PDBsum entry 1bqm

Nucleotidyltransferase

PDB id: 1bqm

Contents

Protein chains

556 a.a. *

430 a.a. *

Ligands

HBY

* Residue conservation analysis

PDB id:

1bqm

Name:

Nucleotidyltransferase

Title:

HIV-1 rt/hby 097

Structure:

Reverse transcriptase. Chain: a. Synonym: HIV-1 rt. Engineered: yes. Mutation: yes. Reverse transcriptase. Chain: b. Synonym: HIV-1 rt. Engineered: yes.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Strain: bh10. Cell_line: 293. Atcc: atcc 1065288. Collection: atcc 1065288. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

3.10Å R-factor: 0.258 R-free: 0.362

Authors:

Y.Hsiou,K.Das,J.Ding,E.Arnold

Key ref:

Y.Hsiou et al. (1998). Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance. J Mol Biol, 284, 313-323. PubMed id: 9813120 DOI: 10.1006/jmbi.1998.2171

Date:

17-Aug-98 Release date: 06-Jan-99

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 556 a.a.*

Protein chain

P03366  (POL_HV1B1) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BH10)

Seq: 1447 a.a.

Struc: 430 a.a.*

* PDB and UniProt seqs differ at 2 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.1998.2171

J Mol Biol 284:313-323 (1998)

PubMed id: 9813120

Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.

Y.Hsiou, K.Das, J.Ding, A.D.Clark, J.P.Kleim, M.Rösner, I.Winkler, G.Riess, S.H.Hughes, E.Arnold.

ABSTRACT

The second generation Hoechst-Bayer non-nucleoside inhibitor, HBY 097 (S-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3, 4-dihydroqui noxalin-2(1H)-thione), is an extremely potent inhibitor of HIV-1 reverse transcriptase (RT) and of HIV-1 infection in cell culture. HBY 097 selects for unusual drug-resistance mutations in HIV-1 RT (e.g. Gly190Glu) when compared with other non-nucleoside RT inhibitors (NNRTIs), such as nevirapine, alpha-APA and TIBO. We have determined the structure of HBY 097 complexed with wild-type HIV-1 RT at 3.1 A resolution. The HIV-1 RT/HBY 097 structure reveals an overall inhibitor geometry and binding mode differing significantly from RT/NNRTI structures reported earlier, in that HBY 097 does not adopt the usual butterfly-like shape. We have determined the structure of the Tyr188Leu HIV-1 RT drug-resistant mutant in complex with HBY 097 at 3.3 A resolution. HBY 097 binds to the mutant RT in a manner similar to that seen in the wild-type RT/HBY 097 complex, although there are some repositioning and conformational alterations of the inhibitor. Conformational changes of the structural elements forming the inhibitor-binding pocket, including the orientation of some side-chains, are observed. Reduction in the size of the 188 side-chain and repositioning of the Phe227 side-chain increases the volume of the binding cavity in the Tyr188Leu HIV-1 RT/HBY 097 complex. Loss of important protein-inhibitor interactions may account for the reduced potency of HBY 097 against the Tyr188Leu HIV-1 RT mutant. The loss of binding energy may be partially offset by additional contacts resulting from conformational changes of the inhibitor and nearby amino acid residues. This would suggest that inhibitor flexibility can help to minimize drug resistance.

Selected figure(s)

Figure 1.
Figure 1. Diagram of HBY 097 (a quinoxaline derivative) contacts with protein residues around the NNIBP in both (a) wild-type HIV-1 RT/HBY 097 and (b) Tyr188Leu mutant HIV-1 RT/HBY 097 complexes. Distances ( slant 3.6 Å) between protein and inhibitor atoms are indicated.

Figure 4.
Figure 4. (a) Stereoview of a difference Fourier m(F[obs] - F[calc]) map showing the electron density of HBY 097 in the wild-type HIV-1 RT/HBY 097 complex. The map is calculated at 3.1 Å resolution with 2s contours (in magenta). The phases were computed from the protein model prior to inclusion of the inhibitor. The green density corresponds to the difference Fourier map (3.7 Å resolution) between HBY 097 and S-0483 complexed with wild-type HIV-1 RT (bromine in S-0483 replaces the methoxy group of HBY 097), contoured at the 5s level, showing the position of the bromine atom and confirming the orientation and placement of the inhibitor. Difference Fourier 2mF[obs] - F[calc] map at 3.3 Å resolution, contoured at 1.2s, (b) of the Tyr188Leu mutant HIV-1 RT/HBY 097 complex at the NNIBP region in p66 showing the absence of any density for the side-chain of Leu188; clear density for HBY 097 is seen in the binding pocket; and of a (c) similar region in the p51 subunit, showing clear electron density for the side-chain at Leu188.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1998, 284, 313-323) copyright 1998.

Figures were selected by an automated process.