The DOI matches its Crossref record; 30 of the 30 references it cites were found in a registry or an index.
Analysis of the human E2 ubiquitin conjugating enzyme protein interaction network
Open accessAbstract
In eukaryotic cells the stability and function of many proteins are regulated by the addition of ubiquitin or ubiquitin-like peptides. This process is dependent upon the sequential action of an E1-activating enzyme, an E2-conjugating enzyme, and an E3 ligase. Different combinations of these proteins confer substrate specificity and the form of protein modification. However, combinatorial preferences within ubiquitination networks remain unclear. In this study, yeast two-hybrid (Y2H) screens were combined with true homology modeling methods to generate a high-density map of human E2/E3-RING interactions. These data include 535 experimentally defined novel E2/E3-RING interactions and >1300 E2/E3-RING pairs with more favorable predicted free-energy values than the canonical UBE2L3-CBL complex. The significance of Y2H predictions was assessed by both mutagenesis and functional assays. Significantly, 74/80 (>92%) of Y2H predicted complexes were disrupted by point mutations that inhibit verified E2/E3-RING interactions, and a approximately 93% correlation was observed between Y2H data and the functional activity of E2/E3-RING complexes in vitro. Analysis of the high-density human E2/E3-RING network reveals complex combinatorial interactions and a strong potential for functional redundancy, especially within E2 families that have undergone evolutionary expansion. Finally, a one-step extended human E2/E3-RING network, containing 2644 proteins and 5087 edges, was assembled to provide a resource for future functional investigations.
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“The ability of E3 ligases to interact with multiple E2 partners is supported by recent global E2-E3 interaction screens (26,27).”
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“However, some of these E2 s failed to interact with Mdm2 in another high throughput approach [26].”
From The p53 orchestra: Mdm2 and Mdmx set the tone (2010) · cites this paper as [26]
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Towards a proteome-scale map of the human protein–protein interaction network
Rual, J.-F. M., Venkatesan, K., Hao, T., Hirozane-Kishikawa, T., Dricot, A., Li, N., Berriz, G. F., Gibbons, F. D., Dreze, M., Ayivi-Guedehoussou, N., et al. (2005) · Nature · doi:10.1038/nature04209 · Cited by 2,904
Self-citationThe FoldX web server: an online force field
Schymkowitz, J., Borg, J., Stricher, F., Nys, R., Rousseau, F., & Serrano, L. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki387 · Cited by 2,759 · cited 1×
“Homology modeling was then achieved by replacing side-chain residues in accordance with structure-based alignments (Supplemental Files 7 and 8) using the BuildModel command of FoldX (Guerois et al. 2002; Schymkowitz et al. 2005a,b) vs 2.7.”
MethodInfluentialSelf-citationA Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome
Stelzl, U., Worm, U., Lalowski, M. M., Haenig, C., Brembeck, F. H., Goehler, H., Strödicke, M., Zenkner, M., Schoenherr, A., Koeppen, S., et al. (2005) · Cell · doi:10.1016/j.cell.2005.08.029 · Cited by 2,433
Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences
Mammalian Gene Collection (MGC) Program Team* (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242603899 · Cited by 1,756
Guerois, R., Nielsen, J. E., & Serrano, L. (2002) · Journal of Molecular Biology · doi:10.1016/s0022-2836(02)00442-4 · Cited by 1,728
Self-citationA proteomics approach to understanding protein ubiquitination
Peng, J., Schwartz, D., Elias, J. E., Thoreen, C. C., Cheng, D., Marsischky, G., Roelofs, J., Finley, D. J., & Gygi, S. P. (2003) · Nature Biotechnology · doi:10.1038/nbt849 · Cited by 1,601
Themes and variations on ubiquitylation
Weissman, A. M. (2001) · Nature Reviews Molecular Cell Biology · doi:10.1038/35056563 · Cited by 1,507
The Tyrosine Kinase Negative Regulator c-Cbl as a RING-Type, E2-Dependent Ubiquitin-Protein Ligase
Joazeiro, C. A. P., Wing, S. S., Huang, H.-K., Leverson, J. D., Hunter, T. R., & Liu, Y. (1999) · Science · doi:10.1126/science.286.5438.309 · Cited by 1,036
Ubiquitin and ubiquitin-like proteins as multifunctional signals
Welchman, R., Gordon, C., & Mayer, R. J. (2005) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm1700 · Cited by 849
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Building ubiquitin chains: E2 enzymes at work
Ye, Y., & Rape, M. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2780 · Cited by 989
The emerging complexity of protein ubiquitination
Komander, D. (2009) · Biochemical Society Transactions · doi:10.1042/bst0370937 · Cited by 821
Self-citationE2 enzymes: more than just middle men
Stewart, M. D., Ritterhoff, T., Klevit, R. E., & Brzović, P. S. (2016) · Cell Research · doi:10.1038/cr.2016.35 · Cited by 585
The p53 orchestra: Mdm2 and Mdmx set the tone
Wade, M., Wang, Y. V., & Wahl, G. M. (2010) · Trends in Cell Biology · doi:10.1016/j.tcb.2010.01.009 · Cited by 450
The family of ubiquitin‐conjugating enzymes (E2s): deciding between life and death of proteins
van Wijk, S. J. L., & Timmers, H. T. M. (2009) · The FASEB Journal · doi:10.1096/fj.09-136259 · Cited by 454
Metadata
- Authors
- Markson, G., Kiel, C., Hyde, R., Brown, S., Charalabous, P., Bremm, A., Semple, J., Woodsmith, J., Duley, S., Salehi-Ashtiani, K., Vidal, M., Komander, D., Serrano, L., Lehner, P., & Sanderson, C. M.
- Affiliations
- University of Cambridge (GB)
- Institució Catalana de Recerca i Estudis Avançats (ES)
- University of Liverpool (GB)
- MRC Laboratory of Molecular Biology (GB)
- Harvard University (US)
- ORCID
- Venue
- Genome Research
- Publisher
- Cold Spring Harbor Laboratory
- Published
- 2009-06-23
- Volume
- 19
- Issue
- 10
- Pages
- 1905-1911
- ISSN
- 1088-9051 (ISSN-L)
- PMC
- PMC2765280
- OpenAlex
- W2135700703
- Cited by
- 157
- References
- 30
- Citations by year
- 2026: 3 · 2025: 2 · 2023: 5 · 2022: 8 · 2021: 4 · 2020: 10 · 2019: 3 · 2018: 11 · 2017: 7 · 2016: 12 · 2015: 19 · 2014: 6 · 2013: 17 · 2012: 18
- Type
- posted content
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Genome Research (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- Wellcome Trust (084957)
- Fonds De La Recherche Scientifique - FNRS
- Fédération Wallonie-Bruxelles
- Medical Research Council
- National Human Genome Research Institute (R01HG001715)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Ubiquitin and proteasome pathways
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Degradation and Inhibitors
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Keywords
- E2 ubiquitin-conjugating enzyme, E3 ubiquitin ligase, RING domain, protein-protein interaction network, ubiquitination, yeast two-hybrid screen, homology modeling, free energy prediction, functional redundancy, human interactome
- MeSH terms
- Amino Acid Sequence, False Positive Reactions, Humans, Protein Binding, Mutagenesis, Site-Directed, Sequence Homology, Amino Acid, K562 Cells, Sequence Analysis, Protein, Two-Hybrid System Techniques, Ubiquitin-Conjugating Enzymes, Ubiquitin-Protein Ligases, Metabolic Networks and Pathways, Protein Interaction Domains and Motifs, Ubiquitination
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