Mining the TRAF6/p62 interactome for a selective ubiquitination motif

BMC Proceedings

Volumn 5, Issue SUPPL. 2, 2011, Pages

  Jadhav, Trafina S ^a   Wooten, Marie W ^a   Wooten, Michael C ^a  

^a AUBURN UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN DERIVED NEUROTROPHIC FACTOR RECEPTOR; LYSINE; NEUROTROPHIC TYROSINE KINASE RECEPTOR 3; NEUROTROPHIN RECEPTOR INTERACTING FACTOR; PROTEIN; PROTEIN P62; PROTEIN TRKC; PROTEIN TYROSINE KINASE; PROTEIN TYROSINE KINASE A; SCAFFOLD PROTEIN; SOLVENT; TUMOR NECROSIS FACTOR RECEPTOR ASSOCIATED FACTOR 6; UBIQUITIN PROTEIN LIGASE E3; UNCLASSIFIED DRUG;

ALGORITHM; ALPHA HELIX; AMINO ACID SEQUENCE; BETA SHEET; CARBOXY TERMINAL SEQUENCE; CONFERENCE PAPER; CONSENSUS SEQUENCE; CONTROLLED STUDY; HYDROPHOBICITY; INTERACTOME; PREDICTION; PRIORITY JOURNAL; PROTEIN MOTIF; PROTEIN PROTEIN INTERACTION; PROTEIN SECONDARY STRUCTURE; PROTEIN STRUCTURE; UBIQUITINATION;

EID: 84859738656     PISSN: None     EISSN: 17536561     Source Type: Journal    
DOI: 10.1186/1753-6561-5-S2-S4     Document Type: Conference Paper

References (48)

