Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase - PubMed (original) (raw)

Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase

Magdalena Korczynska et al. Proc Natl Acad Sci U S A. 2007.

Abstract

The streptogramin combination therapy of quinupristin-dalfopristin (Synercid) is used to treat infections caused by bacterial pathogens, such as methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. However, the effectiveness of this therapy is being compromised because of an increased incidence of streptogramin resistance. One of the clinically observed mechanisms of resistance is enzymatic inactivation of the type B streptogramins, such as quinupristin, by a streptogramin B lyase, i.e., virginiamycin B lyase (Vgb). The enzyme catalyzes the linearization of the cyclic antibiotic via a cleavage that requires a divalent metal ion. Here, we present crystal structures of Vgb from S. aureus in its apoenzyme form and in complex with quinupristin and Mg2+ at 1.65- and 2.8-A resolution, respectively. The fold of the enzyme is that of a seven-bladed beta-propeller, although the sequence reveals no similarity to other known members of this structural family. Quinupristin binds to a large depression on the surface of the enzyme, where it predominantly forms van der Waals interactions. Validated by site-directed mutagenesis studies, a reaction mechanism is proposed in which the initial abstraction of a proton is facilitated by a Mg2+ -linked conjugated system. Analysis of the Vgb-quinupristin structure and comparison with the complex between quinupristin and its natural target, the 50S ribosomal subunit, reveals features that can be exploited for developing streptogramins that are impervious to Vgb-mediated resistance.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Structure of Vgb from S. aureus. (A) Ribbon diagram of Vgb viewed down the central axis. Five active-site residues are also shown together with their corresponding 2 F o − F c density map contoured at 1σ, as observed in the 1.65-Å structure. (B) View rotated 90° about the horizontal axis. The structure is sliced through the center to highlight the depression and the tunnel located on the top and bottom face of Vgb, respectively. Also shown is quinupristin, which binds in the depression.

Fig. 2.

Proposed reaction mechanism for Vgb lyase activity. (A) Chemical structure of quinupristin. The 3-hydroxypicolinic acid, threonyl, and phenylglycyl moieties are colored blue, and the threonyl α-proton is shown in red. (B) Active site of Vgb. Quinupristin is shown using the same color scheme as in A, Mg2+ is shown in purple, active-site residues are displayed in yellow, with the modeled catalytic base His-270 displayed in dark orange, and water molecules are shown as red spheres. Also displayed is the 2_F_ o − F c density map contoured at 1σ for quinupristin and Mg2+. (C) Schematic drawing of the proposed reaction mechanism. Note that only a part of quinupristin is shown, the remainder is represented by R.

Fig. 3.

Comparison between quinupristin binding to Vgb and the ribosome. (A) Shown is the surface of Vgb within 5.5 Å of the bound streptogramin. The surface is colored according to the identity of the associated atoms: N, blue; O, red; C, white; S, yellow. Also shown are residues that contribute significantly to the surface, as well as Mg2+ and the coordinated water molecules. (B) Identical diagram for the 50S ribosomal subunit (Protein Data Bank ID code 1YJW). The view in both images is such that the orientation of the quinupristin matches in the two complexes (rmsd for all quinupristin ring atoms is 0.22 Å).

References

1. Eliopoulos GM. Clin Infect Dis. 2003;36:473–481. -PubMed
1. Cocito C. Microbiol Rev. 1979;43:145–192. -PMC -PubMed
1. Di Giambattista M, Chinali G, Cocito C. J Antimicrob Chemother. 1989;24:485–507. -PubMed
1. Tu D, Blaha G, Moore PB, Steitz TA. Cell. 2005;121:257–270. -PubMed
1. Harms JM, Schlünzen F, Fucini P, Bartels H, Yonath A. BMC Biol. 2004;2:4. -PMC -PubMed

Structural basis for streptogramin B resistance in Staphylococcus aureus by virginiamycin B lyase - PubMed (original) (raw)