PDBsum entry 1jla

Transferase

PDB id: 1jla

Contents

Protein chains

547 a.a. *

408 a.a. *

Ligands

TNK

Waters ×46

* Residue conservation analysis

PDB id:

1jla

Name:

Transferase

Title:

Crystal structure of y181c mutant HIV-1 reverse transcriptase in complex with tnk-651

Structure:

HIV-1 rt a-chain. Chain: a. Fragment: p66. Engineered: yes. HIV-1 rt b-chain. Chain: b. Fragment: p51. Engineered: yes

Source:

HIV-1 m:b_hxb2r. Organism_taxid: 11706. Strain: hxb2 isolate. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.203 R-free: 0.273

Authors:

J.Ren,C.Nichols,L.Bird,P.Chamberlain,K.Weaver,S.Short,D.I.Stuart, D.K.Stammers

Key ref:

J.Ren et al. (2001). Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors. J Mol Biol, 312, 795-805. PubMed id: 11575933 DOI: 10.1006/jmbi.2001.4988

Date:

16-Jul-01 Release date: 03-Oct-01

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 547 a.a.*

Protein chain

P04585  (POL_HV1H2) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)

Seq: 1435 a.a.

Struc: 408 a.a.*

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

Enzyme reactions

• Enzyme class 1: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 2: Chains A, B: 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: Chains A, B: 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: Chains A, B: E.C.3.1.-.-
• Enzyme class 5: Chains A, B: 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: Chains A, B: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 7: Chains A, B: 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: 10.1006/jmbi.2001.4988

J Mol Biol 312:795-805 (2001)

PubMed id: 11575933

Structural mechanisms of drug resistance for mutations at codons 181 and 188 in HIV-1 reverse transcriptase and the improved resilience of second generation non-nucleoside inhibitors.

J.Ren, C.Nichols, L.Bird, P.Chamberlain, K.Weaver, S.Short, D.I.Stuart, D.K.Stammers.

ABSTRACT

Mutations at either Tyr181 or Tyr188 within HIV-1 reverse transcriptase (RT) give high level resistance to many first generation non-nucleoside inhibitors (NNRTIs) such as the anti-AIDS drug nevirapine. By comparison second generation inhibitors, for instance the drug efavirenz, show much greater resilience to these mutations. In order to understand the structural basis for these differences we have determined a series of seven crystal structures of mutant RTs in complexes with first and second generation NNRTIs as well as one example of an unliganded mutant RT. These are Tyr181Cys RT (TNK-651) to 2.4 A, Tyr181Cys RT (efavirenz) to 2.6 A, Tyr181Cys RT (nevirapine) to 3.0 A, Tyr181Cys RT (PETT-2) to 3.0 A, Tyr188Cys RT (nevirapine) to 2.6 A, Tyr188Cys RT (UC-781) to 2.6 A and Tyr188Cys RT (unliganded) to 2.8 A resolution. In the two previously published structures of HIV-1 reverse transcriptase with mutations at 181 or 188 no side-chain electron density was observed within the p66 subunit (which contains the inhibitor binding pocket) for the mutated residues. In contrast the mutated side-chains can be seen in the NNRTI pocket for all seven structures reported here, eliminating the possibility that disordering contributes to the mechanism of resistance. In the case of the second generation compounds efavirenz with Tyr181Cys RT and UC-781 with Tyr188Cys RT there are only small rearrangements of either inhibitor within the binding site compared to wild-type RT and also for the first generation compounds TNK-651, PETT-2 and nevirapine with Tyr181Cys RT. For nevirapine with the Tyr188Cys RT there is however a more substantial movement of the drug molecule. We conclude that protein conformational changes and rearrangements of drug molecules within the mutated sites are not general features of these particular inhibitor/mutant combinations. The main contribution to drug resistance for Tyr181Cys and Tyr188Cys RT mutations is the loss of aromatic ring stacking interactions for first generation compounds, providing a simple explanation for the resilience of second generation NNRTIs, as such interactions make much less significant contribution to their binding.

Selected figure(s)

Figure 3.
Figure 3. Stereo-diagram comparing the NNRTI binding sites of wild-type and Tyr181Cys mutant RTs for the following complexes: (a) nevirapine, (b) TNK-651, (c) PETT-2, and (d) efavirenz. The thinner bonds show the main-chain backbone with wild-type RT coloured as dark grey and the mutant RT as light grey. Side-chains and the inhibitors are shown with thicker bonds with wild-type RT coloured brown and mutant RT as green. For clarity the side-chain of 181 and inhibitor are shown in red for wild-type RT and in cyan for the mutant. The broken yellow lines represent hydrogen bonds.

Figure 4.
Figure 4. Stereo-diagram comparing the NNRTI binding sites of wild-type and Tyr188Cys mutant RTs for the following: (a) unliganded, (b) nevirapine complex and (c) UC-781 complex. The colour scheme for backbone, inhibitors and side-chains is the same as in Figure 3.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 312, 795-805) copyright 2001.

Figures were selected by an automated process.