SitEx: a computer system for analysis of projections of protein functional sites on eukaryotic genes

Abstract

Search of interrelationships between the structural-functional protein organization and exon structure of encoding gene provides insights into issues concerned with the function, origin and evolution of genes and proteins. The functions of proteins and their domains are defined mostly by functional sites. The relation of the exon-intron structure of the gene to the protein functional sites has been little studied. Development of resources containing data on projections of protein functional sites on eukaryotic genes is needed. We have developed SitEx, a database that contains information on functional site amino acid positions in the exon structure of encoding gene. SitEx is integrated with the BLAST and 3DExonScan programs. BLAST is used for searching sequence similarity between the query protein and polypeptides encoded by single exons stored in SitEx. The 3DExonScan program is used for searching for structural similarity of the given protein with these polypeptides using superimpositions. The developed computer system allows users to analyze the coding features of functional sites by taking into account the exon structure of the gene, to detect the exons involved in shuffling in protein evolution, also to design protein-engineering experiments. SitEx is accessible at http://www-bionet.sscc.ru/sitex/. Currently, it contains information about 9994 functional sites presented in 2021 proteins described in proteomes of 17 organisms.

Figure 1.

A schematic representation of the SitEx system. Headings correspond to table names. Table primary keys are in yellow. Foreign keys fields are in red. Type of field is next to its name. INT, numerical value; VARCHAR, character value; TEXT, text value.

Figure 2.

Superimposition of the 1U8F structure. Superimposition of the query 1U8F structure (d-glyceraldehyde-3-phosphate dehydrogenase, in grey) with the polypeptide encoded by the sixth exon of alcohol dehydrogenase that was found in SitEx database and incorporated into the 1D1T structure (alcohol dehydrogenase, in pink). The functional sites amino acids presented in found polypeptide were coloured on the sequence (the alignment of sequences presented for superimposed polypeptides is presented below) as well as on the 3D structure. The parameters of alignment are Z-score 3.9, RMSD 3.4. It seems to be a convergence due to the similar NAD-binding site because no sequence similarity was found even for exon sequences.

Figure 3.

Visualization of internal pages from SitEx. (A) exon description page. The start and end positions of the exon are shown. They correspond to the Ensembl numeration. AA, amino acid; bp, base pair; (B) a fragment of a page for description of functional site; (C) a query page; (D) result of query using the keyword ‘ATP’ in the ligand line. The functional site, information on the sequence, list of exons, which encode the sequence, their length measured in codons is displayed.