6X3C

Crystal structure of streptogramin A acetyltransferase VatA from Staphylococcus aureus in complex with streptogramin analog F1037 (47)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 

wwPDB Validation   3D Report Full Report



Literature

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: 10.1038/s41586-020-2761-3
  • Primary Citation of Related Structures:  
    6PCH, 6PC6, 6PC5, 6PC8, 6PC7, 6PCR, 6PCQ, 6PCT, 6PCS, 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 a ...

    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 Pharmaceutical Chemistry, Cardiovascular Research Institute, University of California, San Francisco, San Francisco, CA, USA. ian.seiple@ucsf.edu.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Virginiamycin A acetyltransferaseABCDEF207Staphylococcus aureusMutation(s): 0 
Gene Names: vat
EC: 2.3.1
Find proteins for P26839 (Staphylococcus aureus)
Explore P26839 
Go to UniProtKB:  P26839
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 6 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O7S
Query on O7S

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A, B, C, D, E, F
(3R,4R,5E,10E,12E,14S,16R,26aR)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione
C30 H40 F N3 O6
GWIAEMBAGQHJHW-CLECSTCYSA-N
 Ligand Interaction
SXA
Query on SXA

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A, B, C, E, F
THIOACETIC ACID S-{2-[3-(2-HYDROXY-3,3-DIMETHYL-4-PHOSPHONOOXY-BUTYRYLAMINO)-PROPIONYLAMINO]-ETHYL} ESTER
C13 H25 N2 O8 P S
AJFWMDFTVVFMHY-LLVKDONJSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B, D
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
PO4
Query on PO4

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A, B, C, D, E, F
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
CL
Query on CL

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A, C, D, E, F
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
MG
Query on MG

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B, E
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.234 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 105.54α = 90
b = 105.62β = 90
c = 178.2γ = 90
Software Package:
Software NamePurpose
PHENIXrefinement
PHENIXphasing
xia2data reduction
xia2data scaling

Structure Validation

View Full Validation Report



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 

  • Version 1.0: 2020-11-18
    Type: Initial release