Fig 7. Sequences and structures of Ty1 PR and representative retroviral and retroviral-like proteases.

(A) Sequences of Ty1, DNA damage-inducible protein 1 (Ddi1), equine infectious anemia virus (EIAV), xenotropic murine leukemia virus-related virus (XMRV), and human immunodeficiency virus type 1 (HIV-1) proteases were aligned. Arrangement of secondary structural elements is shown based on prediction for Ty1 PR, and based on crystal structures of Ddi1, EIAV, XMRV, and HIV-1 PRs, using DSSP (dictionary of protein secondary structure) images available in Protein Data Bank. Sequence numbering is shown for Ty1 PR. β-sheets and α-helices are indicated by orange and red, respectively. D-S/T-G-A catalytic motif residues are bold and underlined. (B) Cartoon representations are shown based on crystal structures of HIV-1, XMRV, and Ddi1 PRs, and based on homology model structure of Ty1 PR (41–164 residues). Upper panel shows the front views of the proteases, whereas bottom panel shows the enlarged views of dimer interfaces, together with the organizations of β-sheets. Additional helical inserts in the proximities of flaps (shown by arrows) are present only in the case of Ddi1 and Ty1 PRs. Catalytic aspartates are shown sticks and dots, while the monomers are differentiated by lighter and darker shades. N- and C-terminal extensions are not shown for Ty1 PR, structures of the full-length protease are shown in S3 Fig.