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Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP

Nature Structural Biology volume 5, pages 803–811 (1998)Cite this article

A Correction to this article was published on 01 October 1998

Abstract

N-ethylmaleimide-sensitive factor (NSF) is a hexameric ATPase which primes and/or dissociates SNARE complexes involved in intracellular fusion events. Each NSF protomer contains three domains: an N-terminal domain required for SNARE binding and two ATPase domains, termed D1 and D2, with D2 being required for oligomerization. We have determined the 1.9 Å crystal structure of the D2 domain of NSF complexed with ATP using multi-wavelength anomalous dispersion phasing. D2 consists of a nucleotide binding subdomain with a Rossmann fold and a C-terminal subdomain, which is structurally unique among nucleotide binding proteins. There are interactions between the ATP moiety and both the neighboring D2 protomer and the C-terminal subdomain that may be important for ATP-dependent oligomerization. Of particular importance are three well-ordered and conserved lysine residues that form ionic interactions with the β- and γ-phosphates, one of which likely contributes to the low hydrolytic activity of D2.

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Figure 1: Sequence alignment of NSF homologs from Chinese Hamster Ovary (SWISSPROT-P18708), mouse (P46460), human (P46459), fly isoform 1 (P46461), fly isoform 2 (P54351) and yeast (P18759).
Figure 2: Electron density maps around the ATP binding site, contoured at 1.25 σ
Figure 3: a,Ribbon diagram of the NSF-D2 hexamer, as viewed from the N-terminal end down the six-fold symmetry axis.
Figure 4: a,Ribbon diagram of theNSF-D2 protomer consisting of two subdomains, an upper N-terminal subdomain in green and a lower C-terminal subdomain in blue-green.
Figure 5: a,Molscript and POV-ray rendering of the hydrogen bonds between Arg 617 from one protomer (blue) and the Phe 618 backbone oxygen from the neighboring protomer (green) in the pore of the D2 domain.
Figure 6: a,Contact regions between subdomains of a protomer, in red and orange, and between neighboring protomers, in yellow and purple.

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Acknowledgements

The authors thank S.C. Stroupe and D. Fasshauer for stimulating discussions, R.B. Sutton for expert advise during the course of the project, C. Ostermeier for aid with crystallization, S.R. Sprang for critical reading of the manuscript, L. Esser for assistance in figure preparation, H. Bellamy for assistance with data collection at SSRL 1-5 (SSRL is funded by the Department of Energy, Office of Basic Energy Sciences; the SSRL Biotechnology Program is supported by the NIH, Biomedical Research Technology Program, Division of Research Resources; further SSRL support is provided by the Department of Energy, Office of Health and Environmental Research), and A. Joachimiak and the Structural Biology Center for assistance with data collection at APS (collected at the 19ID beamline of the Structural Biology Center at the Advanced Photon Source at Argonne National Laboratory: this national user facility is supported by the Office of Health and Environmental Research, U.S. Department of Energy). Support by the National Institutes of Health to A.T.B. is gratefully acknowledged.

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  1. The Howard Hughes Medical Institute and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, 06520, Connecticut, USA

    Richard C. Yu & Axel T. Brünger

  2. Department of Cell Biology and Physiology, Washington University School of Medicine, St. Louis, 63110, Missouri, USA

    Phyllis I. Hanson

  3. Department of Neurobiology, Max-Planck-Institute for Biophysical Chemistry, D-37077, Göttingen, Germany

    Reinhard Jahn

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Correspondence to Axel T. Brünger.

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Yu, R., Hanson, P., Jahn, R. et al. Structure of the ATP-dependent oligomerization domain of N-ethylmaleimide sensitive factor complexed with ATP. Nat Struct Mol Biol 5, 803–811 (1998). https://doi.org/10.1038/1843

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