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Anti-TRAP (AT) is a small zinc-binding protein that regulates tryptophan biosynthesis inBacillus subtilis by binding to tryptophan-boundtrp RNA-binding attenuation protein (TRAP), thereby preventing it from binding RNA, and allowing transcription and translation of thetrp EDCFBA operon. Crystallographic and sedimentation studies have shown that AT can homooligomerize to form a dodecamer, AT12 , composed of a tetramer of trimers, AT3 . Structural and biochemical studies suggest that only trimeric AT is active for binding to TRAP. Our chromatographic and spectroscopic data revealed that a large fraction of recombinantly overexpressed AT retains the N-formyl group (fAT), presumably due to incomplete N-formyl-methionine processing by peptide deformylase. Hydrodynamic parameters from NMR relaxation and diffusion measurements showed that fAT is exclusively trimeric (AT3 ), while (deformylated) AT exhibits slow exchange between both trimeric and dodecameric forms. We examined this equilibrium using NMR spectroscopy and found that oligomerization of active AT3 to form inactive AT12 is linked to protonation of the amino terminus. Global analysis of the pH dependence of the trimer-dodecamer equilibrium revealed a near physiologicalpK a for the N-terminal amine of AT and yielded a pH-dependent oligomerization equilibrium constant. Estimates of excluded volume effects due to molecular crowding suggest the oligomerization equilibrium may be physiologically important. Because deprotonation favors “active” trimeric AT and protonation favors “inactive” dodecameric AT, our findings illuminate a possible mechanism for sensing and responding to changes in cellular pH.

proceedings of the national academy of sciences of the united states of america

Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of <i>Bacillus subtilis</i> anti- <i>trp</i> RNA-binding attenuation protein

Mechanism for pH-dependent gene regulation by amino-terminus-mediated homooligomerization of Bacillus subtilis anti- trp RNA-binding attenuation protein