Structural basis of diverse sequence-dependent target recognition by the 8 kDa dynein light chain

Dyneins are multi-subunit molecular motors that translocate molecular cargoes along microtubules. Otherthan acting as an essential component of the dynein motor complex, the 89-residue subunit of dynein light chain (DLC8) alsoregulates a number of other biological events by binding to various proteins and enzymes. Currently known DLC8 targets includeneuronal nitric oxide synthase; the proapoptotic Bcl-2 family member protein designated Bim; a Drosophila RNA localizationprotein Swallow, myosin V, neuronal scaffolding protein GKAP, and IκBα, an inhibitor of the NFκB transcription factor.The DLC8-binding domains of the various targets are confined within a short, continuous stretch of amino acid residues. However,these domains do not share any obvious sequence homology with each other. Here, the three-dimensional structures of DLC8 complexedwith two peptides corresponding to the DLC8-binding domains of neuronal nitric oxide synthase and Bim, respectively, weredetermined by NMR spectroscopy. Although the two DLC8-binding peptides have entirely different amino acid sequences, both peptidesbind to the protein with a remarkable similar conformation by engaging the symmetric DLC8 dimer through antiparallel β-sheetaugmentation via the β2 strand of the protein. Structural comparison indicates that the two target peptides usedifferent regions within the conformational flexible peptide-binding channels to achieve binding specificity. We have alsore-determined the apo-form solution structure of DLC8 in this work. The structures of the DLC8/target peptide complexes,together with the dynamic properties of the protein, provide a molecular basis of DLC8’s diverse amino acid sequence-dependenttarget recognition.