1. Structure and functional properties of the ubiquitin binding protein p62. Geetha T, Wooten MW, FEBS Lett 2002 512 19 24 10.1016/S0014-5793(02)02286-X 11852044 (Pubitemid 34164443)
2. Defining an embedded code for protein ubiquitination. Jadhav T, Wooten MW, J Proteomics Bioinform 2009 2 316 333 10.4172/jpb.1000091 20148194
3. Lysine 63 polyubiquitination of the nerve growth factor receptor TrkA directs internalization and signaling. Geetha T, Jiang J, Wooten MW, Mol Cell 2005 20 301 312 10.1016/j.molcel.2005.09.014 16246731 (Pubitemid 41484174)
4. TRAF6-mediated ubiquitination regulates nuclear translocation of NRIF, the p75 receptor interactor. Geetha T, Kenchappa RS, Wooten MW, Carter BD, EMBO J 2005 24 3859 3868 10.1038/sj.emboj.7600845 16252010 (Pubitemid 41637993)
5. Site-specific Lys-63-linked tumor necrosis factor receptor-associated factor 6 auto-ubiquitination is a critical determinant of IkappaB kinase activation. Lamothe B, Besse A, Campos AD, Webster WK, Wu H, Darnay BG, J Biol Chem 2007 282 4102 4112 10.1074/jbc.M609503200 17135271 (Pubitemid 47084488)
6. RING Domain E3 Ubiquitin Ligases. Deshaies R, Joazeiro C, Annu Rev Biochem 2009 78 399 434 10.1146/annurev.biochem.78.101807.093809 19489725
7. Role of the TAB2-related protein TAB3 in IL-1 and TNF signaling. Ishitani T, Takaesu G, Ninomiya-Tsuji J, Shibuya H, Gaynor RB, Matsumoto K, EMBO J 2003 22 6277 6288 10.1093/emboj/cdg605 14633987 (Pubitemid 37522585)
8. Genome-wide and functional annotation of human E3 ubiquitin ligases identifies MULAN, a mitochondrial E3 that regulates the organelle's dynamics and signaling. Li W, Bengtson MH, Ulbrich A, Matsuda A, Reddy VA, Orth A, Chanda SK, Batalov S, Joazeiro CA, PLoS One 2008 3 1487 10.1371/journal.pone.0001487 18213395 (Pubitemid 351803431)
9. Appetite for destruction: E3 ubiquitin-ligase protection in cardiac disease. Willis MS, Schisler JC, Patterson C, Future Cardiol 2008 4 65 75 10.2217/14796678.4.1.65 19543439
10. Ubiquitin ligases and the immune response. Liu YC, Annu Rev Immunol 2004 22 81 127 10.1146/annurev.immunol.22.012703.104813 15032575 (Pubitemid 38680419)
11. A proteomics approach to understanding protein ubiquitination. Peng J, Schwartz D, Elias JE, Thoreen CC, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi SP, Nat Biotechnol 2003 21 921 926 10.1038/nbt849 12872131 (Pubitemid 36936199)
12. Large-scale analysis of the human ubiquitin-related proteome. Matsumoto M, Hatakeyama S, Oyamada K, Oda Y, Nishimura T, Nakayama KI, Proteomics 2005 5 4145 4151 10.1002/pmic.200401280 16196087 (Pubitemid 41626082)
13. A proteomics approach to identify the ubiquitinated proteins in mouse heart. Jeon HB, Choi ES, Yoon JH, Hwang JH, Chang JW, Lee EK, Choi HW, Park ZY, Yoo YJ, Biochem Biophys Res Commun 2007 357 731 736 10.1016/j.bbrc.2007.04.015 17451654 (Pubitemid 46653841)
14. Identification of a consensus site for TRAF6/p62 polyubiquitination. Jadhav T, Geetha T, Jiang J, Wooten MW, Biochem Biophys Res Commun 2008 371 521 524 10.1016/j.bbrc.2008.04.138 18457658
15. Mining the TRAF6/p62 interactome for preferred substrates and target ubiquitination sites: developing a code hypothesis Jadhav T, Ph.D. dissertation. Auburn University, Program in Cell and Molecular Biology, Department of Biological Sciences 2010
16. Human Protein Reference Database - 2009 update. Keshava TS Prasad, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, et al., Nucleic Acids Res 2009 37 Database issue 767 D772 10.1093/nar/gkn892 18988627
17. The BioGRID Interaction Database: 2008 update. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, Livstone M, Oughtred R, Lackner DH, Bähler J, Wood V, et al. Nucleic Acids Res 2008 Database issue 637 D640 18000002
18. Entrez Gene: gene-centered information at NCBI. Maglott D, Ostell J, Pruitt KD, Tatusova T, Nucleic Acids Res 2005 33 Database issue 54 D58 10.1093/nar/gki031 15608257 (Pubitemid 40207830)
19. Pearson ES, Hartley HD, Biometrika tables for statisticians 1 London: Cambridge University Press 1972
20. Sokal RR, Rohlf FJ, Biometry: The principles and practice of statistics in biological research New York: W. H. Freeman and Company 1995
21. Sequence Logos: A new way to display consensus sequences. Schneider TD, Stephens RM, Nucleic Acids Res 1990 18 6097 6100 10.1093/nar/18.20.6097 2172928
22. WebLogo: A sequence logo generator. Crooks GE, Hon G, Chandonia JM, Brenner SE, Genome Res 2004 14 1188 1190 10.1101/gr.849004 15173120 (Pubitemid 38811555)
23. Protein secondary structure prediction based on position-specific scoring matrices. Jones DT, J Mol Biol 1999 292 195 202 10.1006/jmbi.1999.3091 10493868 (Pubitemid 29435759)
24. Protein structure prediction servers at University College London. Bryson K, McGuffin LJ, Marsden RL, Ward JJ, Sodhi JS, Jones DT, Nucleic Acids Res 2005 33 36 W38 10.1093/nar/gki410 15980489 (Pubitemid 44529876)
25. MeDor: a metaserver for predicting protein disorder. Lieutaud P, Canard B, Longhi S, BMC Genomics 2008 9 25 10.1186/1471-2164-9-S2-S25 18831791
