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High-resolution structure of a retroviral protease folded as a monomer.

Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M - Acta Crystallogr. D Biol. Crystallogr. (2011)

Bottom Line: The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins.The overall fold of the protein follows the retropepsin canon, but the C(α) deviations are large and the active-site 'DTG' loop (here NTG) deviates up to 2.7 Å from the standard conformation.This structure of a monomeric retropepsin determined at high resolution (1.6 Å) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including AIDS.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland.

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Electrostatic potential surface of retroviral protease protomers. The M-PMV PR monomer (a) is shown in the same orientation and on the same scale as the HIV-1 PR protomer (b) extracted from the dimeric molecule (PDB entry 3hvp). The complete HIV-1 PR dimer is generated by the action of a vertical dyad, which creates a second copy facing the first molecule on the right. In this view, the N- and C-­termini (missing in M-PMV PR) are at the bottom and the flap loops are at the top. The active-site cavity is marked by the Asn26/Asp25 residue (ball-and-stick representation). In M-PMV PR the cavity is completely covered by the curled flap. The area of positive potential on this M-PMV PR surface is influenced by the D26N substitution, but it is of note that this mutation does not influence the tendency of the protein to fold as a monomer. The electrostatic potential (negative, red; positive, blue) was calculated in APBS (Baker et al., 2001 ▶).
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fig4: Electrostatic potential surface of retroviral protease protomers. The M-PMV PR monomer (a) is shown in the same orientation and on the same scale as the HIV-1 PR protomer (b) extracted from the dimeric molecule (PDB entry 3hvp). The complete HIV-1 PR dimer is generated by the action of a vertical dyad, which creates a second copy facing the first molecule on the right. In this view, the N- and C-­termini (missing in M-PMV PR) are at the bottom and the flap loops are at the top. The active-site cavity is marked by the Asn26/Asp25 residue (ball-and-stick representation). In M-PMV PR the cavity is completely covered by the curled flap. The area of positive potential on this M-PMV PR surface is influenced by the D26N substitution, but it is of note that this mutation does not influence the tendency of the protein to fold as a monomer. The electrostatic potential (negative, red; positive, blue) was calculated in APBS (Baker et al., 2001 ▶).

Mentions: When the present M-PMV PR molecule is viewed from the direction of its absent dimerization partner, one sees a uniformly positively charged surface (Fig. 4 ▶). This is different from a similar view of the HIV-1 PR protomer, in which both charges and hydrophobic patches are seen, and may partly explain why in the absence of substrate/inhibitor the M-PMV protein can stably exist as a monomer, at least with the D26N mutation. Fig. 4 ▶ also illustrates that the curled flap closely covers the active-site cavity, while in the HIV-1 PR protomer extracted from the dimeric enzyme the cavity would be freely accessible.


High-resolution structure of a retroviral protease folded as a monomer.

Gilski M, Kazmierczyk M, Krzywda S, Zábranská H, Cooper S, Popović Z, Khatib F, DiMaio F, Thompson J, Baker D, Pichová I, Jaskolski M - Acta Crystallogr. D Biol. Crystallogr. (2011)

Electrostatic potential surface of retroviral protease protomers. The M-PMV PR monomer (a) is shown in the same orientation and on the same scale as the HIV-1 PR protomer (b) extracted from the dimeric molecule (PDB entry 3hvp). The complete HIV-1 PR dimer is generated by the action of a vertical dyad, which creates a second copy facing the first molecule on the right. In this view, the N- and C-­termini (missing in M-PMV PR) are at the bottom and the flap loops are at the top. The active-site cavity is marked by the Asn26/Asp25 residue (ball-and-stick representation). In M-PMV PR the cavity is completely covered by the curled flap. The area of positive potential on this M-PMV PR surface is influenced by the D26N substitution, but it is of note that this mutation does not influence the tendency of the protein to fold as a monomer. The electrostatic potential (negative, red; positive, blue) was calculated in APBS (Baker et al., 2001 ▶).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3211970&req=5

fig4: Electrostatic potential surface of retroviral protease protomers. The M-PMV PR monomer (a) is shown in the same orientation and on the same scale as the HIV-1 PR protomer (b) extracted from the dimeric molecule (PDB entry 3hvp). The complete HIV-1 PR dimer is generated by the action of a vertical dyad, which creates a second copy facing the first molecule on the right. In this view, the N- and C-­termini (missing in M-PMV PR) are at the bottom and the flap loops are at the top. The active-site cavity is marked by the Asn26/Asp25 residue (ball-and-stick representation). In M-PMV PR the cavity is completely covered by the curled flap. The area of positive potential on this M-PMV PR surface is influenced by the D26N substitution, but it is of note that this mutation does not influence the tendency of the protein to fold as a monomer. The electrostatic potential (negative, red; positive, blue) was calculated in APBS (Baker et al., 2001 ▶).
Mentions: When the present M-PMV PR molecule is viewed from the direction of its absent dimerization partner, one sees a uniformly positively charged surface (Fig. 4 ▶). This is different from a similar view of the HIV-1 PR protomer, in which both charges and hydrophobic patches are seen, and may partly explain why in the absence of substrate/inhibitor the M-PMV protein can stably exist as a monomer, at least with the D26N mutation. Fig. 4 ▶ also illustrates that the curled flap closely covers the active-site cavity, while in the HIV-1 PR protomer extracted from the dimeric enzyme the cavity would be freely accessible.

Bottom Line: The flap has an unusual curled shape and a different orientation from both the open and closed states known from dimeric retropepsins.The overall fold of the protein follows the retropepsin canon, but the C(α) deviations are large and the active-site 'DTG' loop (here NTG) deviates up to 2.7 Å from the standard conformation.This structure of a monomeric retropepsin determined at high resolution (1.6 Å) provides important extra information for the design of dimerization inhibitors that might be developed as drugs for the treatment of retroviral infections, including AIDS.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Crystallography, Faculty of Chemistry, A. Mickiewicz University, 60-780 Poznan, Poland.

Show MeSH
Related in: MedlinePlus