Mechanism

The four nucleotide-binding sites

These nucleotide-binding sites in which the four ADP molecules bind to, exists as an interface between the α/β and α submodules of one AAA+, as well as the neighboring α/β submodule. Note that this is very similar to the structural organisation of ATPases.


Hover to see residues involved in recognising ADP to bind: 

Nucleotide binding sites for modules AAA1-4 (click to see original size)
Note the residues involved in each of these four sites have similar structural frameworks, except AAA2 shows particular characteristic residues: 1) sensor-II motif replaced by L2531, 2) glycine takes the place by glutamic acid in ATP hydrolysis in Walker-B motif, 3) AAA3 contributes two arginine fingers to stabilise phosphates of bound ADP. This makes the AAA2 site only binds but not hydrolyse ATP, i.e. only AAA1, 3, 4 can hydrolyse. 

Open and closed ring conformations

The 6 modules are placed such that they are asymmetrical in arrangement, hence becomes two half-rings of 3 α/β-submodules each: AAA5-AAA6-AAA1 and AAA-2-AAA-3-AAA4. They are loosely attached and therefore allows space for arginine finger to extend from AAA2 to 1 and AAA5 to 4, to facilitate ATP hydrolysis when ATP binds. This gap is meant to close off during ATPase cycles so that the arginine finger can interact with γ-phosphate on ATP, and shortens the distance between the fingers and ATP, for the fingers to participate in ATP hydrolysis. 

Dynein AAA+ ring pre powerstroke

Dynein AAA+ ring post powerstroke

Linker and ring interactions

The swing-like motion of the linker is thought to be a drive for dynein's power stroke, considering that electron microscopy analysis shows that its position is close to the powerstroke state. The linker might seem like a bridge between AAA1&4, but is in fact just tightly hanging on the edge of AAA2,3&4. The linker only connects at two interfaces of the chain: at AAA1-α/β and H2 insert β-hairpin and PS-I insert loop. There are multiple points of interactions at these two interfaces. A mutant experiment was used to test the functional significance of the structures (namely H2 and PS-I) at theses interfaces. They were considered to have critical roles in linker swing, because altering their flexibility, would deplete or replace residues involved in linker interaction. A relationship could be possibly drawn between the open-closed transition of the AAA1-AAA2 with the H2 and PS-I inserts, potentially driving the linker swing.

3VKH & 3VKG surface protein:
the linkers are deep blue and lime yellow on the molecule