A Ras-like domain in the light intermediate chain bridges the dynein motor to a cargo-binding region

Abstract

Cytoplasmic dynein, a microtubule-based motor protein, transports many intracellular cargos by means of its light intermediate chain (LIC). In this study, we have determined the crystal structure of the conserved LIC domain, which binds the motor heavy chain, from a thermophilic fungus. We show that the LIC has a Ras-like fold with insertions that distinguish it from Ras and other previously described G proteins. Despite having a G protein fold, the fungal LIC has lost its ability to bind nucleotide, while the human LIC1 binds GDP preferentially over GTP. We show that the LIC G domain binds the dynein heavy chain using a conserved patch of aromatic residues, whereas the less conserved C-terminal domain binds several Rab effectors involved in membrane transport. These studies provide the first structural information and insight into the evolutionary origin of the LIC as well as revealing how this critical subunit connects the dynein motor to cargo.

DOI: http://dx.doi.org/10.7554/eLife.03351.001

eLife digest

Living cells are constantly bustling with activity. They take in nutrients, carefully split their genetic information between new cells when they divide, and move their internal components into the right positions. To move these cargos around, the cell uses proteins—such as dynein—that essentially walks along the cell's internal scaffolding by making step-like movements. However, how a dynein motor protein is tethered to its cargo is not known in detail.

One part of the dynein structure thought to play an important role in binding the motor to its cargo is called the light intermediate chain (LIC). Schroeder et al. used X-ray crystallography to solve the structure of the light intermediate chain of dynein motors from a fungus. This information with other experimental techniques reveals that the LIC subunit has two distinct regions: one that binds to three different proteins that serve as adapters for cargo attachment, and one that binds to the rest of the dynein motor.

The structure of the LIC includes a fold that is also found in many proteins belonging to a family of enzymes called GTPases, suggesting that the LIC evolved from this family. GTPases use a molecule called GTP to release energy and often act as on–off switches for various processes inside cells. However, the fungal LIC subunit cannot bind to molecules called nucleotides—which can act as energy sources—the way GTPases do. This prevents the LIC subunit from acting as a molecular switch.

In contrast, the human version of the LIC is able to bind to some nucleotides, in particular one called GDP. However, since the LIC cannot bind to the high-energy nucleotide GTP, the human LICs most likely also do not act as on–off switches: Schroeder et al. instead propose that the LIC may use GDP only to stabilize the protein.

It remains to be seen how cargo attachment to the LIC is regulated. Further structural work and biochemistry with the LIC bound to the dynein motor and cargo will provide more insight into the mechanism of intracellular cargo transport.

DOI: http://dx.doi.org/10.7554/eLife.03351.002