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Crystal structure of autotaxin and insight into GPCR activation by lipid mediators

Nature Structural & Molecular Biology volume 18, pages 205–212 (2011)Cite this article

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Abstract

Autotaxin (ATX, also known as Enpp2) is a secreted lysophospholipase D that hydrolyzes lysophosphatidylcholine to generate lysophosphatidic acid (LPA), a lipid mediator that activates G protein–coupled receptors to evoke various cellular responses. Here, we report the crystal structures of mouse ATX alone and in complex with LPAs with different acyl-chain lengths and saturations. These structures reveal that the multidomain architecture helps to maintain the structural rigidity of the lipid-binding pocket, which accommodates the respective LPA molecules in distinct conformations. They indicate that a loop region in the catalytic domain is a major determinant for the substrate specificity of the Enpp family enzymes. Furthermore, along with biochemical and biological data, these structures suggest that the produced LPAs are delivered from the active site to cognate G protein–coupled receptors through a hydrophobic channel.

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Figure 1: Overall architecture.
Figure 2: Active site.
Figure 3: Interdomain interaction.
Figure 4: Structural determinant of the substrate specificity.
Figure 5: Biochemical characterization of the wild-type and mutant ATXs.
Figure 6: Hydrophobic channel.

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Acknowledgements

We are grateful to the beam-line staffs at NW12A and NE3A of KEK PF-AR and BL41XU of SPring-8 for assistance in data collection. We thank L. Bonnefond (University of Tokyo, Japan) for critical reading of the manuscript. This work was supported by a grant for the National Project on Protein Structural and Functional Analyses from the Ministry of Education, Culture, Sports, Science and Technology (MEXT) to O.N. and J.A., by a National Institute of Biomedical Innovation (Japan) grant to J.A. and by MEXT grants to R.I. and O.N.

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Authors and Affiliations

  1. Department of Biophysics and Biochemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan

    Hiroshi Nishimasu, Ryuichiro Ishitani & Osamu Nureki

  2. Graduate School of Pharmaceutical Sciences, Tohoku University, Miyagi, Japan

    Shinichi Okudaira, Kotaro Hama, Asuka Inoue & Junken Aoki

  3. Institute for Protein Research, Osaka University, Osaka, Japan

    Emiko Mihara & Junichi Takagi

  4. Biomolecular Characterization Team and CREST/JST, RIKEN, Saitama, Japan

    Naoshi Dohmae

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  1. Hiroshi Nishimasu
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Contributions

H.N. crystallized and determined the structure of ATX and wrote the paper; S.O., K.H. and A.I. conducted biochemical and cell biological analyses of the wild-type and mutant ATXs; E.M. and J.T. prepared the recombinant ATX proteins; A.I., N.D. and J.A. did the mass spectrometry analysis of endogenous LPA; R.I. assisted with the structural determination; and O.N. designed the work and also assisted with the structure determination. All authors discussed the results and commented on the manuscript; O.N., J.A. and J.T. supervised the work.

Corresponding authors

Correspondence to Junichi Takagi, Junken Aoki or Osamu Nureki.

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The authors declare no competing financial interests.

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Supplementary Figures 1–8, Supplementary Table 1 and Supplementary Discussion (PDF 4596 kb)

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Nishimasu, H., Okudaira, S., Hama, K. et al. Crystal structure of autotaxin and insight into GPCR activation by lipid mediators. Nat Struct Mol Biol 18, 205–212 (2011). https://doi.org/10.1038/nsmb.1998

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