub and phosphorylated Ubl domain triggers parkin activation
Condos, T., Dunkerley, K. M., Freeman, E. A., Barber, K. R., Aguirre, J. D., Chaugule, V. K., Xiao, Y., Konermann, L., Walden, H., & Shaw, G. S. (2018) · The EMBO Journal · doi:10.15252/embj.2018100014 · Cited by 61
Structural insights into E1 recognition and the ubiquitin-conjugating activity of the E2 enzyme Cdc34
Williams, K. M., Qie, S., Atkison, J. H., Salazar-Arango, S., Diehl, J. A., & Olsen, S. K. (2019) · Nature Communications · doi:10.1038/s41467-019-11061-8 · Cited by 64
A peroxisomal ubiquitin ligase complex forms a retrotranslocation channel
Feng, P., Wu, X., Erramilli, S. K., Paulo, J. A., Knejski, P. P., Gygi, S. P., Kossiakoff, A. A., & Rapoport, T. A. (2022) · Nature · doi:10.1038/s41586-022-04903-x · Cited by 65
Specificity and disease in the ubiquitin system
Chaugule, V. K., & Walden, H. (2016) · Biochemical Society Transactions · doi:10.1042/bst20150209 · Cited by 65
Structural insights into the mechanism and E2 specificity of the RBR E3 ubiquitin ligase HHARI
Yuan, L., Lv, Z., Atkison, J. H., & Olsen, S. K. (2017) · Nature Communications · doi:10.1038/s41467-017-00272-6 · Cited by 61
Structural basis of specific H2A K13/K15 ubiquitination by RNF168
Horn, V., Uckelmann, M., Zhang, H., Eerland, J., Aarsman, I., le Paige, U. B., Davidovich, C., Sixma, T. K., & van Ingen, H. (2019) · Nature Communications · doi:10.1038/s41467-019-09756-z · Cited by 60
The activity of TRAF RING homo- and heterodimers is regulated by zinc finger 1
Middleton, A. J., Budhidarmo, R., Das, A., Zhu, J., Foglizzo, M., Mace, P. D., & Day, C. L. (2017) · Nature Communications · doi:10.1038/s41467-017-01665-3 · Cited by 59
Regulation of ubiquitin transfer by XIAP, a dimeric RING E3 ligase
Nakatani, Y., Kleffmann, T., Linke, K., Condon, S. M., Hinds, M. G., & Day, C. L. (2013) · Biochemical Journal · doi:10.1042/bj20121702 · Cited by 62
DELTEX E3 ligases ubiquitylate ADP-ribosyl modification on nucleic acids
Zhu, K., Suskiewicz, M. J., Chatrin, C., Strømland, Ø., Dorsey, B. W., Aucagne, V., Ahel, D., & Ahel, I. (2023) · Nucleic Acids Research · doi:10.1093/nar/gkad1119 · Cited by 58
Role of ubiquitin and the HPV E6 oncoprotein in E6AP-mediated ubiquitination
Mortensen, F., Schneider, D., Barbic, T., Sladewska-Marquardt, A., Kühnle, S., Marx, A., & Scheffner, M. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1505923112 · Cited by 57
Monoubiquitination of Histone H2B Is Intrinsic to the Bre1 RING Domain-Rad6 Interaction and Augmented by a Second Rad6-binding Site on Bre1
Turco, E., Gallego, L. D., Schneider, M., & Köhler, A. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.626788 · Cited by 58
The ubiquitin ligation machinery in the defense against bacterial pathogens
Tripathi‐Giesgen, I., Behrends, C., & Alpi, A. F. (2021) · EMBO Reports · doi:10.15252/embr.202152864 · Cited by 54
Conformational dynamics control ubiquitin-deubiquitinase interactions and influence in vivo signaling
Phillips, A. H., Zhang, Y., Cunningham, C. N., Zhou, L., Forrest, W. F., Liu, P. S., Steffek, M., Lee, J., Tam, C., Helgason, E., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1302407110 · Cited by 56
S. pombe Uba1-Ubc15 Structure Reveals a Novel Regulatory Mechanism of Ubiquitin E2 Activity
Lv, Z., Rickman, K. A., Yuan, L., Williams, K. M., Selvam, S. P., Woosley, A. N., Howe, P. H., Öğretmen, B., Smogorzewska, A., & Olsen, S. K. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.01.008 · Cited by 56
Resequencing 200 Flax Cultivated Accessions Identifies Candidate Genes Related to Seed Size and Weight and Reveals Signatures of Artificial Selection
Guo, D., Jiang, H., Yan, W., Yang, L., Ye, J., Wang, Y., Yan, Q., Chen, J., Gao, Y., Duan, L., et al. (2020) · Frontiers in Plant Science · doi:10.3389/fpls.2019.01682 · Cited by 56
RING domains act as both substrate and enzyme in a catalytic arrangement to drive self-anchored ubiquitination
