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1.
FIGURE 1.

FIGURE 1. From: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space.

Example of high resolution (0.98 Å) data. A region of the AVP structure is depicted with the 2FoFc map contoured at 1.5 σ. The amino acid residues, Phe-29, Pro-30, Gly-31, and Phe-32, are conserved among AVP genes and lie in the His activation pathway. All figures were generated with PyMOL (49).

Mary Lynn Baniecki, et al. J Biol Chem. 2013 January 18;288(3):2081-2091.
2.
FIGURE 6.

FIGURE 6. From: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space.

Structural transition in the activation of AVP by pVIc via the activation pathways. A top view of the aligned structures is shown in graphic form. In A, AVP is shown with the residues involved in the common pathway colored green, the His-54 pathway colored yellow, and the Tyr-84 pathway colored blue. His-54 (pink) and Tyr-84 (tan) are shown in stick form. In B, the orientations of those residues are depicted in the AVP-pVIc structure. The cation-π interaction of His-54 and Tyr-84 is shown by the overlapping side chains, and pVIc is colored red.

Mary Lynn Baniecki, et al. J Biol Chem. 2013 January 18;288(3):2081-2091.
3.
FIGURE 5.

FIGURE 5. From: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space.

The NT- and CT-pockets on AVP and the AVP-pVIc complex into which the two termini of pVIc bind. In A, the accessible surface of AVP is shown with the active site cysteine colored orange, residues that form the NT-pocket in the AVP-pVIc complex colored dark pink, and those residues whose positions could be determined in the structure that aid in forming the CT binding pocket colored tan. In B, pVIc is shown in green with the residues that interact in the binding pockets shown as van der Waals spheres; the NT-pocket residues are in olive, and the CT-pocket residues are in blue. Those residues of pVIc that aid in forming the CT-pocket are shown as a light brown surface. In C, the AVP-pVIc complex is shown with the NT- and CT-pockets colored as in A and the pVIc colored as in B. Three residues that aid in forming the CT-pocket are undefined in the AVP structure.

Mary Lynn Baniecki, et al. J Biol Chem. 2013 January 18;288(3):2081-2091.
4.
FIGURE 4.

FIGURE 4. From: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space.

Movements of amino acids in the activation of AVP by pVIc. In A, the orientation of the Cys-His-Glu triad of the AVP-pVIc complex is shown. In B, that triad in AVP is shown along with the position of the His from the AVP-pVIc complex. The arrow indicates the rotation and distance His-54 must move to align with the catalytic Cys. In C, the catalytic triad of AVP-pVIc and Tyr-84 is shown in an orientation to highlight the cation-π interaction of Tyr-84 with His-54 (green mesh). In D, the location of Tyr-84 (red) in AVP, with an arrow showing the direction and distance it must move to form the cation-π interaction in AVP-pVIc, is shown. In E and F, the occlusion of the active site groove in AVP by the loop containing His-54 is shown. In E, the location of the loop relative to the active site residues in AVP is shown. The residues extending across the loop blocking the groove (Gly-52 and Val-53) are colored red, and the active site residues are shown in stick form and colored green. In F, the location of the same residues in the AVP-pVIc complex structure indicating that the groove is no longer blocked is shown. Unblocking the groove also enabled His-54 to move opposite the Cys-122 to render it nucleophilic.

Mary Lynn Baniecki, et al. J Biol Chem. 2013 January 18;288(3):2081-2091.
5.
FIGURE 2.

FIGURE 2. From: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space.

Structural comparisons between AVP and the AVP-pVIc complex. A and B, secondary structure elements of AVP are depicted below the amino acid sequence for both AVP (A) and the AVP-pVIc complex (B). The two structures, AVP and the AVP-pVIc complex, were superimposed by least squares fitting. For C and D, helices are colored red, strands are colored yellow, and coils are colored green. In C, the secondary structure representation of AVP is shown. In D, the secondary structure representation of the AVP-pVIc complex is shown with the pVIc peptide depicted in magenta. N-term, N terminus; C-term, C terminus. In E and F, the aligned structures of C and D have been rotated ∼60° on the x axis and 20° on the y axis to highlight the structural changes. In E, the aligned structural graphic of AVP is shown with residues colored by r.m.s.d. using a spectrum from blue, similar in structure, through red, highly different in structure. Those amino acid residues that are essentially identical in structure are colored tan. In F, the alignment of AVP-pVIc with AVP is shown with residues colored as in C.

Mary Lynn Baniecki, et al. J Biol Chem. 2013 January 18;288(3):2081-2091.
6.
FIGURE 3.

FIGURE 3. From: Regulation of a Viral Proteinase by a Peptide and DNA in One-dimensional Space.

Repositioning of His-54 and comparisons of the active site of AVP-pVIc complexes with the “active” site of AVP. Repositioning of His-54 was determined. In A, residues 52 through 56 of AVP are shown with the 2FoFc electron density map describing the model contoured at 1.5 σ around the residues. In B, residues 52 through 56 of the AVP-pVIc complex are shown with the 2FoFc electron density map describing the model contoured at 1.5 σ around the residues. The nucleophile Cys-122 is shown without electron density to indicate its position relative to His-54 in both A and B. Nitrogen atoms are colored blue, oxygen atoms are colored red, sulfur atoms are colored light orange, and carbon atoms are colored gray except for those on His-54, which are colored yellow. Comparisons of the active site of AVP-pVIc complexes with the “active” site of AVP and repositioning of His-54 are shown. In C, the secondary structure representation of the AVP-pVIc complex is shown with the residues involved in catalysis shown in stick form and colored green. The pVIc peptide is colored yellow. In D, the secondary structure of AVP is shown with the same residues depicted in stick form and colored red. In C and D, the positions of the residues that block the active site groove in AVP are colored semitransparent spheres. In E, the positions of the amino acids involved in catalysis in AVP (red) and in the AVP-pVIc complex (green) are overlaid to reveal the differences in position. Only His-54 and Tyr-84 are in different positions in the two structures. Hydrogen bonds from Glu-71 to His-54 and His-54 to Cys-122 are depicted as dashed lines.

Mary Lynn Baniecki, et al. J Biol Chem. 2013 January 18;288(3):2081-2091.

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