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Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin

Nature Structural & Molecular Biology volume 15, pages 1067–1075 (2008)Cite this article

Abstract

Mg-ADP release is considered to be a crucial process for the regulation and motility of kinesin. To gain insight into the structural basis of this process, we solved the atomic structures of kinesin superfamily protein-1A (KIF1A) during and after Mg2+ release. On the basis of new structural and mutagenesis data, we propose a model mechanism for microtubule activation of Mg-ADP release from KIF1A. In our model, a specific interaction between loop L7 of KIF1A and β-tubulin reconfigures the KIF1A active site by shifting the relative positions of switches I and II. This leads to the sequential release of a group of water molecules that sits over the Mg2+ in the active site, followed by Mg2+ and finally the ADP. We further propose that this set of events is linked to a strain-dependent docking of the neck linker to the motor core, which produces a two-step power stroke.

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Figure 1: Inhibitory effect of Mg2+ on basal KIF1A ATPase activity and its reversal by microtubules.
Figure 2: The overall conformational change of KIF1A during Mg2+ release.
Figure 3: Conformational change of switch I to open the nucleotide binding pocket.
Figure 4: Microtubule-activating pathway of Mg-ADP release.
Figure 5: Sequential docking of the neck linker and the return movement of the microtubule binding interface switch II.
Figure 6: Three-dimensional rotation of switch II rearranges the microtubule binding surface of KIF1A.
Figure 7: Phenotypes of the neck linker mutants.
Figure 8: Schema to illustrate the 'two-door system' of the nucleotide binding pocket of kinesin.
Figure 9: Structure-based model of the gating behavior of dimeric kinesin.

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Acknowledgements

We thank H. Fukuda, H. Sato and T. Akamatsu for assistance, and M. Kikkawa, H. Yajima, T. Ogawa, H. Ueno, H. Miki, E. Nitta and other colleagues for comments and technical assistance. This work was supported by a Center of Excellence Grant-in-Aid from the Ministry of Education, Culture, Sports, Science and Technology of Japan to N.H.

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  1. Department of Cell Biology and Anatomy, University of Tokyo, Graduate School of Medicine, 7-3-1 Hongo, Bunkyo-ku, 113-0033, Tokyo, Japan

    Ryo Nitta, Yasushi Okada & Nobutaka Hirokawa

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  1. Ryo Nitta
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  2. Yasushi Okada
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  3. Nobutaka Hirokawa
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Corresponding author

Correspondence to Nobutaka Hirokawa.

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–4, Supplementary Tables 1 and 2 (PDF 2600 kb)

Supplementary Video 1

This movie supplements Figure 3. Ribbon models of the crucial proteinous elements for ADP/ATP exchange are shown. ADP, the Mg2+-stabilizer and the latch are shown as stick models. The Mg2+-water cap is shown as a ball model. Keys: Mg, cyan; H2O, red; P-loop, blue; L7, purple; switch I, green; switch II, yellow. (MOV 166 kb)

Supplementary Video 2

This movie supplements Figure 5. The main chains of the neck-linker, β0, and L13 are shown as sphere models. The side chains of conserved residues Val6 (blue), Leu285 (yellow), Asn322 (orange), Ile354 (red) and Asn361 (red) are also shown as sphere models. Key: β0, cyan; α4, yellow; α5-L13, light-orange; α6, brown; neck-linker, pink. (MOV 528 kb)

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Nitta, R., Okada, Y. & Hirokawa, N. Structural model for strain-dependent microtubule activation of Mg-ADP release from kinesin. Nat Struct Mol Biol 15, 1067–1075 (2008). https://doi.org/10.1038/nsmb.1487

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