plosone-phylo
pone.0040786.g001.png
E2 UBC domain and phylogenetic tree of E2 family 3. A) The 3D structure of the E2 UBC domain is shown, along with the conserved residues in the E2 superfamily. The loops L7, L4 and L8, the catalytic cysteine, the invariant Trp, the HPN (His-Pro-Asn) motif, as well as the proline-rich motif (PPxxP) are indicated as reported in (26). The structure has been adapted by the 3D X-ray structure of Ube2g2 (PDB code 2CYX). B) The unrooted phylogenetic tree was obtained by PHYLIP package from multiple sequence alignments of E2 family 3 sequences, reported in Table S1. For each protein a label referred to the different sub-families (R, R1, R2, G1, G2 and #) is reported. In the lower-left box the conservation degree of each residues of L7 loop is indicated according to different scoring function. The consensus pattern for L4, L7 and L8 are also reported. C) The 3D structure of Ube2g2 is used as a reference and each residue coloured with different shade of green according to Cα rmsf values calculated from the MD simulations (from light green to dark green for increasing rmsf values). The rmsf intensity of each residue of L7 is indicated on the primary sequence of L7 in the upper box. The data from MD simulations of each E2 enzymes of family 3 considered in this study are reported in Text S1.
pone.0040786.g001.png
E2 UBC domain and phylogenetic tree of E2 family 3. A) The 3D structure of the E2 UBC domain is shown, along with the conserved residues in the E2 superfamily. The loops L7, L4 and L8, the catalytic cysteine, the invariant Trp, the HPN (His-Pro-Asn) motif, as well as the proline-rich motif (PPxxP) are indicated as reported in (26). The structure has been adapted by the 3D X-ray structure of Ube2g2 (PDB code 2CYX). B) The unrooted phylogenetic tree was obtained by PHYLIP package from multiple sequence alignments of E2 family 3 sequences, reported in Table S1. For each protein a label referred to the different sub-families (R, R1, R2, G1, G2 and #) is reported. In the lower-left box the conservation degree of each residues of L7 loop is indicated according to different scoring function. The consensus pattern for L4, L7 and L8 are also reported. C) The 3D structure of Ube2g2 is used as a reference and each residue coloured with different shade of green according to Cα rmsf values calculated from the MD simulations (from light green to dark green for increasing rmsf values). The rmsf intensity of each residue of L7 is indicated on the primary sequence of L7 in the upper box. The data from MD simulations of each E2 enzymes of family 3 considered in this study are reported in Text S1.