Central to the transcriptional control of the Escherichia coli heat shock regulon is the stress-dependent inhibition of the sigma(32) subunit of RNA polymerase by reversible association with the DnaK chaperone, mediated by the DnaJ cochaperone. Here we identified two distinct sites in sigma(32) as binding sites for DnaK and DnaJ. DnaJ binding destabilizes a distant region of sigma(32) in close spatial vicinity of the DnaK-binding site, and DnaK destabilizes a region in the N-terminal domain, the primary target for the FtsH protease, which degrades sigma(32) in vivo. Our findings suggest a molecular mechanism for the DnaK- and DnaJ-mediated inactivation of sigma(32) as part of the heat shock response. They furthermore demonstrate that DnaK and DnaJ binding can induce conformational changes in a native protein substrate even at distant sites, a feature that we propose to be of general relevance for the action of Hsp70 chaperone systems.