Bioinformatical detection of recognition factors for ubiquitin and SUMO

Methods in Molecular Biology

Volumn 832, Issue , 2012, Pages 249-261

  Vogt, Benjamin ^a,b   Hofmann, Kay ^b  

^a UNIVERSITY OF COLOGNE   (Germany)

^b MILTENYI BIOTEC GMBH   (Germany)

Author keywords

Homology domain; Linear motif; SIM; SUMO; UBD; Ubiquitin

Indexed keywords

SUMO PROTEIN; UBIQUITIN;

AMINO ACID SEQUENCE; ARTICLE; BINDING SITE; BIOLOGY; CHEMISTRY; INTERNET; METABOLISM; METHODOLOGY; PROTEIN BINDING; PROTEIN DATABASE; PROTEIN MOTIF; PROTEIN TERTIARY STRUCTURE; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; SUMOYLATION; UBIQUITINATION;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; BINDING SITES; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; INTERNET; PROTEIN BINDING; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SIGNAL TRANSDUCTION; SMALL UBIQUITIN-RELATED MODIFIER PROTEINS; SUMOYLATION; UBIQUITIN; UBIQUITINATION;

EID: 84858217420     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-474-2_18     Document Type: Article

References (28)

1. Andersen KM, Hofmann K, Hartmann- Petersen R (2005) Ubiquitin-binding proteins: Similar, but different. Essays Biochem 41 : 49-67.
2. Hurley JH, Lee S, Prag G (2006) Ubiquitinbinding domains. Biochem J 399 :361-372.
3. Dikic I, Wakatsuki S, Walters KJ (2009) Ubiquitin-binding domains - From structures to functions. Nat Rev Mol Cell Biol 10 : 659-671.
4. Hofmann K (2009) Ubiquitin-binding domains and their role in the DNA damage response. DNA Repair (Amst) 8 :544-556.
5. Minty A, Dumont X, Kaghad M, Caput D (2000) Covalent modifi cation of p73alpha by SUMO-1. Two-hybrid screening with p73 identifi es novel SUMO-1-interacting proteins and a SUMO-1 interaction motif. J Biol Chem 275 :36316-36323.
6. Song J, Durrin LK, Wilkinson TA et al (2004) Identifi cation of a SUMO-binding motif that recognizes SUMO-modifi ed proteins. Proc Natl Acad Sci USA 101 :14373-14378.
7. Hecker CM, Rabiller M, Haglund K et al (2006) Specifi cation of SUMO1- and SUMO2- interacting motifs. J Biol Chem 281 : 16117-16127.
8. Uzunova K, Gottsche K, Miteva M et al (2007) Ubiquitin-dependent proteolytic control of SUMO conjugates. J Biol Chem 282 : 34167-34175.
9. Miteva M, Keusekotten K, Hofmann K et al (2011) Sumoylation as a signal for polyubiquitylation and proteasomal degradation. Subcell Biochem 54 :195-214.
10. Trempe JF, Chen CX, Grenier K et al (2009) SH3 domains from a subset of BAR proteins defi ne a Ubl-binding domain and implicate parkin in synaptic ubiquitination. Mol Cell 36 :1034-1047.
11. Bucher P, Karplus K, Moeri N, Hofmann K (1996) A fl exible motif search technique based on generalized profi les. Comput Chem 20 : 3-23.
12. Eddy SR (1998) Profi le hidden Markov models. Bioinformatics 14 :755-763.
13. Finn RD, Mistry J, Tate J et al (2011) The Pfam protein families database. Nucleic Acids Res 38 :D211-222.
14. Hunter S, Apweiler R, Attwood TK et al (2009) InterPro: The integrative protein signature database. Nucleic Acids Res 37 :D211-215.
15. Letunic I, Doerks T, Bork P (2009) SMART 6: recent updates and new developments. Nucleic Acids Res 37 :D229-232.
16. Sigrist CJ, Cerutti L, de Castro E et al (2011) PROSITE, a protein domain database for functional characterization and annotation. Nucleic Acids Res 38 :D161-166.
17. Wilson D, Pethica R, Zhou Y et al (2009) SUPERFAMILY - sophisticated comparative genomics, data mining, visualization and phylogeny. Nucleic Acids Res 37 :D380-386.
18. Reverter D, Lima CD (2005) Insights into E3 ligase activity revealed by a SUMO-RanGAP1- Ubc9-Nup358 complex. Nature 435 : 687-692.
19. Song J, Zhang Z, Hu W, Chen Y (2005) Small ubiquitin-like modifi er (SUMO) recognition of a SUMO binding motif: A reversal of the bound orientation. J Biol Chem 280 : 40122-40129.
20. Sekiyama N, Ikegami T, Yamane T et al (2008) Structure of the small ubiquitin-like modifi er (SUMO)-interacting motif of MBD1- containing chromatin-associated factor 1 bound to SUMO-3. J Biol Chem 283 : 35966-35975.
21. Escobar-Cabrera E, Okon M, Lau DK et al (2011) Characterizing the N- and C-terminal SUMO interacting motifs of the scaffold protein DAXX. J Biol Chem.
22. Altschul SF, Madden TL, Schaffer AA et al (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res 25 :3389-3402.
23. Edgar RC (2004) MUSCLE: A multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5 :113.
24. Katoh K, Kuma K, Toh H, Miyata T (2005) MAFFT version 5: Improvement in accuracy of multiple sequence alignment. Nucleic Acids Res 33 :511-518.
25. Gould CM, Diella F, Via A et al (2011) ELM: The status of the 2010 eukaryotic linear motif resource. Nucleic Acids Res 38 :D167-180.
26. Linding R, Russell RB, Neduva V, Gibson TJ (2003) GlobPlot: Exploring protein sequences for globularity and disorder. Nucleic Acids Res 31 :3701-3708.
27. Dosztanyi Z, Csizmok V, Tompa P, Simon R (2005) IUPred: web server for the rediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics 21 :3433-3434.
28. Schneider TD, Stephens RM (1990) Sequence logos: A new way to display consensus sequences. Nucleic Acids Res 18 :6097-6100.