Kiss, L., Clift, D., Renner, N., Neuhaus, D., & James, L. C. (2021) · Nature Communications · doi:10.1038/s41467-021-21443-6 · Cited by 55
Structural basis for RNA polymerase II ubiquitylation and inactivation in transcription-coupled repair
Kokić, G., Yakoub, G., van den Heuvel, D., Wondergem, A. P., van der Meer, P. J., van der Weegen, Y., Chernev, A., Fianu, I., Fokkens, T. J., Lorenz, S., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01207-0 · Cited by 54
Activation of UbcH5c∼Ub Is the Result of a Shift in Interdomain Motions of the Conjugate Bound to U-Box E3 Ligase E4B
Soss, S. E., Klevit, R. E., & Chazin, W. (2013) · Biochemistry · doi:10.1021/bi3015949 · Cited by 55
The molecular basis of lysine 48 ubiquitin chain synthesis by Ube2K
Middleton, A. J., & Day, C. L. (2015) · Scientific Reports · doi:10.1038/srep16793 · Cited by 57
Suramin inhibits cullin-RING E3 ubiquitin ligases
Wu, K., Chong, R. A., Yu, Q., Bai, J., Spratt, D. E., Ching, K., Lee, C., Miao, H., Tappin, I., Hurwitz, J., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1601089113 · Cited by 55
Chemical Synthesis of Atomically Tailored SUMO E2 Conjugating Enzymes for the Formation of Covalently Linked SUMO–E2–E3 Ligase Ternary Complexes
Zhang, Y., Hirota, T., Kuwata, K., Oishi, S., Gramani, S. G., & Bode, J. W. (2019) · Journal of the American Chemical Society · doi:10.1021/jacs.9b06820 · Cited by 55
The deSUMOylase SENP2 coordinates homologous recombination and nonhomologous end joining by independent mechanismsPreprint
Garvin, A. J., Walker, A. K., Densham, R. M., Chauhan, A. S., Stone, H. R., Mackay, H. L., Jamshad, M., Starowicz, K., Daza-Martín, M., Ronson, G. E., et al. (2019) · Genes & Development · doi:10.1101/gad.321125.118 · Cited by 55
The BRCA1 Ubiquitin ligase function sets a new trend for remodelling in DNA repair
Densham, R. M., & Morris, J. R. (2016) · Nucleus · doi:10.1080/19491034.2016.1267092 · Cited by 55
Decoding the messaging of the ubiquitin system using chemical and protein probes
Henneberg, L. T., & Schulman, B. A. (2021) · Cell chemical biology · doi:10.1016/j.chembiol.2021.03.009 · Cited by 53
Ubiquitin-Dependent Regulation of Stem Cell Biology
Werner, A. A., Manford, A. G., & Rapé, M. (2017) · Trends in Cell Biology · doi:10.1016/j.tcb.2017.04.002 · Cited by 52
Structural Studies of HHARI/UbcH7∼Ub Reveal Unique E2∼Ub Conformational Restriction by RBR RING1
Dove, K. K., Olszewski, J. L., Martino, L., Duda, D. M., Wu, X. S., Miller, D. J., Reiter, K. H., Rittinger, K., Schulman, B. A., & Klevit, R. E. (2017) · Structure · doi:10.1016/j.str.2017.04.013 · Cited by 52
Structure of UBE2K–Ub/E3/polyUb reveals mechanisms of K48-linked Ub chain extension
Nakasone, M. A., Majorek, K. A., Gabrielsen, M., Sibbet, G. J., Smith, B. O., & Huang, D. T. C. (2022) · Nature Chemical Biology · doi:10.1038/s41589-021-00952-x · Cited by 54
SUMO Rules: Regulatory Concepts and Their Implication in Neurologic Functions
Droescher, M., Chaugule, V. K., & Pichler, A. (2013) · NeuroMolecular Medicine · doi:10.1007/s12017-013-8258-6 · Cited by 50
DUB-Resistant Ubiquitin to Survey Ubiquitination Switches in Mammalian Cells
Békés, M., Okamoto, K., Crist, S. B., Jones, M. V., Chapman, J. R., Brasher, B. B., Melandri, F. D., Ueberheide, B. M., Denchi, E. L., & Huang, T. T. (2013) · Cell Reports · doi:10.1016/j.celrep.2013.10.008 · Cited by 51
Structural insight into SUMO chain recognition and manipulation by the ubiquitin ligase RNF4
Xu, Y., Plechanovová, A., Simpson, P. J., Marchant, J., Leidecker, O., Kraatz, S. H. W., Hay, R. T., & Matthews, S. (2014) · Nature Communications · doi:10.1038/ncomms5217 · Cited by 51
Self-citation
ARMC5 is part of an RPB1-specific ubiquitin ligase implicated in adrenal hyperplasia
Lao, L., Bourdeau, I., Gagliardi, L., He, X., Shi, W., Hao, B., Tan, M., Hu, Y., Peng, J., Coulombe, B., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac483 · Cited by 52
