Modulation of the protein environment in the hydrophilic pore of the ammonia transporter protein AmtB upon GlnK protein binding

Edited by Maurice Montal

Received 22 June 2007; received in revised form 30 July 2007; accepted 31 July 2007. published online 15 August 2007.

Abstract

The conduction of ammonia/ammonium () through the channel protein AmtB is inhibited by the binding of the signal transduction protein GlnK. In the AmtB–GlnK binding interface, there exists an binding site – Am6. The calculated pKa values at the Am6 sites in both the AmtB–GlnK complex and isolated AmtB implies the dominance of an uncharged NH3 state. The GlnK protein binding causes a significant downshift in the Am6 pKa value of the AmtB. However, this downshift is perfectly compensated by the reorientation of the protein backbone (carbonyl group of Cys312 from the AmtB part) upon AmtB–GlnK complex formation.

Abbreviations: AmtB conformational change, conformational change that occurs inside the AmtB part, AmtB–GlnK complex, crystal structure of the AmtB protein bound by the GlnK protein, Amt protein, ammonium transport protein, GlnK-depleted complex, crystal structure of the AmtB protein obtained by the depletion of the GlnK coordinates of the AmtB–GlnK complex, GlnK influence, influence of the GlnK part on the AmtB–GlnK complex, Isolated AmtB, crystal structure of the free AmtB protein, LPB equation, linear Poisson–Boltzmann equation, PDB, protein data bank

Keywords: AmtB–GlnK complex, Protein conformational change, Ion channel, Proton transfer pathway, Ammonia/ammonium transport inhibition

417 SGM Building, Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA

Fax: +1 213 740 2701.

PII: S0014-5793(07)00878-2

doi:10.1016/j.febslet.2007.07.085

29 of 41