Transcription Factor Allosteric Regulation Through Substrate Coordination to Zinc

The development of new synthetic biology circuits for biotechnology and medicine requires deeper mechanistic insight on allosteric transcription factors (aTFs). Here we studied the aTF UxuR in the free form and bound to the inducer D-fructuronate or the analog D-glucuronate. We employed molecular dynamics simulations, principal component analysis and electrostatic potential surface calculations. We furthermore constructed a sensor plasmid for Dfructuronate in E. coli and performed site-directed mutagenesis. Our results show that zinc coordination is necessary for UxuR function and that when the inducer is bound, UxuR acquires an open conformation with a more pronounced negative charge at the surface of the N-terminal DNA binding domains. In opposition, in the free and D-glucuronate bond forms the protein acquires closed conformations, with a more positive character at the surface of the DNA binding regions. These processes can be more general than anticipated and harnessed for biological systems engineering.