2BKK

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

Summary for 2BKK

• Entry DOI: 10.2210/pdb2bkk/pdb
• Related: 1J7I 1J7L 1J7U 1K1A 1K1B 1L8T 1L8U 1MJ0 1N0Q 1N0R 2BKG
• Descriptor: AMINOGLYCOSIDE 3'-PHOSPHOTRANSFERASE, DESIGNED ANKYRIN REPEAT INHIBITOR AR_3A, ADENOSINE-5'-DIPHOSPHATE, ... (5 entities in total)
• Functional Keywords: transferase/peptide, transferase-designed protein complex, ankyrin repeat, co-crystallization, inhibitor design, drug design, enzyme inhibition, kinase inhibition, designed repeat protein, antibiotic resistance, atp-binding, kinase, plasmid, transferase, transferase-peptide complex
• Biological source: ENTEROCOCCUS FAECALIS; More
• Total number of polymer chains: 4
• Total formula weight: 100117.13

Authors

Kohl, A.,Amstutz, P.,Parizek, P.,Binz, H.K.,Briand, C.,Capitani, G.,Forrer, P.,Pluckthun, A.,Grutter, M.G. (deposition date: 2005-02-16, release date: 2005-08-09, Last modification date: 2023-12-13)

Primary citation

Kohl, A.,Amstutz, P.,Parizek, P.,Binz, H.K.,Briand, C.,Capitani, G.,Forrer, P.,Pluckthun, A.,Grutter, M.G.
Allosteric Inhibition of Aminoglycoside Phosphotransferase by a Designed Ankyrin Repeat Protein
Structure, 13:1131-, 2005

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 2.15 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.

PubMed: 16084385
DOI: 10.1016/J.STR.2005.04.020

Experimental method

X-RAY DIFFRACTION (2.15 Å)