Crystal Structure of Vat(D) in Complex with Virginiamycin and Coenzyme A

Experimental Data Snapshot

  • Resolution: 2.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 

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Crystal structure of Vat(D): an acetyltransferase that inactivates streptogramin group A antibiotics.

Sugantino, M.Roderick, S.L.

(2002) Biochemistry 41: 2209-2216

  • DOI: https://doi.org/10.1021/bi011991b
  • Primary Citation of Related Structures:  
    1KHR, 1KK4, 1KK5, 1KK6

  • PubMed Abstract: 

    The streptogramin class of antibiotics act to inhibit bacterial protein synthesis, and their semisynthetic derivatives, such as dalfopristin-quinupristin (Synercid), are used to treat serious or life-threatening infections due to multiply antibiotic resistant bacteria. Acquired resistance of the nosocomial pathogen Enterococcus faecium to the group A component of natural and semisynthetic streptogramin mixtures is a prerequisite for the streptogramin resistance phenotype and is mediated by a streptogramin acetyltransferase. The crystal structure of Vat(D), a streptogramin acetyltransferase from a human urinary isolate of E. faecium, has been determined as an apoenzyme and in complex with either acetyl-CoA or virginiamycin M1 and CoA. These structures illustrate the location and arrangement of residues at the active site, and point to His 82 as a residue that may function as a general base. The structural similarity of Vat(D) to the xenobiotic acetyltransferase from Pseudomonas aeruginosa indicates similarities in the catalytic mechanism for these enzymes as well as several shared and distinctive antibiotic binding interactions between these enzymes and their respective substrates. These results reveal the molecular basis for a reaction by which Gram-positive cocci acquire resistance to a last resort antibiotic.

  • Organizational Affiliation

    Department of Biochemistry, Albert Einstein College of Medicine, 1300 Morris Park Avenue, Bronx, New York 10461, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B, C, D, E
A, B, C, D, E, F
209Enterococcus faeciumMutation(s): 0 
Gene Names: satA
EC: 2.3.1
Find proteins for P50870 (Enterococcus faecium)
Explore P50870 
Go to UniProtKB:  P50870
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP50870
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.80 Å
  • R-Value Free: 0.251 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.189 
  • Space Group: F 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 186.1α = 90
b = 185.9β = 90
c = 186.9γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-GENdata reduction
XDSdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-02-20
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-11
    Changes: Refinement description
  • Version 1.4: 2024-02-14
    Changes: Data collection, Database references, Derived calculations