PDBsum entry 1t03

Transferase/antibody/DNA

PDB id: 1t03

Contents

Protein chains

558 a.a. *

429 a.a. *

211 a.a. *

225 a.a. *

DNA/RNA

Metals

_MG

* Residue conservation analysis

PDB id:

1t03

Name:

Transferase/antibody/DNA

Title:

HIV-1 reverse transcriptase crosslinked to tenofovir terminated template-primer (complex p)

Structure:

Synthetic oligonucleotide template. Chain: t. Engineered: yes. Synthetic oligonucleotide primer. Chain: p. Engineered: yes. Pol polyprotein. Chain: a. Fragment: reverse transcriptase, p66 subunit.

Source:

Synthetic: yes. Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Mus musculus. House mouse. Organism_taxid: 10090.

Biol. unit:

Dimer (from PQS)

Resolution:

3.10Å R-factor: 0.256 R-free: 0.295

Authors:

S.Tuske,S.G.Sarafianos,J.Ding,E.Arnold

Key ref:

S.Tuske et al. (2004). Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir. Nat Struct Mol Biol, 11, 469-474. PubMed id: 15107837 DOI: 10.1038/nsmb760

Date:

07-Apr-04 Release date: 11-May-04

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: 429 a.a.*

Protein chain

No UniProt id for this chain

Struc: 211 a.a.

Protein chain

No UniProt id for this chain

Struc: 225 a.a.

* PDB and UniProt seqs differ at 3 residue positions (black crosses)

DNA/RNA chains

G-C-A-T-G-G-C-G-C-C-C-G-A-A-C-A-G-G-G-A-C-T-G 23 bases

C-A-G-T-C-C-C-T-G-T-T-C-G-G-MRG-C-G-C-C-TFO 20 bases

Enzyme reactions

• Enzyme class 2: Chains A, B: E.C.2.7.7.- - ?????
• Enzyme class 3: 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 4: 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 5: Chains A, B: E.C.3.1.-.-
• Enzyme class 6: 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 7: Chains A, B: E.C.3.1.26.13 - retroviral ribonuclease H.
• Enzyme class 8: 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: 10.1038/nsmb760

Nat Struct Mol Biol 11:469-474 (2004)

PubMed id: 15107837

Structures of HIV-1 RT-DNA complexes before and after incorporation of the anti-AIDS drug tenofovir.

S.Tuske, S.G.Sarafianos, A.D.Clark, J.Ding, L.K.Naeger, K.L.White, M.D.Miller, C.S.Gibbs, P.L.Boyer, P.Clark, G.Wang, B.L.Gaffney, R.A.Jones, D.M.Jerina, S.H.Hughes, E.Arnold.

ABSTRACT

Tenofovir, also known as PMPA, R-9-(2-(phosphonomethoxypropyl)adenine, is a nucleotide reverse transcriptase (RT) inhibitor. We have determined the crystal structures of two related complexes of HIV-1 RT with template primer and tenofovir: (i) a ternary complex at a resolution of 3.0 A of RT crosslinked to a dideoxy-terminated DNA with tenofovir-diphosphate bound as the incoming substrate; and (ii) a RT-DNA complex at a resolution of 3.1 A with tenofovir at the 3' primer terminus. The tenofovir nucleotide in the tenofovir-terminated structure seems to adopt multiple conformations. Some nucleoside reverse transcriptase inhibitors, including 3TC and AZT, have elements ('handles') that project beyond the corresponding elements on normal dNTPs (the 'substrate envelope'). HIV-1 RT resistance mechanisms to AZT and 3TC take advantage of these handles; tenofovir's structure lacks handles that could protrude through the substrate envelope to cause resistance.

Selected figure(s)

Figure 1.
Figure 1. Comparison of the chemical structures of tenofovir, dTMP and the NRTIs 3TCMP and AZTMP. The azido group of AZTMP and the sulfur of the L- -oxathialone ring of 3TCMP protrude through the envelope of normal substrates and can serve as handles for the development of NRTI resistance.

Figure 4.
Figure 4. The active site of the RT(P) -tenofovir complex with tenofovir in two conformations. In one conformation (tenofovir I), tenofovir stacks with the penultimate primer residue but does not engage in Watson-Crick base-pairing with the template dTMP. The dashed lines for the two base pairs upstream of the 3' terminus are labeled 1 -3 and 1' -3' for the template and primer strands, respectively. In the second conformation (tenofovir II), the adenine of tenofovir is flipped out by ~180° relative to the position of adenine in the first conformation.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Struct Mol Biol (2004, 11, 469-474) copyright 2004.

Figures were selected by an automated process.