PDBsum entry 3cyw

Hydrolase

PDB id: 3cyw

Contents

Protein chains

99 a.a. *

Ligands

017

GOL

Metals

_CL ×5

Waters ×189

* Residue conservation analysis

PDB id:

3cyw

Name:

Hydrolase

Title:

Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir

Structure:

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

Source:

Human immunodeficiency virus type 1. Gene: gag-pol. Expressed in: escherichia coli.

Resolution:

1.40Å R-factor: 0.169 R-free: 0.234

Authors:

F.Liu,I.T.Weber

Key ref:

F.Liu et al. (2008). Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir. J Mol Biol, 381, 102-115. PubMed id: 18597780 DOI: 10.1016/j.jmb.2008.05.062

Date:

27-Apr-08 Release date: 27-May-08

Protein chains

P04587  (POL_HV1B5) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH5)

Seq: 1447 a.a.

Struc: 99 a.a.*

* PDB and UniProt seqs differ at 6 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: E.C.2.7.7.- - ?????
• Enzyme class 2: E.C.2.7.7.49 - RNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 3: E.C.2.7.7.7 - DNA-directed Dna polymerase.
• Reaction: DNA(n) + a 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) + diphosphate
• Enzyme class 4: E.C.3.1.-.-
• Enzyme class 5: 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 6: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: 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.2008.05.062

J Mol Biol 381:102-115 (2008)

PubMed id: 18597780

Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.

F.Liu, A.Y.Kovalevsky, Y.Tie, A.K.Ghosh, R.W.Harrison, I.T.Weber.

ABSTRACT

HIV-1 (human immunodeficiency virus type 1) protease (PR) and its mutants are important antiviral drug targets. The PR flap region is critical for binding substrates or inhibitors and catalytic activity. Hence, mutations of flap residues frequently contribute to reduced susceptibility to PR inhibitors in drug-resistant HIV. Structural and kinetic analyses were used to investigate the role of flap residues Gly48, Ile50, and Ile54 in the development of drug resistance. The crystal structures of flap mutants PR(I50V) (PR with I50V mutation), PR(I54V) (PR with I54V mutation), and PR(I54M) (PR with I54M mutation) complexed with saquinavir (SQV) as well as PR(G48V) (PR with G48V mutation), PR(I54V), and PR(I54M) complexed with darunavir (DRV) were determined at resolutions of 1.05-1.40 A. The PR mutants showed changes in flap conformation, interactions with adjacent residues, inhibitor binding, and the conformation of the 80s loop relative to the wild-type PR. The PR contacts with DRV were closer in PR(G48V)-DRV than in the wild-type PR-DRV, whereas they were longer in PR(I54M)-DRV. The relative inhibition of PR(I54V) and that of PR(I54M) were similar for SQV and DRV. PR(G48V) was about twofold less susceptible to SQV than to DRV, whereas the opposite was observed for PR(I50V). The observed inhibition was in agreement with the association of G48V and I50V with clinical resistance to SQV and DRV, respectively. This analysis of structural and kinetic effects of the mutants will assist in the development of more effective inhibitors for drug-resistant HIV.

Selected figure(s)

Figure 3.
Fig. 3. F[o] − F[c] omit maps of SQV (upper panel) and DRV (lower panel) contoured at 3.3 σ. SQV is colored by atom type from complex PR[I54V]–SQV. DRV is from complex PR[I54V]–DRV, showing alternate conformations of 60%/40% occupancy. The major conformation is colored by atom type, whereas the minor conformation is shown in pink.

Figure 5.
Fig. 5. PR[I54M] interactions with inhibitors. (a) Major orientation of SQV. (b) Major orientation of DRV. Hydrogen bonds are indicated in red; CH–π interactions, in blue; and C–H…O interactions, in purple. Interatomic distances are shown in angstrom. Note that the water-mediated interaction of the NH2 of DRV with the Asp30 side chain is replaced by a direct hydrogen bond in the wild-type PR and the other mutant structures.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2008, 381, 102-115) copyright 2008.

Figures were selected by an automated process.