PDBsum entry: 1mr9

Transferase

PDB id: 1mr9

Contents

Protein chains

(+ 0 more) 203 a.a. *

Ligands

ACO ×6

* Residue conservation analysis

PDB id:

1mr9

Name:

Transferase

Title:

Crystal structure of streptogramin a acetyltransferase with bound

Structure:

Streptogramin a acetyltransferase. Chain: a, b, c, x, y, z. Engineered: yes

Source:

Enterococcus faecium. Organism_taxid: 1352. Expressed in: escherichia coli. Expression_system_taxid: 562.

Biol. unit:

Trimer (from PQS)

Resolution:

3.00Å R-factor: 0.246 R-free: 0.295

Authors:

L.E.Kehoe,J.Snidwongse,P.Courvalin,J.B.Rafferty,I.A.Murray

Key ref:

L.E.Kehoe et al. (2003). Structural basis of Synercid (quinupristin-dalfopristin) resistance in Gram-positive bacterial pathogens. J Biol Chem, 278, 29963-29970. PubMed id: 12771141 DOI: 10.1074/jbc.M303766200

Date:

18-Sep-02 Release date: 26-Aug-03

Protein chains

P50870  (VATD_ENTFC) -  Streptogramin A acetyltransferase

Seq: 209 a.a.

Struc: 203 a.a.

 Gene Ontology (GO) functional annotation 

• Biological process: response to antibiotic (1 term)
• Biochemical function: transferase activity (2 terms)

DOI no: 10.1074/jbc.M303766200

J Biol Chem 278:29963-29970 (2003)

PubMed id: 12771141

Structural basis of Synercid (quinupristin-dalfopristin) resistance in Gram-positive bacterial pathogens.

L.E.Kehoe, J.Snidwongse, P.Courvalin, J.B.Rafferty, I.A.Murray.

ABSTRACT

Synercid, a new semisynthetic streptogramin-derived antibiotic containing dalfopristin and quinupristin, is used in treatment of life-threatening infections caused by glycopeptide-resistant Enterococcus faecium and other bacterial pathogens. However, dissemination of genes encoding virginiamycin acetyltransferases, enzymes that confer resistance to streptogramins, threatens to limit the medical utility of the quinupristin-dalfopristin combination. Here we present structures of virginiamycin acetyltransferase D (VatD) determined at 1.8 A resolution in the absence of ligands, at 2.8 A resolution bound to dalfopristin, and at 3.0 A resolution in the presence of acetyl-coenzyme A. Dalfopristin is bound by VatD in a similar conformation to that described previously for the streptogramin virginiamycin M1. However, specific interactions with the substrate are altered as a consequence of a conformational change in the pyrollidine ring that is propagated to adjacent constituents of the dalfopristin macrocycle. Inactivation of dalfopristin involves acetyl transfer from acetyl-coenzyme A to the sole (O-18) hydroxy group of the antibiotic that lies close to the side chain of the strictly conserved residue, His-82. Replacement of residue 82 by alanine is accompanied by a fall in specific activity of >105-fold, indicating that the imidazole moiety of His-82 is a major determinant of catalytic rate enhancement by VatD. The structure of the VatD-dalfopristin complex can be used to predict positions where further structural modification of the drug might preclude enzyme binding and thereby circumvent Synercid resistance.

Selected figure(s)

Figure 1.
FIG. 1. Stereo images. a, the final |2Fo-Fc| electron density map contoured at 1.0 of a representative portion of the 1.8 Å E. faecium VatD structure. b, the final |2Fo-Fc| electron density map contoured at 1.0 of dalfopristin molecule H at 2.8 Å. c, the final |2Fo-Fc| electron density map contoured at 1.0 of AcCoA molecule H at 3.0 Å. d, arrangement of secondary structural elements in the VatD monomer. This figure was produced using TURBO-FRODO (18), MOLSCRIPT (40), and Raster3D (41).

Figure 2.
The active site of VatD. a, stereo image of the VatD trimer showing AcCoA superimposed on the model of the dalfopristin complex. Carbon atoms are colored yellow (AcCoA) and gray (dalfopristin), with non-carbon atoms colored according to atom type (N blue, O red, P purple, and S black). b, chemical structure and atom numbering scheme for dalfopristin. Natural product streptogramin A antibiotics (e.g. VM) lack the sulfonyl triethylamine substituent (atoms 39 through 48) on the pyrollidine ring. c, stereo image of dalfopristin bound at the VatD active site. Amino acid residues shown are those making contacts (<4 Å) with the substrate. Asterisks denote residues from a symmetry-related subunit. Atoms, other than S (yellow) and the carbon atoms of dalfopristin (green), are colored as in a, and secondary structural elements of VatD are colored in red, green, and yellow for helices, {beta} -strands, and turns, respectively. d, stereo image showing the conformation of dalfopristin (green) bound to VatD superimposed on the complex of the same enzyme with VM (pink) (11). Non-carbon atoms are colored as in c. The altered positions of the pyrollidine groups (and proximal elements of the macrocycle) arise because the C-1-C-2 double bond of VM becomes saturated, when the additional C-2 substituent is introduced to produce dalfopristin, changing the pyrollidine ring from a planar to a puckered conformation. e, stereo image ofthe AcCoA-VatD complex showing amino acid residues that form contacts (<4 Å) with the substrate. Atoms and secondary structural elements are colored as in c, and asterisks indicate residues associated with a symmetry-related subunit of the trimer. The figure was produced using MOLSCRIPT (40), Raster3D (41), and ISIS DRAW v2.4 (MDL Information Systems Inc.).

The above figures are reprinted by permission from the ASBMB: J Biol Chem (2003, 278, 29963-29970) copyright 2003.

Figures were selected by an automated process.