PDBsum entry 1tvr

Aspartyl protease

PDB id: 1tvr

Contents

Protein chains

558 a.a. *

427 a.a. *

Ligands

TB9

* Residue conservation analysis

PDB id:

1tvr

Name:

Aspartyl protease

Title:

HIV-1 rt/9-cl tibo

Structure:

Reverse transcriptase. Chain: a. Engineered: yes. Mutation: yes. Reverse transcriptase. Chain: b. Engineered: yes. Mutation: yes

Source:

Human immunodeficiency virus type 1 (clone 12). Organism_taxid: 11679. Strain: bh10. Cell_line: 293. Atcc: accession number 1065288. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: human immunodeficiency virus type 1 (HIV-1) subcloned from bh10 isolate. Expressed and processed by bacterial escherichia

Biol. unit:

Dimer (from PQS)

Resolution:

3.00Å R-factor: 0.259

Authors:

K.Das,J.Ding,Y.Hsiou,E.Arnold

Key ref:

K.Das et al. (1996). Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant. J Mol Biol, 264, 1085-1100. PubMed id: 9000632 DOI: 10.1006/jmbi.1996.0698

Date:

16-Apr-96 Release date: 12-Mar-97

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: 427 a.a.*

* PDB and UniProt seqs differ at 2 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.1996.0698

J Mol Biol 264:1085-1100 (1996)

PubMed id: 9000632

Crystal structures of 8-Cl and 9-Cl TIBO complexed with wild-type HIV-1 RT and 8-Cl TIBO complexed with the Tyr181Cys HIV-1 RT drug-resistant mutant.

K.Das, J.Ding, Y.Hsiou, A.D.Clark, H.Moereels, L.Koymans, K.Andries, R.Pauwels, P.A.Janssen, P.L.Boyer, P.Clark, R.H.Smith, M.B.Kroeger Smith, C.J.Michejda, S.H.Hughes, E.Arnold.

ABSTRACT

Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) is an important target for chemotherapeutic agents used in the treatment of AIDS; the TIBO compounds are potent non-nucleoside inhibitors of HIV-1 RT (NNRTIs). Crystal structures of HIV-1 RT complexed with 8-Cl TIBO (R86183, IC50 = 4.6 nM) and 9-Cl TIBO (R82913, IC50 = 33 nM) have been determined at 3.0 A resolution. Mutant HIV-1 RT, containing Cys in place of Tyr at position 181 (Tyrl81Cys), is highly resistant to many NNRTIs and HIV-1 variants containing this mutation have been selected in both cell culture and clinical trials. We also report the crystal structure of Tyrl81Cys HIV-1 RT in complex with 8-Cl TIBO (IC50 = 130 nM) determined at 3.2 A resolution. Averaging of the electron density maps computed for different HIV-1 RT/NNRTI complexes and from diffraction datasets obtained using a synchrotron source from frozen (-165 degrees C) and cooled (-10 degrees C) crystals of the same complex was employed to improve the quality of electron density maps and to reduce model bias. The overall locations and conformations of the bound inhibitors in the complexes containing wild-type HIV-1 RT and the two TIBO inhibitors are very similar, as are the overall shapes and volumes of the non-nucleoside inhibitor-binding pocket (NNIBP). The major differences between the two wild-type HIV-1 RT/TIBO complexes occur in the vicinity of the TIBO chlorine substituents and involve the polypeptide segments around the beta5-beta6 connecting loop (residues 95 to 105) and the beta13-beta14 hairpin (residues 235 and 236). In all known structures of HIV-1 RT/NNRTI complexes, including these two, the position of the beta12-beta13 hairpin or the "primer grip" is significantly displaced relative to the position in the structure of HIV-1 RT complexed with a double-stranded DNA and in unliganded HIV-1 RT structures. Since the primer grip helps to position the template-primer, this displacement suggests that binding of NNRTIs would affect the relative positions of the primer terminus and the polymerase active site. This could explain biochemical data showing that NNRTI binding to HIV-1 RT reduces efficiency of the chemical step of DNA polymerization, but does not prevent binding of either dNTPs or DNA. When the structure of the Tyr181Cys mutant HIV-1 RT in complex with 8-Cl TIBO is compared with the corresponding structure containing wild-type HIV-1 RT, the overall conformations of Tyr181Cys and wild-type HIV-1 RT and of the 8-Cl TIBO inhibitors are very similar. Some positional changes in the polypeptide backbone of the beta6-beta10-beta9 sheet containing residue 181 are observed when the Tyr181Cys and wild-type complexes are compared, particularlty near residue Val179 of beta9. In the p51 subunit, the Cys181 side-chain is oriented in a similar direction to the Tyr181 side-chain in the wild-type complex. However, the electron density corresponding to the sulfur of the Cys181 side-chain in the p66 subunit is very weak, indicating that the thiol group is disordered, presumably because there is no significant interaction with either 8-Cl TIBO or nearby amino acid residues. In the mutant complex, there are slight rearrangements of the side-chains of other amino acid residues in the NNIBP and of the flexible dimethylallyl group of 8-Cl TIBO; these conformational changes could potentially compensate for the interactions that were lost when the relatively large tyrosine at position 181 was replaced by a less bulky cysteine residue. In the corresponding wild-type complex, Tyr181 iin the p66 subunit has significant interactions with the bound inhibitor and the position of the Tyr181 side-chain is well defined in both subunits. Apparently the Tyr181 --> Cys mutation eliminates favorable contacts of the aromatic ring of the tyrosine and the bou

Selected figure(s)

Figure 1.
Figure 1. Chemical structures with the numbering scheme used and distances (E3.6 Å ) between atoms of the TIBO inhibitor and of the amino acid residues of the NNIBP for: (a) 8-Cl TIBO (R86183, tivirapine) complexed with wild- type HIV-1 RT; (b) 8-Cl TIBO complexed with Tyr181Cys mutant HIV-1 RT; and (c) 9-Cl TIBO (R82913) complexed with wild-type HIV-1 RT. An NNIBP residue is shown only if atoms of that residue are E3.6 Å from an inhibitor atom with the exception of Cys181 in (b). The wings I and II portions of the inhibitors in the butterfly-like anal- ogy for NNRTIs (Ding et al., 1995a) are indicated here and in sub- sequent Figures by Roman nu- merals I and II. The dotted line in (a) indicates the subdivision of atoms between wings I and II.

Figure 5.
Figure 5. A stereoview of the superposition (based on the C a atoms of the b6-b10-b9 sheet) of the HIV-1 RT/DNA/Fab complex structure (in gray) (Jacobo-Molina et al., 1993) on the HIV-1 RT/9-Cl TIBO complex structure (in cyan) in the regions near the NNIBP and the polymerase active site showing the disposition of the b12-b13-b14 sheet containing the primer grip. Bound 9-Cl TIBO in the HIV-1 RT/9-Cl TIBO complex is shown in gold and the two 3'-terminal nucleotides 17 and 18 of the primer strand in the HIV-1 RT/DNA/Fab complex are shown with a yellow ball-and-stick model. The broken line represents interactions between the primer grip and the primer terminal phosphate in the HIV-1 RT/DNA/Fab complex and the arrow indicates the movement of the primer grip that accompanies NNRTI binding.

The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 264, 1085-1100) copyright 1996.

Figures were selected by an automated process.