4HUS

Crystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with virginiamycin M1


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free: 
    0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work: 
    0.184 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 
    0.186 (Depositor) 

Starting Model: experimental
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Ligand Structure Quality Assessment 

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Literature

Potential for Reduction of Streptogramin A Resistance Revealed by Structural Analysis of Acetyltransferase VatA.

Stogios, P.J.Kuhn, M.L.Evdokimova, E.Courvalin, P.Anderson, W.F.Savchenko, A.

(2014) Antimicrob Agents Chemother 58: 7083-7092

  • DOI: https://doi.org/10.1128/AAC.03743-14
  • Primary Citation of Related Structures:  
    4HUR, 4HUS, 4MYO

  • PubMed Abstract: 

    Combinations of group A and B streptogramins (i.e., dalfopristin and quinupristin) are "last-resort" antibiotics for the treatment of infections caused by Gram-positive pathogens, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecium. Resistance to streptogramins has arisen via multiple mechanisms, including the deactivation of the group A component by the large family of virginiamycin O-acetyltransferase (Vat) enzymes. Despite the structural elucidation performed for the VatD acetyltransferase, which provided a general molecular framework for activity, a detailed characterization of the essential catalytic and antibiotic substrate-binding determinants in Vat enzymes is still lacking. We have determined the crystal structure of S. aureus VatA in apo, virginiamycin M1- and acetyl-coenzyme A (CoA)-bound forms and provide an extensive mutagenesis and functional analysis of the structural determinants required for catalysis and streptogramin A recognition. Based on an updated genomic survey across the Vat enzyme family, we identified key conserved residues critical for VatA activity that are not part of the O-acetylation catalytic apparatus. Exploiting such constraints of the Vat active site may lead to the development of streptogramin A compounds that evade inactivation by Vat enzymes while retaining binding to their ribosomal target.


  • Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada Center for Structural Genomics of Infectious Diseases (CSGID).


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virginiamycin A acetyltransferase
A, B, C
220Staphylococcus aureusMutation(s): 0 
Gene Names: vat
EC: 2.3.1
UniProt
Find proteins for P26839 (Staphylococcus aureus)
Explore P26839 
Go to UniProtKB:  P26839
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP26839
Sequence Annotations
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  • Reference Sequence
Small Molecules
Ligands 7 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
VIR
Query on VIR

Download Ideal Coordinates CCD File 
S [auth A]VIRGINIAMYCIN M1
C28 H35 N3 O7
DAIKHDNSXMZDCU-FQTGFAPKSA-N
PGE
Query on PGE

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FA [auth B],
GA [auth B]
TRIETHYLENE GLYCOL
C6 H14 O4
ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG
Query on PEG

Download Ideal Coordinates CCD File 
EA [auth B],
P [auth A],
Q [auth A],
R [auth A]
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
D [auth A]
E [auth A]
F [auth A]
HA [auth C]
IA [auth C]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
AA [auth B]
BA [auth B]
CA [auth B]
DA [auth B]
L [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
H [auth A]
I [auth A]
J [auth A]
JA [auth C]
K [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA
Query on NA

Download Ideal Coordinates CCD File 
G [auth A]SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.36 Å
  • R-Value Free:  0.228 (Depositor), 0.230 (DCC) 
  • R-Value Work:  0.184 (Depositor), 0.190 (DCC) 
  • R-Value Observed: 0.186 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 93.308α = 90
b = 184.735β = 90
c = 98.567γ = 90
Software Package:
Software NamePurpose
HKL-3000data collection
PHENIXmodel building
PHENIXrefinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 

Created with Raphaël 2.3.0Worse 01 BetterLigand structure goodness of fit to experimental dataBest fitted VIRClick on this verticalbar to view details

Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2012-11-21
    Type: Initial release
  • Version 1.1: 2014-09-24
    Changes: Database references
  • Version 1.2: 2014-12-24
    Changes: Database references
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description