Group II intron EcI5 and its IEP. (A) Predicted secondary structure of EcI5 RNA; data adapted from Dai and Zimmerly (2002b). The structure consists of six double-helical domains (DI–DVI). The 5′- and 3′-splice sites are indicated by arrows. The putative Shine–Dalgarno (SD) sequence, initiation and termination codons of the intron ORF, and sequences involved in tertiary interactions (Greek letters) are boxed. The inset (top right) shows the predicted secondary structure of DIVb of the EcI5-ΔORF intron, which has an MluI site (boxed) added at the site of the ORF deletion. (B) EcI5 IEP. Conserved protein domains shared with other group II IEPs are RT, containing conserved amino acid sequence blocks 1–7 characteristic of the finger and palm regions of retroviral RTs; X, region associated with maturase activity corresponding in part to the RT thumb; D, DNA binding; and En, DNA endonuclease. (0) region conserved in RTs of non-LTR retroelements. Conserved amino acids that are sites of mutations and the boundaries of the ΔD/En and ΔEn truncations analyzed in the present work are shown below.
