PDBsum entry 1rkw

Transcription

PDB id: 1rkw

Contents

Protein chains

186 a.a. *

Ligands

SO4 ×22

PNT

Waters ×80

* Residue conservation analysis

PDB id:

1rkw

Name:

Transcription

Title:

Crystal structure of the multidrug binding transcriptional repressor qacr bound to pentamadine

Structure:

Transcriptional regulator qacr. Chain: b, d, a, e. Engineered: yes. Mutation: yes

Source:

Staphylococcus aureus. Organism_taxid: 1280. Gene: qacr, savp031. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Dimer (from PQS)

Resolution:

2.62Å R-factor: 0.224 R-free: 0.275

Authors:

D.S.Murray,M.A.Schumacher,R.G.Brennan

Key ref:

D.S.Murray et al. (2004). Crystal structures of QacR-diamidine complexes reveal additional multidrug-binding modes and a novel mechanism of drug charge neutralization. J Biol Chem, 279, 14365-14371. PubMed id: 14726520 DOI: 10.1074/jbc.M313870200

Date:

23-Nov-03 Release date: 01-Jun-04

Protein chains

P0A0N4  (QACR_STAAU) -  HTH-type transcriptional regulator QacR from Staphylococcus aureus

Seq: 188 a.a.

Struc: 186 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

DOI no: 10.1074/jbc.M313870200

J Biol Chem 279:14365-14371 (2004)

PubMed id: 14726520

Crystal structures of QacR-diamidine complexes reveal additional multidrug-binding modes and a novel mechanism of drug charge neutralization.

D.S.Murray, M.A.Schumacher, R.G.Brennan.

ABSTRACT

The Staphylococcus aureus multidrug-binding protein QacR represses transcription of the plasmid-encoded membrane protein QacA, a multidrug efflux transporter. QacR is induced by multiple structurally dissimilar monovalent and bivalent cationic lipophilic compounds, many of which are effluxed from the cell by QacA via the proton motive force. The multidrug-binding pocket of QacR has been shown to be quite extensive and features several glutamates and multiple aromatic residues. To date, the structure of only one QacR-bivalent cationic drug complex (that of QacR bound to dequalinium) has been determined, and how other longer or shorter bivalent cationic compounds bind is unknown. Here we report the crystal structures of QacR bound to two cytotoxic bivalent diamidines, pentamidine and hexamidine. These compounds are structurally similar, differing by only one methylene carbon in the alkyl chain linker. However, this small difference results in very dissimilar binding modes. Similar to dequalinium, hexamidine spans the multidrug-binding pocket, and its positively charged benzamidine groups are neutralized by residues Glu-57 and Glu-120. Pentamidine binds QacR in a novel fashion whereby one of its benzamidine groups interacts with residue Glu-63, and the other is neutralized by carbonyl and side chain oxygen atoms. Thus, these structures demonstrate that a formal negative charge is not a prerequisite for binding positively charged drugs and underscore the versatility of the QacR and, likely, all multidrug-binding pockets.

Selected figure(s)

Figure 4.
FIG. 4. Stereoview of the pentamidine-QacR-binding pocket. For clarity, the side chains of only selected residues are shown (not shown are residues Leu-54, Lys-60, and Gln-96) as sticks, whereby oxygen atoms are red, nitrogens are blue, carbons are gray, and the backbone of the drug-bound subunit is aquamarine with germane helices labeled in blue. Solvent molecules within the hydrogen-bonding distance of the protein or drug are shown as red spheres. The hydrogen-bonding network between W1, W2, and QacR is depicted with black dashed lines. W1 is 3.1 Å from the hydroxyl oxygen of residue Tyr-93, 3.4 Å from the hydroxyl of Tyr-123, and 2.8 Å from W2; W2 is hydrogen-bonded to the hydroxyl oxygen of residue Y123 (2.5 Å) and the backbone carbonyl oxygen of residue L54 (2.9 Å); W3 engages in a weak hydrogen bond with residue Asn-157 (3.6 Å), and van der Waals contacts with the pentamidine phenyl ring (closest approach 3.4 Å). The binding pocket subsites, Site 1 and Site 2, are labeled.

Figure 5.
FIG. 5. Close up stereoview of the Site 1 drug-binding site of pentamidine. Interaction distances are given in angstrom. Hydrogen bonds are depicted by red dashed lines, van der Waals contacts are depicted by a black dashed line, a -cation interaction is depicted by a green dashed line, and stacking interactions (closest contact) are depicted by purple dashed lines. Note that no negatively charged side chains are found within 6 Å of either of the amidinic nitrogens.

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2004, 279, 14365-14371) copyright 2004.

Figures were selected by an automated process.