Crystal structure of streptogramin A acetyltransferase VatA from Staphylococcus aureus in complex with streptogramin analog F0224 (46)

Experimental Data Snapshot

  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 

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Synthetic group A streptogramin antibiotics that overcome Vat resistance.

Li, Q.Pellegrino, J.Lee, D.J.Tran, A.A.Chaires, H.A.Wang, R.Park, J.E.Ji, K.Chow, D.Zhang, N.Brilot, A.F.Biel, J.T.van Zundert, G.Borrelli, K.Shinabarger, D.Wolfe, C.Murray, B.Jacobson, M.P.Muhle, E.Chesneau, O.Fraser, J.S.Seiple, I.B.

(2020) Nature 586: 145-150

  • DOI: https://doi.org/10.1038/s41586-020-2761-3
  • Primary Citation of Related Structures:  
    6PC5, 6PC6, 6PC7, 6PC8, 6PCH, 6PCQ, 6PCR, 6PCS, 6PCT, 6WYV, 6X3C, 6X3J

  • PubMed Abstract: 

    Natural products serve as chemical blueprints for most antibiotics in clinical use. The evolutionary process by which these molecules arise is inherently accompanied by the co-evolution of resistance mechanisms that shorten the clinical lifetime of any given class of antibiotics 1 . Virginiamycin acetyltransferase (Vat) enzymes are resistance proteins that provide protection against streptogramins 2 , potent antibiotics against Gram-positive bacteria that inhibit the bacterial ribosome 3 . Owing to the challenge of selectively modifying the chemically complex, 23-membered macrocyclic scaffold of group A streptogramins, analogues that overcome the resistance conferred by Vat enzymes have not been previously developed 2 . Here we report the design, synthesis, and antibacterial evaluation of group A streptogramin antibiotics with extensive structural variability. Using cryo-electron microscopy and forcefield-based refinement, we characterize the binding of eight analogues to the bacterial ribosome at high resolution, revealing binding interactions that extend into the peptidyl tRNA-binding site and towards synergistic binders that occupy the nascent peptide exit tunnel. One of these analogues has excellent activity against several streptogramin-resistant strains of Staphylococcus aureus, exhibits decreased rates of acetylation in vitro, and is effective at lowering bacterial load in a mouse model of infection. Our results demonstrate that the combination of rational design and modular chemical synthesis can revitalize classes of antibiotics that are limited by naturally arising resistance mechanisms.

  • Organizational Affiliation

    Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Virginiamycin A acetyltransferase,VatA
A, B, C, D, E
A, B, C, D, E, F
209Staphylococcus aureusMutation(s): 0 
Gene Names: vat
EC: 2.3.1
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
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
O7V (Subject of Investigation/LOI)
Query on O7V

Download Ideal Coordinates CCD File 
BA [auth F]
G [auth A]
J [auth B]
K [auth B]
O [auth C]
BA [auth F],
G [auth A],
J [auth B],
K [auth B],
O [auth C],
U [auth E]
(2R)-2-[(3S,4R,5E,10E,12E,14S,16R,26aR)-16-fluoro-14-hydroxy-4,12-dimethyl-1,7,22-trioxo-4,7,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,3H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosin-3-yl]propyl isoquinolin-3-ylcarbamate
C38 H44 F N5 O8
Query on SXA

Download Ideal Coordinates CCD File 
AA [auth E]
FA [auth F]
GA [auth F]
I [auth A]
N [auth B]
AA [auth E],
FA [auth F],
GA [auth F],
I [auth A],
N [auth B],
T [auth D]
C13 H25 N2 O8 P S
Query on PO4

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H [auth A],
Z [auth E]
O4 P
Query on CL

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CA [auth F]
DA [auth F]
EA [auth F]
L [auth B]
M [auth B]
CA [auth F],
DA [auth F],
EA [auth F],
L [auth B],
M [auth B],
P [auth C],
Q [auth C],
V [auth E],
W [auth E],
X [auth E],
Y [auth E]
Query on MG

Download Ideal Coordinates CCD File 
R [auth C],
S [auth D]
Experimental Data & Validation

Experimental Data

  • Resolution: 2.70 Å
  • R-Value Free: 0.271 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 104.8α = 90
b = 109.22β = 90
c = 173.03γ = 90
Software Package:
Software NamePurpose
xia2data reduction
xia2data scaling

Structure Validation

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Ligand Structure Quality Assessment 

Entry History & Funding Information

Deposition Data

Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM128656

Revision History  (Full details and data files)

  • Version 1.0: 2020-11-18
    Type: Initial release
  • Version 1.1: 2023-10-18
    Changes: Advisory, Data collection, Database references, Refinement description