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![[Figure 1]](dw5203fig1mag.jpg)
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Figure 1
(a) The canonical fold of retroviral protease based on EIAV PR (PDB entry 2fmb). Common structural elements in the N/C-terminal halves of the protein are indicated with colors: A1/A2 hairpins, green; B1/B2 loops, light orange; C1/C2 helices, pink; D1/D2 hairpins, lime. The side chains of the catalytic aspartates (from the DTG triads), shown in ball-and-stick representation, point towards the binding pocket. (b) Secondary-structure elements of the 3MI model shown in a slightly different view for better visibility. (c) Structural alignment of retroviral proteases. The color of the background indicates the secondary structure assigned by DSSP. Green denotes β-ladder, red denotes α-helix, magenta denotes 310-helix, blue denotes hydrogen-bonded turn, yellow denotes bend, dark green with a white font denotes isolated β-bridges and black denotes residues that are not present in a given model. The analysis is based on data retrieved from the Protein Data Bank (and identified by PDB code) for the HIV-1 PR apo structure (3hvp) and that with an inhibitor (4hvp), HIV-2 PR (1ivp), SIV PR (1az5), RSV PR (1bai), FIV PR (4fiv), EIAV PR (2fmb), HTLV-1 PR (3liy), XMRV PR (3slz) and M-PMV PR in a monomeric state (3sqf). M-PMV PR in a dimeric state is represented by chains B of 1M and 3MI. The last row represents the structural regions highlighted in (a). Secondary-structure elements (green arrows, β-strands, β; red cylinder, α-helix, α; magenta cylinder, 310-helix, η; black lines, loops, L) are shown above the sequences as pictograms for the present M-PMV PR 3MI model shown in (b). |
![[Figure 1]](dw5203fig1.jpg)
 | STRUCTURAL BIOLOGY |
ISSN: 2059-7983
