Title

Authors

Sunil Archak¹* & Javaregowda Nagaraju²

Affiliation

¹Division of Genomic Resources, National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi INDIA; ²Laboratory of Molecular Genetics, Centre for DNA Fingerprinting and Diagnostics, Hyderabad India

Email

sunil.archak@gmail.com; *Corresponding author

Article Type

Hypothesis

Date

Received January 19, 2014; Accepted January 26, 2014; Published February 19, 2014

Eicosapenta peptide repeats (EPRs) occur exclusively in flowering plant genomes and exhibit very high amino acid residue conservation across occurrence. DNA and amino acid sequence searches yielded no indications about the function due to absence of similarity to known sequences. Tertiary structure of an EPR protein coded by rice (Oryza sativa japonica) cDNA (GI: 32984786) was determined based on ab initio methodology in order to draw clues on functional significance of EPRs. The resultant structure comprised of seven α-helices and thirteen anti-parallel β-sheets. Surface-mapping of conserved residues onto the structure deduced that (i) regions equivalent to β12 and α4 with α4-β7 junction actually represent conserved regions as well as two functional sites, (ii) the primary function of EPR protein could be Ca2+ binding, and (iii) the putative EPR Ca2+ binding domain is structurally similar to calcium-binding domains of plant lectins. Additionally, the phylogenetic analysis showed an evolving taxa-specific distribution of EPR proteins observed in some GNA-like lectins. 

Keywords

ab initio structure prediction, function prediction, repeat proteins, surface mapping, taxa-specific.

Citation

Archak & Nagaraju,   Bioinformation 10(2): 063-067 (2014)
 

Edited by

P Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.