PDBsum entry 1c9r

Transferase/immune system/DNA

PDB id: 1c9r

Contents

Protein chains

558 a.a.

430 a.a.

214 a.a.

220 a.a.

DNA/RNA

Obsolete entry

PDB id:

1c9r

Name:

Transferase/immune system/DNA

Title:

Crystal structure of met184ile mutant of HIV-1 reverse transcriptase in complex with double stranded DNA template- primer

Structure:

HIV-1 reverse transcriptase (chain a). Chain: a. Synonym: HIV-1 rt. Engineered: yes. Mutation: yes. HIV-1 reverse transcriptase (chain b). Chain: b. Synonym: HIV-1 rt. Engineered: yes.

Source:

Human immunodeficiency virus type 1. Expressed in: escherichia coli. Mus musculus. Mouse. Synthetic: yes. Synthetic: yes

Biol. unit:

Octamer (from PQS)

Resolution:

3.50Å R-factor: 0.262 R-free: 0.338

Authors:

S.G.Sarafianos,K.Das,E.Arnold

Key ref:

S.G.Sarafianos et al. (1999). Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids. Proc Natl Acad Sci U S A, 96, 10027-10032. PubMed id: 10468556 DOI: 10.1073/pnas.96.18.10027

Date:

03-Aug-99 Release date: 01-Sep-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: 558 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.*

Protein chain

No UniProt id for this chain

Struc: 214 a.a.

Protein chain

No UniProt id for this chain

Struc: 220 a.a.

* PDB and UniProt seqs differ at 110 residue positions (black crosses)

DNA/RNA chains

A-T-G-G-C-G-C-C-C-G-A-A-C-A-G-G-G-A-C 19 bases

G-T-C-C-C-T-G-T-T-C-G-G-G-C-G-C-C-A 18 bases

Enzyme reactions

• Enzyme class: 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

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

Added reference

DOI no: 10.1073/pnas.96.18.10027

Proc Natl Acad Sci U S A 96:10027-10032 (1999)

PubMed id: 10468556

Lamivudine (3TC) resistance in HIV-1 reverse transcriptase involves steric hindrance with beta-branched amino acids.

S.G.Sarafianos, K.Das, A.D.Clark, J.Ding, P.L.Boyer, S.H.Hughes, E.Arnold.

ABSTRACT

An important component of triple-drug anti-AIDS therapy is 2', 3'-dideoxy-3'-thiacytidine (3TC, lamivudine). Single mutations at residue 184 of the reverse transcriptase (RT) in HIV cause high-level resistance to 3TC and contribute to the failure of anti-AIDS combination therapy. We have determined crystal structures of the 3TC-resistant mutant HIV-1 RT (M184I) in both the presence and absence of a DNA/DNA template-primer. In the absence of a DNA substrate, the wild-type and mutant structures are very similar. However, comparison of crystal structures of M184I mutant and wild-type HIV-1 RT with and without DNA reveals repositioning of the template-primer in the M184I/DNA binary complex and other smaller changes in residues in the dNTP-binding site. On the basis of these structural results, we developed a model that explains the ability of the 3TC-resistant mutant M184I to incorporate dNTPs but not the nucleotide analog 3TCTP. In this model, steric hindrance is expected for NRTIs with beta- or L- ring configurations, as with the enantiomer of 3TC that is used in therapy. Steric conflict between the oxathiolane ring of 3TCTP and the side chain of beta-branched amino acids (Val, Ile, Thr) at position 184 perturbs inhibitor binding, leading to a reduction in incorporation of the analog. The model can also explain the 3TC resistance of analogous hepatitis B polymerase mutants. Repositioning of the template-primer as observed in the binary complex (M184I/DNA) may also occur in the catalytic ternary complex (M184I/DNA/3TCTP) and contribute to 3TC resistance by interfering with the formation of a catalytically competent closed complex.

Selected figure(s)

Figure 2.
Fig. 2. Superposition of the polymerase active sites of wild-type HIV-1 RT/DNA/Fab and M184I HIV-1 RT/DNA/Fab. The wild-type RT complex is shown in white, the mutant RT complex in cyan. The wild-type and M184I RT structures were superimposed on the basis of the core of the p66 palm subdomains (residues 107 to 112 and 151 to 215 of their corresponding p66 subunits).

Figure 3.
Fig. 3. Ribbon diagram of the superimposed polymerase active sites of wild-type HIV-1 RT/DNA/Fab and M184I HIV-1 RT/DNA/Fab. The wild-type protein and DNA are shown in gray, the mutant protein in red, and DNA in the mutant RT/DNA complex in yellow.

Figures were selected by an automated process.