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Bioinformatics Advance Access published online on December 1, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti767
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Published by Oxford University Press 2005
Received May 4, 2005
Revised November 1, 2005
Accepted November 4, 2005

Discovery note

The ASCH superfamily: novel domains with a fold related to the PUA domain and a potential role in RNA metabolism

Lakshminarayan M. Iyer 1, A. Maxwell Burroughs 1, and L. Aravind 1 *

1 National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA

* To whom correspondence should be addressed.
L. Aravind, E-mail: aravind{at}ncbi.nlm.nih.gov


  Abstract

Several studies show that transcription coactivators are often bi-functional ribonucleoprotein complexes that also regulate pre-mRNA processing and splicing decisions. Using sensitive sequence profile searches and structural comparisons we show that the C-terminal domain of the human coactivator protein ASC-1 defines a novel superfamily, the ASC-1 homology (ASCH) domain. The approximately 110 amino acid long ASCH domains are widely represented in all the three superkingdoms of life and several prokaryotic viruses. We show that the ASCH superfamily adopts a beta-barrel fold similar to the PUA domain superfamily. Using multiple lines of evidence, we suggest that members of the ASCH superfamily are likely to function as RNA-binding domains in contexts related to co-activation, RNAprocessing and possibly prokaryotic translation regulation. Structural analysis of ASCH domains reveals the presence of a potential RNA-binding cleft associated with a conserved sequence motif, which is characteristic of this superfamily. Despite their similar structure, the ASCH and PUA domains appear to occupy distinct functional niches, with the former domains typically occurring in a standalone form in polypeptides, and the latter domains showing fusions to a variety of RNA-modifying enzymes.


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