PDBsum entry 1hqu

Transferase

PDB id: 1hqu

Contents

Protein chains

556 a.a. *

430 a.a. *

Ligands

HBY

* Residue conservation analysis

PDB id:

1hqu

Name:

Transferase

Title:

Human immunodeficiency virus type 1

Structure:

Pol polyprotein. Chain: a. Fragment: p66 subunit. Synonym: reverse transcriptase. Engineered: yes. Mutation: yes. Pol polyprotein. Chain: b. Fragment: p51 subunit.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: HIV-1 clone 12. Other_details: HIV-1 clone 12

Biol. unit:

Dimer (from PQS)

Resolution:

2.70Å R-factor: 0.249 R-free: 0.345

Authors:

Y.Hsiou,J.Ding,E.Arnold

Key ref:

Y.Hsiou et al. (2001). The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance. J Mol Biol, 309, 437-445. PubMed id: 11371163 DOI: 10.1006/jmbi.2001.4648

Date:

19-Dec-00 Release date: 30-May-01

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 4 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.2001.4648

J Mol Biol 309:437-445 (2001)

PubMed id: 11371163

The Lys103Asn mutation of HIV-1 RT: a novel mechanism of drug resistance.

Y.Hsiou, J.Ding, K.Das, A.D.Clark, P.L.Boyer, P.Lewi, P.A.Janssen, J.P.Kleim, M.Rösner, S.H.Hughes, E.Arnold.

ABSTRACT

Inhibitors of human immunodeficiency virus (HIV) reverse transcriptase (RT) are widely used in the treatment of HIV infection. Loviride (an alpha-APA derivative) and HBY 097 (a quinoxaline derivative) are two potent non-nucleoside RT inhibitors (NNRTIs) that have been used in human clinical trials. A major problem for existing anti-retroviral therapy is the emergence of drug-resistant mutants with reduced susceptibility to the inhibitors. Amino acid residue 103 in the p66 subunit of HIV-1 RT is located near a putative entrance to a hydrophobic pocket that binds NNRTIs. Substitution of asparagine for lysine at position 103 of HIV-1 RT is associated with the development of resistance to NNRTIs; this mutation contributes to clinical failure of treatments employing NNRTIs. We have determined the structures of the unliganded form of the Lys103Asn mutant HIV-1 RT and in complexes with loviride and HBY 097. The structures of wild-type and Lys103Asn mutant HIV-1 RT in complexes with NNRTIs are quite similar overall as well as in the vicinity of the bound NNRTIs. Comparison of unliganded wild-type and Lys103Asn mutant HIV-1 RT structures reveals a network of hydrogen bonds in the Lys103Asn mutant that is not present in the wild-type enzyme. Hydrogen bonds in the unliganded Lys103Asn mutant but not in wild-type HIV-1 RT are observed between (1) the side-chains of Asn103 and Tyr188 and (2) well-ordered water molecules in the pocket and nearby pocket residues. The structural differences between unliganded wild-type and Lys103Asn mutant HIV-1 RT may correspond to stabilization of the closed-pocket form of the enzyme, which could interfere with the ability of inhibitors to bind to the enzyme. These results are consistent with kinetic data indicating that NNRTIs bind more slowly to Lys103Asn mutant than to wild-type HIV-1 RT. This novel drug-resistance mechanism explains the broad cross-resistance of Lys103Asn mutant HIV-1 RT to different classes of NNRTIs. Design of NNRTIs that make favorable interactions with the Asn103 side-chain should be relatively effective against the Lys103Asn drug-resistant mutant.

Selected figure(s)

Figure 3.
Figure 3. Stereoview of a SIGMAA weighted 2mFo - DFc difference Fourier map showing the electron density in the NNIBP region of p66 in the unliganded Lys103Asn mutant HIV-1 RT structure. The phases were computed from the final model at 2.7 Å resolution and the map was contoured at 2s. Selected hydrogen-bonding interactions are indicated with broken lines.

Figure 4.
Figure 4. Energy diagram for the binding of an NNRTI to wild-type and Lys103Asn mutant RT. The Lys103Asn mutant RT with the additional hydrogen bonding network in the NNIBP region is assumed to be more stable than wild-type HIV-1 RT. The relative stab- ility of wild-type and Lys103Asn mutant HIV-1 RT com- plexes with NNRTIs will depend on the inhibitor.

The above figures are reprinted by permission from Elsevier: J Mol Biol (2001, 309, 437-445) copyright 2001.

Figures were selected by an automated process.