(a) E. histolytica AspRS dimer. One monomer is colored from blue (N-terminal) to red (C-terminal). The second monomer is in grey. The three helices (α6, α7, α8) of the hinge region between the N-terminal anticodon binding domain and the C-terminal Class II aaRS catalytic domain are separately labelled. The two monomers are crystallographically independent, but are essentially identical in conformation except for the angle at which an extended arm protrudes from the hinge region. The arms (highlighted by grey circles) are more than 15Å longer than the homologous structures of yeast AspRS, with the extension formed by an Entamoeba-specific 43 residue insertion. The active site is indicated by placement of a model for aspartyladenylate (blue CPK spheres) based on superposition of the binding mode seen in a bacterial AspRS:aspartyladenylate complex (PDB entry 1c0a).
(b) Model of tRNA binding to E. histolytica AspRS. Superposition of tRNA^Asp (gold surface) from the Yeast AspRS:tRNA complex (PDB 1asy) onto the current structure of E. histolytica AspRS (monomer B in dark blue, monomer A in light blue). The tRNA interacts only with one monomer. The 12 well-ordered residues from the Entamoeba-specific insertion are shown in magenta; 30 additional residues are not well-ordered in the crystal structure and are represented by dots.

Structure-based sequence alignment of cytosolic AspRS from E. histolytica (residues 10–544), yeast (residues 57–557), and human (residues 11–501). Secondary structure is shown for the current structure. Conserved features including the three signature motifs characteristic of all Class II aaRS are indicated in blue. An Entamoeba-specific 43-residue insertion extends the hinge region between the N-terminal anti-codon binding domain and the conserved Class II aaRS catalytic core domain. Sequence differences at the active site are indicated by red boxes.