PDBsum entry 2azc

Hydrolase/hydrolase inhibitor

PDB id: 2azc

Contents

Protein chains

99 a.a. *

Ligands

3TL ×2

Waters ×154

* Residue conservation analysis

PDB id:

2azc

Name:

Hydrolase/hydrolase inhibitor

Title:

HIV-1 protease nl4-3 6x mutant

Structure:

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

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: r8. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: protease nl4-3

Biol. unit:

Tetramer (from PQS)

Resolution:

2.01Å R-factor: 0.227 R-free: 0.278

Authors:

H.Heaslet,V.Kutilek,G.M.Morris,Y.-C.Lin,J.H.Elder,B.E.Torbett, C.D.Stout

Key ref:

H.Heaslet et al. (2006). Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3. J Mol Biol, 356, 967-981. PubMed id: 16403521 DOI: 10.1016/j.jmb.2005.11.094

Date:

10-Sep-05 Release date: 28-Feb-06

Protein chains

P03367  (POL_HV1BR) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)

Seq: 1447 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 8 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 2: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.3.1.13.2 - exoribonuclease H.
• Reaction: Exonucleolytic cleavage to 5'-phosphomonoester oligonucleotides in both 5'- to 3'- and 3'- to 5'-directions.
• Enzyme class 4: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 5: E.C.3.4.23.16 - HIV-1 retropepsin.
• Reaction: Specific for a P1 residue that is hydrophobic, and P1' variable, but often Pro.

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.jmb.2005.11.094

J Mol Biol 356:967-981 (2006)

PubMed id: 16403521

Structural Insights into the Mechanisms of Drug Resistance in HIV-1 Protease NL4-3.

H.Heaslet, V.Kutilek, G.M.Morris, Y.C.Lin, J.H.Elder, B.E.Torbett, C.D.Stout.

ABSTRACT

The development of resistance to anti-retroviral drugs targeted against HIV is an increasing clinical problem in the treatment of HIV-1-infected individuals. Many patients develop drug-resistant strains of the virus after treatment with inhibitor cocktails (HAART therapy), which include multiple protease inhibitors. Therefore, it is imperative that we understand the mechanisms by which the viral proteins, in particular HIV-1 protease, develop resistance. We have determined the three-dimensional structure of HIV-1 protease NL4-3 in complex with the potent protease inhibitor TL-3 at 2.0A resolution. We have also obtained the crystal structures of three mutant forms of NL4-3 protease containing one (V82A), three (V82A, M46I, F53L) and six (V82A, M46I, F53L, V77I, L24I, L63P) point mutations in complex with TL-3. The three protease mutants arose sequentially under ex vivo selective pressure in the presence of TL-3, and exhibit fourfold, 11-fold, and 30-fold resistance to TL-3, respectively. This series of protease crystal structures offers insights into the biochemical and structural mechanisms by which the enzyme can overcome inhibition by TL-3 while recovering some of its native catalytic activity.

Selected figure(s)

Figure 1.
Figure 1. Conformation of HIV-1 protease NL4-3 in complex with the inhibitor TL-3. TL-3 forms an intricate hydrogen bonding network with wild-type NL4-3 protease. The network between TL-3 and residues in the catalytic loop and flap regions is mediated by seven ordered water molecules (W1-W4, W1'-W3'). The majority of the protein-inhibitor hydrogen bonds are formed between main-chain atoms. See Table 2 for hydrogen bond distances. The positions of Met46 and Phe53 are indicated in parentheses. This Figure and Figure 2, Figure 4 and Figure 5 were generated using WebLab ViewerLite 3.20 (Accelrys, San Diego, CA, USA).

Figure 2.
Figure 2. Effects of the 1X and 3X mutants on interactions with TL-3. (a) Conformational changes observed at the P1/P1' position of TL-3 in the 1X mutant protease. Comparisons of the TL-3 complexes with wild-type protease (grey) and 1X protease (yellow) reveals conformational changes at the P1/P1' position of the inhibitor. The mutation of residue 82 from valine to alanine in the 1X mutant protease weakens the packing contact formed with the P1/P1' position of TL-3, allowing the P1/P1' phenyl ring to shift away from the side-chain of Pro81 by 0.8 Å and rotate by 25° about the x1 torsion angle. (b) Residues in the flap region of protease form stabilizing contacts. The side-chain of Phe53 adopts two conformations in wild-type and 1X proteases. In one conformation it forms a van der Waals interaction with the side-chain of Met46. In the other conformation it forms a hydrophobic contact with the P4 phenyl ring of TL-3. The side-chain of Met46 is packed between the side-chains of Phe53 and Lys55 in the wild-type and 1X structures. In the 3X mutant protease residue 46 is mutated to an Ile and residue 53 is mutated to a Leu (indicated in parentheses). Loss of the stabilizing contacts due to these mutations increases the overall mobility of the flaps (see Figure 3(a)) and alters the water structure near the tips of the flaps (see Table 2). The positions of Ile50, Gly51 and Gly52 are indicated.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2006, 356, 967-981) copyright 2006.

Figures were selected by an automated process.