2BKK

Crystal structure of Aminoglycoside Phosphotransferase APH(3')-IIIa in complex with the inhibitor AR_3a


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 

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Literature

Allosteric Inhibition of Aminoglycoside Phosphotransferase by a Designed Ankyrin Repeat Protein

Kohl, A.Amstutz, P.Parizek, P.Binz, H.K.Briand, C.Capitani, G.Forrer, P.Pluckthun, A.Grutter, M.G.

(2005) Structure 13: 1131

  • DOI: 10.1016/j.str.2005.04.020
  • Primary Citation of Related Structures:  
    2BKK

  • PubMed Abstract: 
  • Aminoglycoside phosphotransferase (3')-IIIa (APH) is a bacterial kinase that confers antibiotic resistance to many pathogenic bacteria and shares structural homology with eukaryotic protein kinases. We report here the crystal structure of APH, trapped in an inactive conformation by a tailor-made inhibitory ankyrin repeat (AR) protein, at 2 ...

    Aminoglycoside phosphotransferase (3')-IIIa (APH) is a bacterial kinase that confers antibiotic resistance to many pathogenic bacteria and shares structural homology with eukaryotic protein kinases. We report here the crystal structure of APH, trapped in an inactive conformation by a tailor-made inhibitory ankyrin repeat (AR) protein, at 2.15 A resolution. The inhibitor was selected from a combinatorial library of designed AR proteins. The AR protein binds the C-terminal lobe of APH and thereby stabilizes three alpha helices, which are necessary for substrate binding, in a significantly displaced conformation. BIAcore analysis and kinetic enzyme inhibition experiments are consistent with the proposed allosteric inhibition mechanism. In contrast to most small-molecule kinase inhibitors, the AR proteins are not restricted to active site binding, allowing for higher specificity. Inactive conformations of pharmaceutically relevant enzymes, as can be elucidated with the approach presented here, represent powerful starting points for rational drug design.


    Organizational Affiliation

    Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASEA, C264Enterococcus faecalisMutation(s): 1 
Gene Names: aphA
EC: 2.7.1.95
UniProt
Find proteins for P0A3Y5 (Enterococcus faecalis)
Explore P0A3Y5 
Go to UniProtKB:  P0A3Y5
Entity Groups  
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UniProt GroupP0A3Y5
Protein Feature View
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
DESIGNED ANKYRIN REPEAT INHIBITOR AR_3AB, D169synthetic constructMutation(s): 0 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Protein Feature View
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  • Reference Sequence
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.260 
  • R-Value Work: 0.199 
  • R-Value Observed: 0.200 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 59.67α = 90
b = 98.082β = 110.01
c = 81.3γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing

Structure Validation

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Ligand Structure Quality Assessment 



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-08-09
    Type: Initial release
  • Version 1.1: 2016-12-21
    Changes: Database references, Derived calculations, Non-polymer description, Other, Source and taxonomy, Structure summary, Version format compliance