Systematic identification of novel protein domain families associated with nuclear functions

European Molecular Biology Laboratory, 69114 Heidelberg, Germany.
Genome Research (Impact Factor: 14.63). 02/2002; 12(1):47-56.
Source: PubMed


A systematic computational analysis of protein sequences containing known nuclear domains led to the identification of 28 novel domain families. This represents a 26% increase in the starting set of 107 known nuclear domain families used for the analysis. Most of the novel domains are present in all major eukaryotic lineages, but 3 are species specific. For about 500 of the 1200 proteins that contain these new domains, nuclear localization could be inferred, and for 700, additional features could be predicted. For example, we identified a new domain, likely to have a role downstream of the unfolded protein response; a nematode-specific signalling domain; and a widespread domain, likely to be a noncatalytic homolog of ubiquitin-conjugating enzymes.

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Available from: Tobias Doerks, Jun 03, 2014
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    • "The RWD domain of Gcn2 is related to the ubiquitin-conjugating enzymes (UBC) domain, forming the clade of Ubiquitin-conjugating enzyme/RWD-like domain (InterPro IPR016135, [65]), predicted to have a function in protein–protein interaction [66]. RWD domains including the Gcn2 RWD domain, however, lack the catalytic cysteine residue critical for ubiquitin-conjugating activity [66]. The structure of the GCN2 RWD domain has been solved by NMR [63]. "
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    Biochimica et Biophysica Acta (BBA) - Molecular Cell Research 01/2014; · 5.02 Impact Factor
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    • "Most of Ash1 SET proteins have one SET domain that is preceded by an AWS (associated with SET) domain and followed by a cysteine-rich PostSET domain except for the members in II-2 group that lack the AWS domain (Fig. 1). The AWS domain is a subdomain of the PreSET domain that contains several highly conserved Cys residues, which are often found in association with the SET domain, suggesting a role in methylation of lysine residues in histones and other proteins (Doerks et al. 2002). Compared to other classes of SET domain proteins, in which the SET domain is found very near the C terminus of the protein (Springer et al. 2003; Ng et al. 2007), the members in the II-1 group possess a relatively centrally located SET domain (Fig. 1). "
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    • "In this study, a homologue of P. monodon SARIP1 cDNA and gene were successfully identified. The deduced PmSARIP1 protein contained an RWD domain which is functionally proposed as a protein–protein interaction domain (Doerks et al., 2002). A highly conserved YPXXXP motif of the RWD domain (Nameki et al., 2004) is also found in the deduced PmSARIP1 protein. "
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