4FEX

Crystal structure of the aminoglycoside phosphotransferase APH(3')-Ia, with substrate kanamycin and small molecule inhibitor tyrphostin AG1478


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.71 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.184 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Structure-guided optimization of protein kinase inhibitors reverses aminoglycoside antibiotic resistance.

Stogios, P.J.Spanogiannopoulos, P.Evdokimova, E.Egorova, O.Shakya, T.Todorovic, N.Capretta, A.Wright, G.D.Savchenko, A.

(2013) Biochem.J. 454: 191-200

  • DOI: 10.1042/BJ20130317
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue com ...

    Activity of the aminoglycoside phosphotransferase APH(3')-Ia leads to resistance to aminoglycoside antibiotics in pathogenic Gram-negative bacteria, and contributes to the clinical obsolescence of this class of antibiotics. One strategy to rescue compromised antibiotics such as aminoglycosides is targeting the enzymes that confer resistance with small molecules. We demonstrated previously that ePK (eukaryotic protein kinase) inhibitors could inhibit APH enzymes, owing to the structural similarity between these two enzyme families. However, limited structural information of enzyme-inhibitor complexes hindered interpretation of the results. In addition, cross-reactivity of compounds between APHs and ePKs represents an obstacle to their use as aminoglycoside adjuvants to rescue aminoglycoside antibiotic activity. In the present study, we structurally and functionally characterize inhibition of APH(3')-Ia by three diverse chemical scaffolds, anthrapyrazolone, 4-anilinoquinazoline and PP (pyrazolopyrimidine), and reveal distinctions in the binding mode of anthrapyrazolone and PP compounds to APH(3')-Ia compared with ePKs. Using this observation, we identify PP derivatives that select against ePKs, attenuate APH(3')-Ia activity and rescue aminoglycoside antibiotic activity against a resistant Escherichia coli strain. The structures described in the present paper and the inhibition studies provide an important opportunity for structure-based design of compounds to target aminoglycoside phosphotransferases for inhibition, potentially overcoming this form of antibiotic resistance.


    Organizational Affiliation

    Department of Chemical Engineering and Applied Chemistry, University of Toronto, Ontario, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside 3'-phosphotransferase AphA1-IAB
A, B, C, D, E
272Acinetobacter baumannii (strain AYE)Mutation(s): 0 
EC: 2.7.1.95
Find proteins for B0VD92 (Acinetobacter baumannii (strain AYE))
Go to UniProtKB:  B0VD92
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0TO
Query on 0TO

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A, C, D, E
N-(3-chlorophenyl)-6,7-dimethoxyquinazolin-4-amine
C16 H14 Cl N3 O2
GFNNBHLJANVSQV-UHFFFAOYSA-N
 Ligand Interaction
NA
Query on NA

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Download CCD File 
A, B
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
ACT
Query on ACT

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C
ACETATE ION
C2 H3 O2
QTBSBXVTEAMEQO-UHFFFAOYSA-M
 Ligand Interaction
KAN
Query on KAN

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Download CCD File 
A, B, C, D, E
KANAMYCIN A
C18 H36 N4 O11
SBUJHOSQTJFQJX-NOAMYHISSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

Unit Cell:
Length (Å)Angle (°)
a = 57.669α = 118.84
b = 93.694β = 103.56
c = 96.318γ = 93.44
Software Package:
Software NamePurpose
HKL-2000data scaling
HKL-3000data collection
PHENIXrefinement
HKL-2000data reduction
PHENIXmodel building
PHENIXphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Revision History 

  • Version 1.0: 2012-06-20
    Type: Initial release
  • Version 1.1: 2013-06-26
    Type: Database references
  • Version 1.2: 2013-08-07
    Type: Database references
  • Version 1.3: 2013-09-04
    Type: Database references