PDBsum entry 1rt3

Nucleotidyltransferase

PDB id: 1rt3

Contents

Protein chains

521 a.a. *

398 a.a. *

Ligands

U05

* Residue conservation analysis

PDB id:

1rt3

Name:

Nucleotidyltransferase

Title:

Azt drug resistant HIV-1 reverse transcriptase complexed with 1051u91

Structure:

HIV-1 reverse transcriptase. Chain: a. Engineered: yes. Mutation: yes. HIV-1 reverse transcriptase. Chain: b. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Variant: hxb2 isolate. Cell_line: 293. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.264 R-free: 0.335

Authors:

J.Ren,D.K.Stammers,D.I.Stuart

Key ref:

J.Ren et al. (1998). 3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes. Proc Natl Acad Sci U S A, 95, 9518-9523. PubMed id: 9689112 DOI: 10.1073/pnas.95.16.9518

Date:

29-Jun-98 Release date: 16-Feb-99

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: 521 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: 398 a.a.*

* PDB and UniProt seqs differ at 7 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: 10.1073/pnas.95.16.9518

Proc Natl Acad Sci U S A 95:9518-9523 (1998)

PubMed id: 9689112

3'-Azido-3'-deoxythymidine drug resistance mutations in HIV-1 reverse transcriptase can induce long range conformational changes.

J.Ren, R.M.Esnouf, A.L.Hopkins, E.Y.Jones, I.Kirby, J.Keeling, C.K.Ross, B.A.Larder, D.I.Stuart, D.K.Stammers.

ABSTRACT

HIV reverse transcriptase (RT) is one of the main targets for the action of anti-AIDS drugs. Many of these drugs [e.g., 3'-azido-3'-deoxythymidine (AZT) and 2',3'-dideoxyinosine (ddI)] are analogues of the nucleoside substrates used by the HIV RT. One of the main problems in anti-HIV therapy is the selection of a mutant virus with reduced drug sensitivity. Drug resistance in HIV is generated for nucleoside analogue inhibitors by mutations in HIV RT. However, most of these mutations are situated some distance from the polymerase active site, giving rise to questions concerning the mechanism of resistance. To understand the possible structural bases for this, the crystal structures of AZT- and ddI-resistant RTs have been determined. For the ddI-resistant RT with a mutation at residue 74, no significant conformational changes were observed for the p66 subunit. In contrast, for the AZT-resistant RT (RTMC) bearing four mutations, two of these (at 215 and 219) give rise to a conformational change that propagates to the active site aspartate residues. Thus, these drug resistance mutations produce an effect at the RT polymerase site mediated simply by the protein. It is likely that such long-range effects could represent a common mechanism for generating drug resistance in other systems.

Selected figure(s)

Figure 1.
Fig. 1. Overall structure and drug resistance mutation sites of the RT heterodimer. (Top) The p66 subunit is drawn in dark gray and p51 in light gray. NI resistance mutation sites (26) are shown as green spheres, with RTMC and L74V sites highlighted in yellow. In the p51 subunit, residues 215 and 219 are disordered; their positions are not shown. NNI resistance mutation sites (27) are shown as blue spheres. The three polymerase active site aspartate residues and the bound NNI are shown in red and magenta, respectively. Double-stranded DNA (shown as a spiral ladder with the template strand in green and the primer in red) was modeled into our RT-nevirapine structure (6) from the C and phosphate coordinates of the RT-DNA-Fab complex (5) by superimposing the p66 palm domain of the two structures. (Bottom) A close-up view of the polymerase active site and the drug resistance mutation sites in the p66 subunit. The coloring scheme is the same as in the top panel; however, the side chains for mutated residues are shown in ball-and-stick representation and the van der Waals surface for the bound NNI (nevirapine) is shown semitransparent.

Figure 3.
Fig. 3. The NNI binding site and polymerase active site. (a) A stereodiagram showing the superposition of the NNI binding site in RTMC and wild-type RT. The protein backbone is shown by thin sticks. The NNIs (thick bonds) and side chains that have contacts with the NNIs are shown as ball-and-stick representations. The RTMC is colored in green with residue 181 and the bound 1051U91 highlighted in red. The wild-type RT is colored in blue with residue 181 and bound 1051U91 highlighted in yellow. (b) A stereodiagram of the superposition of the active sites in RTMC (green), the wild type unliganded (red), and six NNI-bound RT structures (blue for RT-1051U91, gray for others) showing the structural changes at the active site in RTMC caused by 215 and 219 mutations. The C trace and side chains for residues 110, 185, 186, 215, and 219 are shown for RTMC, wild-type unliganded RT, and RT-1051U91; the C traces only are shown for RT-Cl-TIBO, RT-BHAP, RT-nevirapine, RT-MKC-442, and RT- -APA. In the p51 subunit, residues 215 and 219 are disordered whereas residues 67 and 70 do not show significant rearrangement from the wild-type p51.

Figures were selected by an automated process.