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In Silico Biology 5, 0034 (2005); ©2005, Bioinformation Systems e.V.  



A new domain family in the superfamily of alkaline phosphatases

Rana Bhadra1, Narayanaswamy Srinivasan1* and Shashi B. Pandit2

1 Molecular Biophysics Unit, Indian Institute of Science, Bangalore 560 012, India
2 Present address: Center of Excellence in Bioinformatics, University at Buffalo, New York, USA

* Corresponding author; Email: ns@mbu.iisc.ernet.in


Edited by E. Wingender; received March 06, 2005; revised May 13, 2005; accepted May 15, 2004; published May 21, 2005


Abstract

During the course of our large-scale genome analysis a conserved domain, currently detectable only in the genomes of Drosophila melanogaster, Caenorhabditis elegans and Anopheles gambiae, has been identified. The function of this domain is currently unknown and no function annotation is provided for this domain in the publicly available genomic, protein family and sequence databases. The search for the homologues of this domain in the non-redundant sequence database using PSI-BLAST, resulted in identification of distant relationship between this family and the alkaline phosphatase-like superfamily, which includes families of aryl sulfatase, N-acetylgalactosomine-4-sulfatase, alkaline phosphatase and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase (iPGM). The fold recognition procedures showed that this new domain could adopt a similar 3-D fold as for this supefamily. Most of the phosphatases and sulfatases of this superfamily are characterized by functional residues Ser and Cys respectively in the topologically equivalent positions. This functionally important site aligns with Ser/Thr in the members of the new family. Additionally, set of residues responsible for a metal binding site in phosphatases and sulphtases are conserved in the new family. The in-depth analysis suggests that the new family could possess phosphatase activity.


Keywords: functional domains, phosphatases, protein domains, sequence analysis, sulfatases