Establishing the principles of recognition in the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3′)-IIIa]

David D. Boehr, Adam R. Farley, Frank J. LaRonde, Tera Rica Murdock, Gerard D. Wright, James R. Cox

Research output: Contribution to journalArticlepeer-review

19 Scopus citations

Abstract

The protein-based molecular recognition of the adenine ring has implications throughout biological systems. In this paper, we discuss the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3′)-IIIa], which serves as an excellent model system for proteins that bind the adenine ring. This enzyme employs a hydrogen-bonding network involving water molecules along with enzyme backbone/ side-chain atoms and a π-π stacking interaction to recognize the adenine ring. Our approach utilized site-directed mutagenesis, adenosine analogues and a variety of biophysical methods to probe the contacts in the adenine-binding region of APH(3′)-IIIa. The results point to the polar nature of an adenine-Met90 contact in this binding pocket and the important role that Met90, the "gatekeeper" residue in structurally similar Ser/Thr protein kinases, plays in adenine binding. The results also suggest that small changes in the structure of the adenine ring can lead to significant changes in the ability of these analogues to occupy the adenine-binding region of the enzyme. Additional computational experiments indicate that both size and electronic factors are important in the binding of aromatic systems in this interaction-rich pocket. The principles governing adenine recognition established in this study may be applied to other protein-ligand complexes and used to navigate future studies directed at discovering potent and selective inhibitors of APH-type enzymes.

Original languageEnglish (US)
Pages (from-to)12445-12453
Number of pages9
JournalBiochemistry
Volume44
Issue number37
DOIs
StatePublished - Sep 20 2005

All Science Journal Classification (ASJC) codes

  • Biochemistry

Fingerprint

Dive into the research topics of 'Establishing the principles of recognition in the adenine-binding region of an aminoglycoside antibiotic kinase [APH(3′)-IIIa]'. Together they form a unique fingerprint.

Cite this