PDBsum entry 1rt3

Nucleotidyltransferase

PDB id: 1rt3

Contents

Protein chains

521 a.a. *

398 a.a. *

Ligands

U05

* Residue conservation analysis

References listed in PDB file

Key reference

Title

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

Authors

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.

Ref.

Proc Natl Acad Sci U S A, 1998, 95, 9518-9523. [DOI no: 10.1073/pnas.95.16.9518]

PubMed id

9689112

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.

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.

Secondary reference #1

Title

Unique features in the structure of the complex between HIV-1 reverse transcriptase and the bis(heteroaryl)piperazine (bhap) u-90152 explain resistance mutations for this nonnucleoside inhibitor.

Authors

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

Ref.

Proc Natl Acad Sci U S A, 1997, 94, 3984-3989. [DOI no: 10.1073/pnas.94.8.3984]

PubMed id

9108091

Figure 2.
Fig. 2. Stereo diagram showing F[obs] F[calc] omit electron density for U-90152 contoured at 3 U-90152 is shown in ball-and-stick representation and the surrounding protein structure is shown by thin sticks. Residue Tyr-318, which would otherwise obscure the BHAP carbonyl group, is omitted from the figure for clarity.

Figure 4.
Fig. 4. Interactions between the indole ring of U-90152 and Pro-236. U-90152 is shown with thick bonds, residues 235-237 with thin bonds and interatomic distances <3.6 Å by broken lines. With so many interactions it is not surprising that mutations of this residue (such as Pro-236-Leu) disrupt the binding of BHAPs.

Secondary reference #2

Title

Complexes of HIV-1 reverse transcriptase with inhibitors of the hept series reveal conformational changes relevant to the design of potent non-Nucleoside inhibitors.

Authors

A.L.Hopkins, J.Ren, R.M.Esnouf, B.E.Willcox, E.Y.Jones, C.Ross, T.Miyasaka, R.T.Walker, H.Tanaka, D.K.Stammers, D.I.Stuart.

Ref.

J Med Chem, 1996, 39, 1589-1600. [DOI no: 10.1021/jm960056x]

PubMed id

8648598

Secondary reference #3

Title

The structure of HIV-1 reverse transcriptase complexed with 9-Chloro-Tibo: lessons for inhibitor design.

Authors

J.Ren, R.Esnouf, A.Hopkins, C.Ross, Y.Jones, D.Stammers, D.Stuart.

Ref.

Structure, 1995, 3, 915-926. [DOI no: 10.1016/S0969-2126(01)00226-X]

PubMed id

8535785

Figure 1.
Figure 1. The structure of 9-chloro-TIBO (R82913) showing the numbering of atoms in the ring system and the required stereospecificity of the 5-methyl substituent. Figure 1. The structure of 9-chloro-TIBO (R82913) showing the numbering of atoms in the ring system and the required stereospecificity of the 5-methyl substituent.

Figure 5.
Figure 5. Ribbon diagram of the form E RT/Cl-TIBO complex using colour coding to illustrate the structural variation from the unliganded form E RT structure. Cl-TIBO is shown as a space-filling model. The form E RT/Cl-TIBO model was produced by a nine-domain rigid-body refinement of the form F model on to the partial data set of form E. Hence, some artifactual variation can be detected near the domain boundaries (light blue). Figure 5. Ribbon diagram of the form E RT/Cl-TIBO complex using colour coding to illustrate the structural variation from the unliganded form E RT structure. Cl-TIBO is shown as a space-filling model. The form E RT/Cl-TIBO model was produced by a nine-domain rigid-body refinement of the form F model on to the partial data set of form E. Hence, some artifactual variation can be detected near the domain boundaries (light blue).

The above figures are reproduced from the cited reference with permission from Cell Press

Secondary reference #4

Title

High resolution structures of HIV-1 rt from four rt-Inhibitor complexes.

Authors

J.Ren, R.Esnouf, E.Garman, D.Somers, C.Ross, I.Kirby, J.Keeling, G.Darby, Y.Jones, D.Stuart.

Ref.

Nat Struct Biol, 1995, 2, 293-302.

PubMed id

7540934

Secondary reference #5

Title

Mechanism of inhibition of HIV-1 reverse transcriptase by non-Nucleoside inhibitors.

Authors

R.Esnouf, J.Ren, C.Ross, Y.Jones, D.Stammers, D.Stuart.

Ref.

Nat Struct Biol, 1995, 2, 303-308.

PubMed id

7540935

Secondary reference #6

Title

Crystals of HIV-1 reverse transcriptase diffracting to 2.2 a resolution.

Authors

D.K.Stammers, D.O.Somers, C.K.Ross, I.Kirby, P.H.Ray, J.E.Wilson, M.Norman, J.S.Ren, R.M.Esnouf, E.F.Garman.

Ref.

J Mol Biol, 1994, 242, 586-588.

PubMed id

7523679