Importance of the D and E Helices of the Molecular Chaperone DnaK for ATP Binding and Substrate Release

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Abstract
The C-terminal domain of the molecular chaperone DnaK is a compact lid-like structure made up of five α-helices (αA−αE) (residues 508−608) that is followed by a 30-residue disordered, flexible region (609−638). The lid encapsulates the peptide molecule bound in the substrate-binding domain, whereas the function of the 30-residue disordered region is not known. By sequentially deleting the flexible subdomain and the individual lid helices, we deduced the importance of each structural unit to creating long-lived DnaK−peptide complexes. Here we report that (i) the αD helix is essential for long-lived DnaK−peptide complexes. For example, ATP triggers the dissociation of a acrylodan-labeled p5 peptide (ap5, a-CLLLSAPRR) from wtDnaK and DnaK595(A−D) with koff equal to 7.6 and 8.9 s-1, respectively, whereas when the D-helix is deleted, creating DnaK578(A−C), koff jumps to 207 s-1. (ii) The presence of the αB helix impacts the rate of the ATP-induced high-to-low affinity conformational change. For example, ATP induces this conformational change in a lidless variant, DnaK517(1/2A), with a rate constant of 442 s-1, whereas, after adding back the B-helix (residues 518−554), ATP induces this conformational change in DnaK554(A−B) with a rate constant of 2.5 s-1. Our interpretation is that this large decrease occurs because the B-helix of the DnaK554(A−B) is bound in the substrate-binding site. (iii) The deletion analysis also revealed that residues 596−638, which comprise the αE helix and the flexible subdomain, affect ATP binding. Our results are consistent with this part of the lid producing conformational heterogeneity, perhaps by binding to the ATPase domain.