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Open Access Research article

Molecular evolution of dihydrouridine synthases

Joanna M Kasprzak2, Anna Czerwoniec2 and Janusz M Bujnicki12*

Author Affiliations

1 Laboratory of Bioinformatics and Protein Engineering, International Institute of Molecular and Cell Biology, Trojdena 4, PL-02-109, Warsaw, Poland

2 Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Umultowska 89, PL-61-614, Poznan, Poland

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BMC Bioinformatics 2012, 13:153  doi:10.1186/1471-2105-13-153

Published: 28 June 2012

Additional files

Additional file 1:

MSA_tree.aln. Multiple sequence alignment of all DUS sequences from the COG/KOG database used to calculate a phylogenetic tree. Sequences are denoted by the COG/KOG number, species’ name (six-letter abbreviation for genus or species e.g. Bacsub for B.subtilis), followed by the protein name (if assigned) or the sequence name from COG/KOG database. The variable termini and non-conserved insertions have been removed.

Format: ALN Size: 49KB Download file

Open Data

Additional file 2:

structures_superposition.pse. Superposition of DHPDH, DHODH, TthDus and hDus2 model structures. Active site residues, cofactors and ligands are shown in sticks representation and each structure is shown in a different color (DHPDH in blue, DHODH in magenta, TthDus in green and hDus2 in grey). The file is a PyMOL session.

Format: PSE Size: 3MB Download file

Open Data

Additional file 3:

Dus_models_RNAbindingSites.pse. Superposition of structural models of DUS representatives. All proteins are shown in surface representation and putative RNA binding sites are highlighted by different colors. Additionally each protein is shown in surface representation and colored by residue conservation within closest homologs calculated by the Consurf method (the color pattern is the same as in Figure 7). The file is a PyMOL session.

Format: PSE Size: 10.3MB Download file

Open Data