2BKK: Crystal Structure Of Aminoglycoside Phosphotransferase Aph (3')-iiia In Complex With The Inhibitor Ar_3a

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.
PDB ID: 2BKKDownload
MMDB ID: 34914
PDB Deposition Date: 2005/2/16
Updated in MMDB: 2016/12
Experimental Method:
x-ray diffraction
Resolution: 2.15  Å
Source Organism:
synthetic construct
Similar Structures:
Biological Unit for 2BKK: dimeric; determined by author and by software (PQS)
Molecular Components in 2BKK
Label Count Molecule
Proteins (2 molecules)
Aminoglycoside 3'-phosphotransferase
Molecule annotation
Designed Ankyrin Repeat Inhibitor Ar_3a
Molecule annotation
Chemicals (4 molecules)
* Click molecule labels to explore molecular sequence information.

Citing MMDB