KEPE - A motif frequently superimposed on sumoylation sites in metazoan chromatin proteins and transcription factors

Bioinformatics

Volumn 25, Issue 1, 2009, Pages 1-5

  Diella, Francesca ^a   Chabanis, Sophie ^b   Luck, Katja ^a   Chica, Claudia ^a   Ramu, Chenna ^c   Nerlov, Claus ^d   Gibson, Toby J ^a  

^a EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^b European School Karlsruhe   (Germany)

^c MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

^d EUROPEAN MOLECULAR BIOLOGY LABORATORY EMBL   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

CCAAT ENHANCER BINDING PROTEIN; CELL PROTEIN; DNA TOPOISOMERASE; HEPATOCYTE NUCLEAR FACTOR 1ALPHA; HISTONE DEACETYLASE 4; HOMEODOMAIN INTERACTING PROTEIN KINASE 2; KRUPPEL LIKE FACTOR; MIXED LINEAGE LEUKEMIA PROTEIN; NUCLEAR PROTEIN; PROTEIN C JUN; PROTEIN CHD 8; PROTEIN FOS; TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR MAF; TRANSCRIPTION FACTOR NFAT; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ARTICLE; CELLULAR DISTRIBUTION; CHROMATIN; GENETIC CONSERVATION; METAZOON; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN EXPRESSION; PROTEIN MOTIF; SEQUENCE ANALYSIS; SPECIES DIFFERENCE; SUMOYLATION;

METAZOA;

EID: 58149163609     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn594     Document Type: Article

References (33)

1. Camon,E. et al. (2004) The gene ontology annotation (GOA) database: Sharing knowledge in Uniprot with Gene Ontology. Nucleic Acids Res., 32, D262-D266.
2. Chica,C. et al. (2008) A trec-based conservation scoring method for short linear motifs in multiple alignments of protein sequences. BMC Bioinformatics, 9, 229.
3. Copley,R.R. (2005) The EH1 motif in metazoan transcription factors. BMC Genomics, 6, 169.
4. Diella,F. et al. (2008) Understanding eukaryotic linear motifs and their role in cell signaling and regulation. Front. Biosci., 13 6580-6603.
5. Dosztanyi,Z. et al. (2005) IUPred: Web server for the prediction of intrinsically unstructured regions of proteins based on estimated energy content. Bioinformatics, 21, 3433-3434.
6. Dye,B.T. and Schulman,B.A. (2007) Structural mechanisms underlying post-translational modification hy ubiquitin-like proteins. Annu. Rev. Biophys. Biomol. Struct., 36, 131-150.
7. Echols,N. et al. (2002) Comprehensive analysis of amino acid and nucleotide composition in eukaryotic genomes, comparing genes and pseudogenes. Nucleic Acids Res., 30, 2515-2523.
8. Fuxreiter,M. et al. (2007) Local structural disorder imparts plasticity on linear motifs. Bioinformatics, 23, 950-956.
9. Geiss-Friedlander,R. and Melchior,F. (2007) Concepts in sumoylation: A decade on Nat. Rev. Mol. Cell Biol., 8, 947-956.
10. Gibson,T.J. and Spring,J. (1998) Genetic redundancy in vertebrates: polyploidy and persistence of genes encoding multidomain proteins. Trends Genet., 14, 46-40.
11. Girdwood,D.W. et al. (2004) SUMO and transcriptional regulation. Semin. Cell Dev. Biol., 15, 201-210.
12. Harris,M.A. et al. (2004) The Gene Ontology (GO) database and informatics resource. Nucleic Acids Res., 32, D258-D261.
13. Hietakangas,V. et al. (2006) PDSM, a motif for phosphorylation-dependent SUMO modification. Proc. Natl Acad Sci. USA 103, 45-50.
14. Hong,E.L. et al. (2008) Gene Ontology annotations at SGD: New data sources and annotation methods. Nucleic Acids Res., 36, D577-D581.
15. Hubbard,T.J. et al. (2007) Ensembl 2007. Nucleic Acids Res., 35, D610-D617.
16. Kasahara,M. (2007) The 2R hypothesis: An update, Curr. Opin. Immunol. 19, 547-552.
17. Kim,J. et al. (2002) Transcriptional activity of CCAAT/ enhancer-binding proteins is controlled by a conserved inhibitory domain that is a target for sumoylation. J. Biol. Chem., 277, 38037-38044.
18. Letunic,I. et al. (2006) SMART 5: Domains in the context of genomes and networks. Nucleic Acids Res., 34, D257-D260.
19. Meyer,A. and Van de Peer,Y. (2005) From 2R to 3R: Evidence for a fish-specific genome duplication (FSGD). BioEssays, 27, 937-945.
20. Michael,S. et al. (2008) Discovery of candidate KEN-box motifs using cell cycle keyword enrichment combined with native disorder prediction and motif conservation. Bioinformatics, 24, 453-457.
21. Neduva,V. and Russell,R.B. (2005) Linear motifs: Evolutionary interaction switches. FEBS Lett., 579, 3342-3345.
22. Nerlov,C. (2008) C/EBPs: Recipients of extracellular signals through proteome modulation. Curr. Opin. Cell Biol., 20, 180-185.
23. Puntervoll,P. et al. (2003) ELM server: A new resource for investigating short functional sites in modular eukaryotic proteins. Nucleic Acids Res., 31, 3625-3630.
24. Ramu,C. (2003) SIRW: A web server for the simple indexing and retrieval system that combines sequence motif searches with keyword searches. Nucleic Acids Res., 31, 3771-3774.
25. Rodriguez,M.S. et al. (2001) SUMO-1 conjugation in vivo requires both a consensus modification motif and nuclear targeting. J. Biol. Chem., 276, 12654-12659.
26. Rosas-Acosta,G. et al. (2005) A universal strategy for proteomic studies of SUMO and other ubiquitin-like modifiers. Mol. Cell Proteomics, 4, 56-72.
27. Sammut,S.J. et al. (2008) Pfam 10 years on: 10 000 families and still growing. Brief. Bioinform., 9, 210-219.
28. Stankovic-Valentin,N. et al. (2007) An acetylation/ deacetylation-SUMOylation switch through a phylogenetically conserved psiKXEP motif in the tumor suppressor HIC1 regulates transcriptional repression activity. Mol. Cell. Biol., 27, 2661-2675.
29. The_Gene_Ontology_Consortium (2008) The Gene Ontology project in 2008. Nucleic Acids Res., 36, D440-D444.
30. The_UniProt_Consortium (2008) The universal protein resource (UniProt). Nucleic Acids Res., 36, D190-D195.
31. Watts,F.Z. (2004) SUMO modification of proteins other than transcription factors. Semin. Cell Dev. Biol., 15, 211-220.
32. Yang,S.H. et al. (2006) An extended consensus motif enhances the specificity of substrate modification by SUMO. EMBO J., 25, 5093-5093.
33. Zhou,F. et al. (2006) A general user interface for prediction servers of proteins' post-translational modification sites. Nat. Protoc., 3, 1318-1321.