26. SMART, a simple modular architecture research tool: Identification of signaling domains. Schultz J, Milpretz F, Bork O, Ponting CP, Proc Natl Acad Sci USA 1998 95 5857 5864 10.1073/pnas.95.11.5857 9600884 (Pubitemid 28248931)
27. Accurate prediction of solvent accessibility using neural networks-based regression. Adamczak R, Porollo A, Meller J, Proteins 2004 56 753 767 10.1002/prot.20176 15281128 (Pubitemid 39063318)
28. Preferred in vivo ubiquitination sites. Catic A, Collins C, Church GM, Ploegh HL, Bioinformatics 2004 20 3302 3307 10.1093/bioinformatics/bth407 15256413 (Pubitemid 40136763)
29. Differential ubiquitination defines the functional status of the tumor suppressor Smad4. Morén A, Hellman U, Inada Y, Imamura T, Heldin CH, Moustakas A, J Biol Chem 2003 278 33571 33582 10.1074/jbc.M300159200 12794086 (Pubitemid 37055811)
30. Identification of recurring protein structure microenvironments and discovery of novel functional sites around CYS residues. Wu S, Liu T, Altman RB, BMC Struct Biol 2010 10 4 22 10.1186/1472-6807-10-4 20122268
31. Lysine residues in N-terminal and C-terminal regions of human histone H2A are targets for biotinylation by biotinidase. Chew YC, Camporeale G, Kothapalli N, Sarath G, Zempleni J, J Nutr Biochem 2006 17 225 233 10.1016/j.jnutbio.2005. 05.003 16109483
32. TRAF6 and the three C-terminal Lysine sites on IRF7 are required for its ubiquitination-mediated activation by the tumor necrosis factor receptor family member latent membrane protein 1. Ning S, Campos AD, Darnay BG, Bentz GL, Pagano JS, Mol Cell Biol 2008 28 6536 6546 10.1128/MCB.00785-08 18710948
33. SUMOylation of the lens-epithelium-derived growth factor/p75 attenuates its transcriptional activity on the heat shock protein 27 promoter. Bueno MT, Garcia-Rivera JA, Kugelman JR, Morales E, Rosas-Acosta G, Llano M, J Mol Biol 2010 399 221 239 10.1016/j.jmb.2010.03.063 20382164
34. Surface accessibility of protein post-translational modifications. Pang CN, Hayen A, Wilkins MR, J Proteome Res 2007 6 1833 1845 10.1021/pr060674u 17428077 (Pubitemid 46814507)
35. Analysis of protein solvent interactions in glucose dehydrogenase from the extreme halophile Haloferax mediterranei. Britton KL, Baker PJ, Fisher M, Ruzheinikov S, Gilmour DJ, Bonete MJ, Ferrer J, Pire C, Esclapez J, Rice DW, Proc Natl Acad Sci USA 2006 103 4846 4851 10.1073/pnas.0508854103 16551747
36. The Gene Ontology (GO) database and informatics resource. Harris MA, Clark J, Ireland A, Lomax J, Ashburner M, Foulger R, Eilbeck K, Lewis S, Marshall B, Mungall C, et al. Nucleic Acids Res 2004 32 258 D261 10.1093/nar/gkh066 14681407
37. A genome-wide analysis of sumoylation-related biological processes and functions in human nucleus. Zhou F, Xue Y, Lu H, Chen G, Yao X, FEBS Lett 2005 579 3369 3375 10.1016/j.febslet.2005.04.076 15922331 (Pubitemid 40800283)
38. ECRbase: database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes. Loots G, Ovcharenko I, Bioinformatics 2007 23 122 124 10.1093/bioinformatics/btl546 17090579 (Pubitemid 46017865)
39. Conservation of protein phosphorylation sites within gene families and across species. Maathuis FJ, Plant Signal Behav 2008 3 1011 1013 19704437
40. Linear motifs: evolutionary interaction switches. Neduva V, Russell RB, FEBS Lett 2005 579 3342 3345 10.1016/j.febslet.2005.04.005 15943979 (Pubitemid 40804684)
41. PHOSIDA (phosphorylation site database): management, structural and evolutionary investigation, and prediction of phosphosites. Gnad F, Ren S, Cox J, Olsen JV, Macek B, Oroshi M, Mann M, Genome Biol 2007 8 250 10.1186/gb-2007-8-11-r250 18039369 (Pubitemid 351917499)
42. Prediction of post-translational glycosylation and phosphorylation of proteins from the amino acid sequence. Blom N, Sicheritz-Ponten T, Gupta R, Gammeltoft S, Brunak S, Proteomics 2004 4 1633 1649 10.1002/pmic.200300771 15174133 (Pubitemid 38738322)
43. SUMOsp: a web server for sumoylation site prediction. Xue Y, Zhou F, Fu C, Xu Y, Yao X, Nucleic Acids Res 2006 34 254 257 10.1093/nar/gkl207 16845005 (Pubitemid 44529774)
44. NetAcet: Prediction of N-terminal acetylation sites. Kiemer L, Bendtsen JD, Blom N, Bioinformatics 2005 21 1269 1270 10.1093/bioinformatics/bti130 15539450 (Pubitemid 40467956)
45. Protein kinase DYRK2 is a scaffold that facilitates assembly of an E3 ligase. Maddika S, Chen J, Nat Cell Biol 2009 11 379 381 10.1038/ncb1848 19337321
46. Identification of the main ubiquitination site in human erythroid a-spectrin. Galluzzi L, Paiardini M, Lecomte MC, Magnani M, FEBS Lett 2001 489 254 258 10.1016/S0014-5793(00)02333-4 11165260 (Pubitemid 32126419)
47. Proportion of solvent-exposed amino acids in a protein and rate of protein evolution. Lin YS, Hsu WL, Hwang JK, Li WH, Mol Biol Evol 2007 24 1005 1011 10.1093/molbev/msm019 17264066 (Pubitemid 46536711)
48. Local structural disorder imparts plasticity on linear motifs. Fuxreiter M, Tompa P, Simon I, Bioinformatics 2007 23 950 956 10.1093/bioinformatics/ btm035 17387114 (Pubitemid 47050581)