PDBsum entry 2hnd

Transferase

PDB id: 2hnd

Contents

Protein chains

523 a.a. *

394 a.a. *

Ligands

PO4 ×3

NVP

Metals

_MG

Waters ×80

* Residue conservation analysis

PDB id:

2hnd

Name:

Transferase

Title:

Crystal structure of k101e mutant HIV-1 reverse transcriptase in complex with nevirapine

Structure:

Reverse transcriptase/ribonuclease h. Chain: a. Fragment: p66. Engineered: yes. Mutation: yes. Reverse transcriptase/ribonuclease h. Chain: b. Fragment: p51. Engineered: yes.

Source:

Human immunodeficiency virus 1. Organism_taxid: 11676. Gene: pol. Expressed in: escherichia coli. Expression_system_taxid: 562. Expression_system_taxid: 562

Biol. unit:

Dimer (from PQS)

Resolution:

2.50Å R-factor: 0.197 R-free: 0.269

Authors:

J.Ren,C.E.Nichols,A.Stamp,P.P.Chamberlain,D.K.Stammers

Key ref:

J.Ren et al. (2006). Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138. FEBS J, 273, 3850-3860. PubMed id: 16911530 DOI: 10.1111/j.1742-4658.2006.05392.x

Date:

12-Jul-06 Release date: 05-Sep-06

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: 523 a.a.*

Protein chain

P03367  (POL_HV1BR) -  Gag-Pol polyprotein from Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)

Seq: 1447 a.a.

Struc: 394 a.a.*

* PDB and UniProt seqs differ at 3 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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

DNA(n) + 2'-deoxyribonucleoside 5'-triphosphate = DNA(n+1) (Bound ligand (Het Group name = PO4) matches with 55.56% similarity) + 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: 10.1111/j.1742-4658.2006.05392.x

FEBS J 273:3850-3860 (2006)

PubMed id: 16911530

Structural insights into mechanisms of non-nucleoside drug resistance for HIV-1 reverse transcriptases mutated at codons 101 or 138.

J.Ren, C.E.Nichols, A.Stamp, P.P.Chamberlain, R.Ferris, K.L.Weaver, S.A.Short, D.K.Stammers.

ABSTRACT

Lys101Glu is a drug resistance mutation in reverse transcriptase clinically observed in HIV-1 from infected patients treated with the non-nucleoside inhibitor (NNRTI) drugs nevirapine and efavirenz. In contrast to many NNRTI resistance mutations, Lys101(p66 subunit) is positioned at the surface of the NNRTI pocket where it interacts across the reverse transcriptase (RT) subunit interface with Glu138(p51 subunit). However, nevirapine contacts Lys101 and Glu138 only indirectly, via water molecules, thus the structural basis of drug resistance induced by Lys101Glu is unclear. We have determined crystal structures of RT(Glu138Lys) and RT(Lys101Glu) in complexes with nevirapine to 2.5 A, allowing the determination of water structure within the NNRTI-binding pocket, essential for an understanding of nevirapine binding. Both RT(Glu138Lys) and RT(Lys101Glu) have remarkably similar protein conformations to wild-type RT, except for significant movement of the mutated side-chains away from the NNRTI pocket induced by charge inversion. There are also small shifts in the position of nevirapine for both mutant structures which may influence ring stacking interactions with Tyr181. However, the reduction in hydrogen bonds in the drug-water-side-chain network resulting from the mutated side-chain movement appears to be the most significant contribution to nevirapine resistance for RT(Lys101Glu). The movement of Glu101 away from the NNRTI pocket can also explain the resistance of RT(Lys101Glu) to efavirenz but in this case is due to a loss of side-chain contacts with the drug. RT(Lys101Glu) is thus a distinctive NNRTI resistance mutant in that it can give rise to both direct and indirect mechanisms of drug resistance, which are inhibitor-dependent.

Selected figure(s)

Figure 1.
Fig. 1. Simulated annealing omit electron density maps contoured at 3.5 showing bound inhibitors, waters and mutated residues within one of the HIV-1 RT subunits as indicated. (A) Lys101Glu in p66 and nevirapine. (B) Glu138Lys in p51 and nevirapine. (C) Glu138Lys in p51 and PETT-2.

Figure 2.
Fig. 2. Stereo-diagrams comparing the NNRTI binding sites of wild-type and mutant RTs for the following complexes: (A) Lys101Glu and nevirapine, (B) Glu138Lys and nevirapine, and (C) Glu138Lys and PETT-2. The thinner and thicker bonds show the CA backbone and side-chains with wild-type RT coloured orange and the mutant RTs coloured blue, respectively. Inhibitors and water molecules are shown in ball-and-stick representation and coloured red for wild-type RT and cyan for mutant RTs. For clarity, the side-chains at the site of mutation are shown in magenta for wild-type and green for the mutants. Hydrogen bonds linking drug to protein and drug to water molecules are marked in dashed lines, coloured yellow for wild-type and blue for mutant RTs.

The above figures are reprinted by permission from the Federation of European Biochemical Societies: FEBS J (2006, 273, 3850-3860) copyright 2006.