PDBsum entry 1v8j

Structural protein

PDB id: 1v8j

Contents

Protein chain

337 a.a. *

Ligands

ADP

Metals

_MG

Waters ×34

* Residue conservation analysis

References listed in PDB file

Key reference

Title

A common mechanism for microtubule destabilizers-M type kinesins stabilize curling of the protofilament using the class-Specific neck and loops.

Authors

T.Ogawa, R.Nitta, Y.Okada, N.Hirokawa.

Ref.

Cell, 2004, 116, 591-602. [DOI no: 10.1016/S0092-8674(04)00129-1]

PubMed id

14980225

Abstract

Unlike other kinesins, middle motor domain-type kinesins depolymerize the microtubule from its ends. To elucidate its mechanism, we solved the X-ray crystallographic structure of KIF2C, a murine member of this family. Three major class-specific features were identified. The class-specific N-terminal neck adopts a long and rigid helical structure extending out vertically into the interprotofilament groove. This structure explains its dual roles in targeting to the end of the microtubule and in destabilization of the lateral interaction of the protofilament. The loop L2 forms a unique finger-like structure, long and rigid enough to reach the next tubulin subunit to stabilize the peeling of the protofilament. The open conformation of the switch I loop could be reversed by the shift of the microtubule binding L8 loop, suggesting its role as the sensor to trigger ATP hydrolysis. Mutational analysis supports these structural implications.

Figure 3.
Figure 3. The Open Conformation of the Nucleotide Binding Pocket of KIF2C in the AMP-PNP Form(A) Comparison of the structures of KIF2C in the ADP form (red) and in the AMP-PNP form (blue). The interaction between the neck (green) and the KVD-finger (pink) is also shown. Note the disulfide bond (yellow) between the neck and the KVD-finger.(B) Comparison of the configuration of the switch I and switch II regions of KIF1A (purple) and KIF2C (blue). Although both structures are of the AMP-PXP (X = C or N) form, the switch I loop is distant from the γ-phosphate due to the rotation of α3. To move the switch I loop closer to the γ-phosphate, α3 must be rotated as shown by the yellow arrows. This rotation may be triggered by the preceding L8 loop. This open conformation of the switch I loop is similar to the structure of the salt bridge mutant (R598A) of Kar3. The structures of the wild-type (purple) and R598A mutant (blue) of Kar3 are shown for comparison (C). The mutation resulted in the rotation of α3 and the switch I loop moved away from the nucleotide binding pocket (yellow arrow).

Figure 6.
Figure 6. Structural Model of the Mechanism of MT Depolymerization by KIF-M(A) ADP bound KIF-M (light blue) binds to the side wall of the MT.(B) The neck helix (green) interferes with the M loop in the interprotofilament groove, and KIF-M cannot bind tightly to the side wall of the MT. The nucleotide binding pocket is trapped in the open state. Thus, ATP bound KIF-M diffuses along the MT protofilament.(C) When KIF-M reaches the end of the MT, the curved conformation of the protofilament allows full contact with KIF-M. The L8 loop (blue) closes the nucleotide binding pocket and ATP hydrolysis takes place. The neck helix destabilizes the lateral interaction of the protofilament, and the KVD-finger (red) stabilizes the curved conformation of the interdimer groove.(D) Tubulin dimer or oligomer is spontaneously released from the curved end of the protofilament.Hydrolysis of ATP on the tubulin dimer (or oligomer) releases KIF-M and the next cycle starts. Alternatively, only the tubulin dimer is released and KIF-M remains on the protofilament, sliding back to release the next tubulin dimer processively (C′ and D′). The same mechanism can also explain depolymerization from the minus end of MT (E). Dimerization of KIF-M is not required for this mechanism, but will further increase the depolymerization activity (F).

The above figures are reprinted by permission from Cell Press: Cell (2004, 116, 591-602) copyright 2004.