3WRU

Crystal structure of the bacterial ribosomal decoding site in complex with synthetic aminoglycoside with F-HABA group

• PDB DOI: https://doi.org/10.2210/pdb3WRU/pdb
• NAKB: 3WRU

• Classification: RNA/antibiotic
• Mutation(s): No 


• Deposited: 2014-02-27 Released: 2014-11-05 
• Deposition Author(s): Maianti, J.P., Kanazawa, H., Dozzo, P., Feeney, L.A., Armstrong, E.S., Kondo, J., Hanessian, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.262 
• R-Value Work: 0.249 

Literature

Toxicity Modulation, Resistance Enzyme Evasion, and A-Site X-ray Structure of Broad-Spectrum Antibacterial Neomycin Analogs

Maianti, J.P., Kanazawa, H., Dozzo, P., Matias, R.D., Feeney, L.A., Armstrong, E.S., Hildebrandt, D.J., Kane, T.R., Gliedt, M.J., Goldblum, A.A., Linsell, M.S., Aggen, J.B., Kondo, J., Hanessian, S.

(2014) ACS Chem Biol 9: 2067-2073

• PubMed: 25019242 
• DOI: https://doi.org/10.1021/cb5003416
• Primary Citation of Related Structures:  
  3WRU


• PubMed Abstract: 
  

  Aminoglycoside antibiotics are pseudosaccharides decorated with ammonium groups that are critical for their potent broad-spectrum antibacterial activity. Despite over three decades of speculation whether or not modulation of pKa is a viable strategy to curtail aminoglycoside kidney toxicity, there is a lack of methods to systematically probe amine-RNA interactions and resultant cytotoxicity trends. This study reports the first series of potent aminoglycoside antibiotics harboring fluorinated N1-hydroxyaminobutyryl acyl (HABA) appendages for which fluorine-RNA contacts are revealed through an X-ray cocrystal structure within the RNA A-site. Cytotoxicity in kidney-derived cells was significantly reduced for the derivative featuring our novel β,β-difluoro-HABA group, which masks one net charge by lowering the pKa without compromising antibacterial potency. This novel side-chain assists in evasion of aminoglycoside-modifying enzymes, and it can be easily transferred to impart these properties onto any number of novel analogs.

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Organizational Affiliation: 

Department of Chemistry, Université de Montréal , CP 6128 Succ. Centre-Ville, Montréal, Québec H3C3J7, Canada.

Biological Assembly 1  

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

Macromolecule Content

• Total Structure Weight: 16.12 kDa 
• Atom Count: 1,047 
• Modelled Residue Count: 42 
• Deposited Residue Count: 46 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
RNA (5'-R(*UP*UP*GP*CP*GP*UP*CP*AP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3')	A, B	23	N/A

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SJP	C [auth A], D [auth B]	(2R,3R)-4-amino-N-[(1R,2S,3R,4R,5S)-5-amino-4-[(2,6-diamino-2,3,4,6-tetradeoxy-alpha-D-erythro-hexopyranosyl)oxy]-3-{[3-O-(2,6-diamino-2,3,4,6-tetradeoxy-beta-L-threo-hexopyranosyl)-beta-D-ribofuranosyl]oxy}-2-hydroxycyclohexyl]-3-fluoro-2-hydroxybutanamide C27 H52 F N7 O11 XWTWBGQMVSXRIE-ZLDKHCKJSA-N
K	E [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.262 
• R-Value Work: 0.249 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.554	α = 90
b = 32.602	β = 108.5
c = 51.413	γ = 90

Software Package:

Software Name	Purpose
PHENIX	model building
CNS	refinement
CrystalClear	data reduction
CrystalClear	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-11-05 
Deposition Author(s): Maianti, J.P., Kanazawa, H., Dozzo, P., Feeney, L.A., Armstrong, E.S., Kondo, J., Hanessian, S.

Revision History  

• Version 1.0: 2014-11-05
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations