PDBsum entry 2qhc

Hydrolase

PDB id: 2qhc

Contents

Protein chains

99 a.a. *

Ligands

BME ×2

AB1

Waters ×41

* Residue conservation analysis

PDB id:

2qhc

Name:

Hydrolase

Title:

The influence of i47a mutation on reduced susceptibility to the protease inhibitor lopinavir

Structure:

Protease retropepsin. Chain: a, b. Synonym: HIV-1 protease. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. HIV-1. Organism_taxid: 11676. Strain: type b. Gene: gag-pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.80Å R-factor: 0.193 R-free: 0.228

Authors:

J.Brynda,K.G.Saskova,M.Kozisek,M.Lepsik,L.Machala,J.Konvalinka

Key ref:

K.G.Sasková et al. (2008). Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir. Protein Sci, 17, 1555-1564. PubMed id: 18560011 DOI: 10.1110/ps.036079.108

Date:

02-Jul-07 Release date: 22-Jul-08

Protein chains

Q9J2P7  (Q9J2P7_9HIV1) -  Protease (Fragment) from Human immunodeficiency virus 1

Seq: 99 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

DOI no: 10.1110/ps.036079.108

Protein Sci 17:1555-1564 (2008)

PubMed id: 18560011

Enzymatic and structural analysis of the I47A mutation contributing to the reduced susceptibility to HIV protease inhibitor lopinavir.

K.G.Sasková, M.Kozísek, M.Lepsík, J.Brynda, P.Rezácová, J.Václavíková, R.M.Kagan, L.Machala, J.Konvalinka.

ABSTRACT

Lopinavir (LPV) is a second-generation HIV protease inhibitor (PI) designed to overcome resistance development in patients undergoing long-term antiviral therapy. The mutation of isoleucine at position 47 of the HIV protease (PR) to alanine is associated with a high level of resistance to LPV. In this study, we show that recombinant PR containing a single I47A substitution has the inhibition constant (K(i) ) value for lopinavir by two orders of magnitude higher than for the wild-type PR. The addition of the I47A substitution to the background of a multiply mutated PR species from an AIDS patient showed a three-order-of-magnitude increase in K(i) in vitro relative to the patient PR without the I47A mutation. The crystal structure of I47A PR in complex with LPV showed the loss of van der Waals interactions in the S2/S2' subsites. This is caused by the loss of three side-chain methyl groups due to the I47A substitution and by structural changes in the A47 main chain that lead to structural changes in the flap antiparallel beta-strand. Furthermore, we analyzed possible interaction of the I47A mutation with secondary mutations V32I and I54V. We show that both mutations in combination with I47A synergistically increase the relative resistance to LPV in vitro. The crystal structure of the I47A/I54V PR double mutant in complex with LPV shows that the I54V mutation leads to a compaction of the flap, and molecular modeling suggests that the introduction of the I54V mutation indirectly affects the strain of the bound inhibitor in the PR binding cleft.

Selected figure(s)

Figure 1.
Model of HIV-1 PR with highlighted resistance-conferring mutations studied in this work. Mutations in the PR1 isolated from the patient are colored in yellow; color coding for other mutations is: I47A (green), V32I (brown), and I54V (brown stripes).

Figure 4.
Van der Waals interactions between PR and LPV lost due to the I47A mutation. The distances are represented as dashed lines with numbers in angstroms. (A) Wild-type PR (1MUI) complexed with LPV. Segmentation of LPV into P2, P1, P1[prime prime or minute], and P2[prime prime or minute] subsites is depicted. (B) PR3 (I47A) complexed with LPV. (Thin gray lines) Superimposition of LPV as bound to the wild-type PR.

The above figures are reprinted from an Open Access publication published by the Protein Society: Protein Sci (2008, 17, 1555-1564) copyright 2008.

Figures were selected by an automated process.