Biological Assembly 1  

Global Symmetry: Cyclic - C3  (3D View)
Global Stoichiometry: Homo 3-mer - A3 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 79.57 kDa 
• Atom Count: 6,018 
• Modelled Residue Count: 632 
• Deposited Residue Count: 660 
• Unique protein chains: 1

 4HUR

Crystal structure of streptogramin group A antibiotic acetyltransferase VatA from Staphylococcus aureus in complex with acetyl coenzyme A

• PDB DOI:  https://doi.org/10.2210/pdb4HUR/pdb

• Classification: TRANSFERASE
• Organism(s): Staphylococcus aureus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2012-11-03 Released: 2012-11-14 
• Deposition Author(s): Stogios, P.J., Minasov, G., Evdokimova, E., Wawrzak, Z., Yim, V., Krishnamoorthy, M., Di Leo, R., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 

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

• PubMed: 25223995 
• 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Virginiamycin A acetyltransferase	A, B, C	220	Staphylococcus aureus	Mutation(s): 0  Gene Names: vat EC: 2.3.1
UniProt
Find proteins for P26839 (Staphylococcus aureus) Explore P26839  Go to UniProtKB:  P26839

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACO	CA [auth C], D [auth A], T [auth B]	ACETYL COENZYME *A C23 H38 N7 O17 P3 S ZSLZBFCDCINBPY-ZSJPKINUSA-N
SO4	DA [auth C], E [auth A], F [auth A], G [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	EA [auth C], FA [auth C], GA [auth C], H [auth A], HA [auth C], I [auth A], IA [auth C], J [auth A], JA [auth C], K [auth A], KA [auth C], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], O [auth A], P [auth A], Q [auth A], R [auth A], U [auth B], V [auth B], W [auth B], X [auth B], Y [auth B], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	AA [auth B], BA [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	S [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.202 
• R-Value Work: 0.167 
• R-Value Observed: 0.168 
• Space Group: C 2 2 2₁
• Diffraction Data: https://doi.org/10.18430/M34HUR

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 92.91	α = 90
b = 184.545	β = 90
c = 98.997	γ = 90

Software Package:

Software Name	Purpose
HKL-3000	data collection
PHENIX	model building
PHENIX	refinement
HKL-3000	data reduction
HKL-3000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-11-14 
Deposition Author(s): Stogios, P.J., Minasov, G., Evdokimova, E., Wawrzak, Z., Yim, V., Krishnamoorthy, M., Di Leo, R., Courvalin, P., Savchenko, A., Anderson, W.F., Center for Structural Genomics of Infectious Diseases (CSGID)

Revision History  

• Version 1.0: 2012-11-14
  Type: Initial release
  
• Version 1.1: 2012-11-21
  Changes: Other
• Version 1.2: 2014-09-24
  Changes: Database references
• Version 1.3: 2014-12-24
  Changes: Database references