3Q2J

Crystal Structure of 3',5"-Aminoglycoside Phosphotransferase Type IIIa Protein Kinase Inhibitor CKI-7 Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1501 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structures of two aminoglycoside kinases bound with a eukaryotic protein kinase inhibitor.

Fong, D.H.Xiong, B.Hwang, J.Berghuis, A.M.

(2011) Plos One 6: e19589-e19589

  • DOI: 10.1371/journal.pone.0019589
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibiotic resistance is recognized as a growing healthcare problem. To address this issue, one strategy is to thwart the causal mechanism using an adjuvant in partner with the antibiotic. Aminoglycosides are a class of clinically important antibioti ...

    Antibiotic resistance is recognized as a growing healthcare problem. To address this issue, one strategy is to thwart the causal mechanism using an adjuvant in partner with the antibiotic. Aminoglycosides are a class of clinically important antibiotics used for the treatment of serious infections. Their usefulness has been compromised predominantly due to drug inactivation by aminoglycoside-modifying enzymes, such as aminoglycoside phosphotransferases or kinases. These kinases are structurally homologous to eukaryotic Ser/Thr and Tyr protein kinases and it has been shown that some can be inhibited by select protein kinase inhibitors. The aminoglycoside kinase, APH(3')-IIIa, can be inhibited by CKI-7, an ATP-competitive inhibitor for the casein kinase 1. We have determined that CKI-7 is also a moderate inhibitor for the atypical APH(9)-Ia. Here we present the crystal structures of CKI-7-bound APH(3')-IIIa and APH(9)-Ia, the first structures of a eukaryotic protein kinase inhibitor in complex with bacterial kinases. CKI-7 binds to the nucleotide-binding pocket of the enzymes and its binding alters the conformation of the nucleotide-binding loop, the segment homologous to the glycine-rich loop in eukaryotic protein kinases. Comparison of these structures with the CKI-7-bound casein kinase 1 reveals features in the binding pockets that are distinct in the bacterial kinases and could be exploited for the design of a bacterial kinase specific inhibitor. Our results provide evidence that an inhibitor for a subset of APHs can be developed in order to curtail resistance to aminoglycosides.


    Organizational Affiliation

    Department of Biochemistry, McGill University, Montreal, Quebec, Canada.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Aminoglycoside 3'-phosphotransferase
A, B
264Enterococcus faecalisMutation(s): 0 
Gene Names: aphA
EC: 2.7.1.95
Find proteins for P0A3Y5 (Enterococcus faecalis)
Go to UniProtKB:  P0A3Y5
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CKI
Query on CKI

Download SDF File 
Download CCD File 
A, B
N-(2-AMINOETHYL)-5-CHLOROISOQUINOLINE-8-SULFONAMIDE
C11 H12 Cl N3 O2 S
OGKYMFFYOWUTKV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

Download SDF File 
Download CCD File 
A, B
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
CKIKi: 66100 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1501 Å
  • R-Value Free: 0.235 
  • R-Value Work: 0.189 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 49.837α = 90.00
b = 91.852β = 90.00
c = 131.150γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data scaling
CNSrefinement
HKL-2000data reduction
HKL-2000data collection
PHENIXrefinement
CNSphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2011-05-18
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2013-06-19
    Type: Database references