IAPs: Modular regulators of cell signalling
Budhidarmo, R., & Day, C. L. (2014) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2014.12.002 · Cited by 50
Structural Basis for the Inhibition of Host Protein Ubiquitination by Shigella Effector Kinase OspG
Grishin, A. M., Condos, T., Barber, K. R., Campbell‐Valois, F., Parsot, C., Shaw, G. S., & Cygler, M. (2014) · Structure · doi:10.1016/j.str.2014.04.010 · Cited by 49
RNF4 interacts with both SUMO and nucleosomes to promote the DNA damage response
Groocock, L., Nie, M., Prudden, J., Moiani, D., Wang, T., Cheltsov, A. V., Rambo, R. P., Arvai, A. S., Hitomi, C., Tainer, J. A., et al. (2014) · EMBO Reports · doi:10.1002/embr.201338369 · Cited by 49
The Colossus of Ubiquitylation: Decrypting a Cellular Code
Williamson, A. P., Werner, A. A., & Rapé, M. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.028 · Cited by 46
A tri-ionic anchor mechanism drives Ube2N-specific recruitment and K63-chain ubiquitination in TRIM ligases
Kiss, L., Zeng, J., Dickson, C. F., Mallery, D. L., Yang, J., McLaughlin, S. H., Boland, A., Neuhaus, D., & James, L. C. (2019) · Nature Communications · doi:10.1038/s41467-019-12388-y · Cited by 50
Mechanistic insights into nucleosomal H2B monoubiquitylation mediated by yeast Bre1-Rad6 and its human homolog RNF20/RNF40-hRAD6A
Deng, Z., Ai, H., Sun, M., Tong, Z., Du, Y., Qu, Q., Zhang, L., Xu, Z., Tao, S., Shi, Q., et al. (2023) · Molecular Cell · doi:10.1016/j.molcel.2023.08.001 · Cited by 45
DNA activates the Nse2/Mms21 SUMO E3 ligase in the Smc5/6 complex
Varejão, N., Ibars, E., Lascorz, J., Colomina, N., Torres‐Rosell, J., & Reverter, D. (2018) · The EMBO Journal · doi:10.15252/embj.201798306 · Cited by 54
Multivalent interactions of the SUMO-interaction motifs in RING finger protein 4 determine the specificity for chains of the SUMO
Keusekotten, K., Bade, V. N., Meyer-Teschendorf, K., Sriramachandran, A. M., Fischer-Schrader, K., Krause, A., Horst, C., Schwarz, G., Hofmann, K., Dohmen, R. J., et al. (2013) · Biochemical Journal · doi:10.1042/bj20130753 · Cited by 46
Mechanism of ubiquitin transfer promoted by TRAF6
Fu, T., Shen, C., Li, Q., Zhang, P., & Wu, H. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1721788115 · Cited by 47
Prp19/Pso4 Is an Autoinhibited Ubiquitin Ligase Activated by Stepwise Assembly of Three Splicing Factors
de Moura, T. R., Mozaffari‐Jovin, S., Szabó, C. Z. K., Schmitzová, J., Dybkov, O., Cretu, C., Kachala, M., Svergun, D. I., Urlaub, H., Lührmann, R., et al. (2018) · Molecular Cell · doi:10.1016/j.molcel.2018.02.022 · Cited by 52
Analysis of Small Ubiquitin-Like Modifier (SUMO) Targets Reflects the Essential Nature of Protein SUMOylation and Provides Insight to Elucidate the Role of SUMO in Plant Development
Elrouby, N. (2015) · PLANT PHYSIOLOGY · doi:10.1104/pp.15.01014 · Cited by 45
RNF4—A Paradigm for SUMOylation‐Mediated Ubiquitination
Kumar, R., & Sabapathy, K. (2019) · PROTEOMICS · doi:10.1002/pmic.201900185 · Cited by 45
Protein clearance strategies for disease intervention
Hommen, F., Bilican, S., & Vílchez, D. (2021) · Journal of Neural Transmission · doi:10.1007/s00702-021-02431-y · Cited by 48
Mechanism of millisecond Lys48-linked poly-ubiquitin chain formation by cullin-RING ligases
Liwocha, J., Li, J., Purser, N., Rattanasopa, C., Maiwald, S. A., Krist, D. T., Scott, D. C., Steigenberger, B. A., Prabu, J. R., Schulman, B. A., et al. (2024) · Nature Structural & Molecular Biology · doi:10.1038/s41594-023-01206-1 · Cited by 45
Targeting TRIM Proteins: A Quest towards Drugging an Emerging Protein Class
D’Amico, F., Mukhopadhyay, R., Ovaa, H., & Mulder, M. P. C. (2021) · ChemBioChem · doi:10.1002/cbic.202000787 · Cited by 44
Structure of the FA core ubiquitin ligase closing the ID clamp on DNA
Wang, S., Wang, R., Peralta, C., Yaseen, A., & Pavletich, N. P. (2021) · Nature Structural & Molecular Biology · doi:10.1038/s41594-021-00568-8 · Cited by 44

