biostudies-literatureHuang HTNational Institutes of HealthNIGMS NIH HHS324-332https://www.ebi.ac.uk/biostudies/studies/S-EPMC5766909biostudies-literatureUnknown293(1)RcnR, a transcriptional regulator in <i>Escherichia coli</i>, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered flexibility from the N terminus through helix 1 and modulated the RcnR-DNA interaction. Apo-RcnR and RcnR-DNA complexes and the Zn(II)-RcnR complex exhibited similar ²H uptake kinetics, with fast-exchanging segments located in the N terminus, in helix 1 (reThe Journal of biological chemistryCo(II) and Ni(II) binding of the <i>Escherichia coli</i> transcriptional repressor RcnR orders its N terminus, alters helix dynamics, and reduces DNA affinity.PMC5766909R01 GM069696R01-GM069696Iwig JSKaltashov IAChivers PTMaroney MJBobst CEHuang HTfalseCo(II) and Ni(II) binding of the <i>Escherichia coli</i> transcriptional repressor RcnR orders its N terminus, alters helix dynamics, and reduces DNA affinity.RcnR, a transcriptional regulator in <i>Escherichia coli</i>, derepresses the expression of the export proteins RcnAB upon binding Ni(II) or Co(II). Lack of structural information has precluded elucidation of the allosteric basis for the decreased DNA affinity in RcnR's metal-bound states. Here, using hydrogen-deuterium exchange coupled with MS (HDX-MS), we probed the RcnR structure in the presence of DNA, the cognate metal ions Ni(II) and Co(II), or the noncognate metal ion Zn(II). We found that cognate metal binding altered flexibility from the N terminus through helix 1 and modulated the RcnR-DNA interaction. Apo-RcnR and RcnR-DNA complexes and the Zn(II)-RcnR complex exhibited similar ²H uptake kinetics, with fast-exchanging segments located in the N terminus, in helix 1 (re2018-01-01T00:00:00Z2018 Jan2025-04-21T16:16:47.085Z2019-03-26T22:31:20ZS-EPMC57669092915044110.1074/jbc.ra117.00039810.1074/jbc.RA117.000398