5C4K

APH(2")-IVa in complex with GET (G418) at room temperature


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 

Starting Model: experimental
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Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Aminoglycoside binding and catalysis specificity of aminoglycoside 2-phosphotransferase IVa: A thermodynamic, structural and kinetic study.

Kaplan, E.Guichou, J.F.Chaloin, L.Kunzelmann, S.Leban, N.Serpersu, E.H.Lionne, C.

(2016) Biochim Biophys Acta 1860: 802-813

  • DOI: https://doi.org/10.1016/j.bbagen.2016.01.016
  • Primary Citation of Related Structures:  
    5C4K, 5C4L

  • PubMed Abstract: 

    Aminoglycoside O-phosphotransferases make up a large class of bacterial enzymes that is widely distributed among pathogens and confer a high resistance to several clinically used aminoglycoside antibiotics. Aminoglycoside 2″-phosphotransferase IVa, APH(2″)-IVa, is an important member of this class, but there is little information on the thermodynamics of aminoglycoside binding and on the nature of its rate-limiting step. We used isothermal titration calorimetry, electrostatic potential calculations, molecular dynamics simulations and X-ray crystallography to study the interactions between the enzyme and different aminoglycosides. We determined the rate-limiting step of the reaction by the means of transient kinetic measurements. For the first time, Kd values were determined directly for APH(2″)-IVa and different aminoglycosides. The affinity of the enzyme seems to anti-correlate with the molecular weight of the ligand, suggesting a limited degree of freedom in the binding site. The main interactions are electrostatic bonds between the positively charged amino groups of aminoglycosides and Glu or Asp residues of APH. In spite of the significantly different ratio Kd/Km, there is no large difference in the transient kinetics obtained with the different aminoglycosides. We show that a product release step is rate-limiting for the overall reaction. APH(2″)-IVa has a higher affinity for aminoglycosides carrying an amino group in 2' and 6', but tighter bindings do not correlate with higher catalytic efficiencies. As with APH(3')-IIIa, an intermediate containing product is preponderant during the steady state. This intermediate may constitute a good target for future drug design.


  • Organizational Affiliation

    CNRS, FRE3689 - Université de Montpellier, Centre d'études d'agents Pathogènes et Biotechnologies pour la Santé, F-34293 Montpellier, France.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
APH(2'')-Id
A, B
321Enterococcus casseliflavusMutation(s): 2 
Gene Names: aph(2'')-Id
UniProt
Find proteins for O68183 (Enterococcus casseliflavus)
Explore O68183 
Go to UniProtKB:  O68183
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO68183
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GET
Query on GET

Download Ideal Coordinates CCD File 
C [auth A]GENETICIN
C20 H40 N4 O10
BRZYSWJRSDMWLG-DJWUNRQOSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.05 Å
  • R-Value Free: 0.199 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.161 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 78.703α = 90
b = 64.941β = 90.73
c = 78.87γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALAdata scaling
PDB_EXTRACTdata extraction
XDSdata reduction
Cootmodel building

Structure Validation

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Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
French National Research AgencyFranceFDT20140931113

Revision History  (Full details and data files)

  • Version 1.0: 2016-02-03
    Type: Initial release
  • Version 1.1: 2016-02-17
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Author supporting evidence, Data collection, Database references, Refinement description