Authors: Plechanovová, A., Jaffray, E. G., Tatham, M. H., Naismith, J. H., & Hay, R. T.
Affiliations: University of Dundee (GB)
University of St Andrews (GB)
Corresponding author: Hay, Ronald T.
ORCID: Plechanovová, Anna
Jaffray, Ellis G.
Tatham, Michael H.
Naismith, James H.
Hay, Ronald T.
Venue: Nature
Publisher: Springer Science and Business Media LLC
Published: 2012-07-29
Volume: 489
Issue: 7414
Pages: 115-120
ISSN: 0028-0836 (ISSN-L)
1476-4687
DOI: 10.1038/nature11376
PMC: PMC3442243
OpenAlex: W2147542927
Cited by: 521
References: 41
Citations by year: 2026: 25 · 2025: 36 · 2024: 41 · 2023: 24 · 2022: 41 · 2021: 39 · 2020: 41 · 2019: 29 · 2018: 27 · 2017: 44 · 2016: 39 · 2015: 37 · 2014: 47 · 2013: 46 · 2012: 5
FWCI: 17.37
Type: journal article
Language: en
Open access: green
europepmc.org
Licence: www.springer.com/tdm (tdm)
Locations: Nature (publishedVersion)
PubMed (publishedVersion)
Europe PMC (PubMed Central) (acceptedVersion)
PubMed Central (acceptedVersion)
RePEc: Research Papers in Economics (submittedVersion)
Discovery Research Portal (University of Dundee) (submittedVersion)
Funders: Wellcome Trust (098391, 081862, 098391/Z/12/Z)
Cancer Research UK (13067)
Scottish Funding Council
Topics: Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
Life Sciences › Biochemistry, Genetics and Molecular Biology › Structural Biology › Enzyme Structure and Function
Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
Keywords: RING E3 ubiquitin ligase, RNF4, UbcH5a, ubiquitin transfer, isopeptide bonds, ubiquitin binding, crystal structure
MeSH terms: Animals, Humans, Hydrolysis, Models, Molecular, Mutation, Nuclear Proteins, Protein Binding, Transcription Factors, Zinc Fingers, Protein Structure, Tertiary, Crystallography, X-Ray, Catalytic Domain, Ubiquitin, Ubiquitin-Conjugating Enzymes, Ubiquitin-Protein Ligases, Multiprotein Complexes, Rats, Ubiquitination, Biocatalysis

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

Structure of a RING E3 ligase and ubiquitin-loaded E2 primed for catalysis

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Self-check

Citations

Cites

Cited by

Related

Metadata

Record

About these checks