4HUS | pdb_00004hus

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

• PDB DOI: https://doi.org/10.2210/pdb4HUS/pdb

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


• Deposited: 2012-11-03 Released: 2012-11-21 
• 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: 2.36 Å
• R-Value Free: 
  0.228 (Depositor), 0.230 (DCC) 
• R-Value Work: 
  0.184 (Depositor), 0.186 (DCC) 
• R-Value Observed: 
  0.186 (Depositor) 

Starting Model: experimental

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 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).
Center for Structural Genomics of Infectious Diseases (CSGID) Department of Molecular Pharmacology and Biological Chemistry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA.
Unité des Agents Antibactériens, Institut Pasteur, Paris, France.
Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, Ontario, Canada Center for Structural Genomics of Infectious Diseases (CSGID) [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 78.35 kDa 
• Atom Count: 5,825 
• Modeled Residue Count: 635 
• Deposited Residue Count: 660 
• Unique protein chains: 1

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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VIR	S [auth A]	VIRGINIAMYCIN M1 C28 H35 N3 O7 DAIKHDNSXMZDCU-FQTGFAPKSA-N
PGE	FA [auth B], GA [auth B]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
PEG	EA [auth B], P [auth A], Q [auth A], R [auth A]	DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], HA [auth C], IA [auth C], T [auth B], U [auth B], V [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
EDO	AA [auth B], BA [auth B], CA [auth B], DA [auth B], L [auth A], LA [auth C], M [auth A], MA [auth C], N [auth A], NA [auth C], O [auth A], OA [auth C], PA [auth C], QA [auth C], Z [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL	H [auth A], I [auth A], J [auth A], JA [auth C], K [auth A], KA [auth C], W [auth B], X [auth B], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	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), 0.186 (DCC) 
• R-Value Observed: 0.186 (Depositor) 

Diffraction Data: https://doi.org/10.18430/m34hus

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.308	α = 90
b = 184.735	β = 90
c = 98.567	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: 2012-11-21 
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: 2012-11-21
  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