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Crystal structure of hemopexin reveals a novel high-affinity heme site formed between two β-propeller domains

Nature Structural Biology volume 6, pages 926–931 (1999)Cite this article

Abstract

The ubiquitous use of heme in animals poses severe biological and chemical challenges. Free heme is toxic to cells and is a potential source of iron for pathogens. For protection, especially in conditions of trauma, inflammation and hemolysis, and to maintain iron homeostasis, a high-affinity binding protein, hemopexin, is required. Hemopexin binds heme with the highest affinity of any known protein, but releases it into cells via specific receptors. The crystal structure of the heme–hemopexin complex reveals a novel heme binding site, formed between two similar four-bladed β-propeller domains and bounded by the interdomain linker. The ligand is bound to two histidine residues in a pocket dominated by aromatic and basic groups. Further stabilization is achieved by the association of the two β-propeller domains, which form an extensive polar interface that includes a cushion of ordered water molecules. We propose mechanisms by which these structural features provide the dual function of heme binding and release.

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Figure 1: Structure of the heme-hemopexin complex.
Figure 2: Stereo view of electron density at the heme binding site.
Figure 3: Environment around the heme.
Figure 4: Interface interactions between the two b-propeller domains, showing the 'cushion' of 14 ordered water molecules (dark blue) at the center of the interface, plus specific salt bridging interactions Arg 79-Asp 263 and Glu 130-Arg 257 (side chains in magenta).

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Acknowledgements

We thank C. Smith, and staff of the Stanford Synchrotron Radiation Laboratory, for help with data collection; N. Sakabe and staff at the Photon Factory (Tsukuba, Japan) for help with data collection on the deglycosylated hemopexin crystals; T. Kagawa, P. Metcalf and S. Moore for useful discussions; and L. Khalifah, M. Parry and N. Shipulina for isolation and purification of hemopexin. We are also grateful to J. Blackburn, M. Simmonds and B. Luisi for critical reading of the manuscript. This work was supported by the Health Research Council of New Zealand, by the Marsden Fund of New Zealand and by the U.S. National Institutes of Health (to A.S.). E.N.B. also receives research support as an International Research Scholar of the Howard Hughes Medical Institute.

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  1. Massimo Paoli

    Present address: Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QW, United Kingdom

  2. Heather M. Baker & Edward N. Baker

    Present address: School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand

Authors and Affiliations

  1. School of Biological Sciences, University of Auckland, Auckland,, New Zealand

    Massimo Paoli, Heather M. Baker & Edward N. Baker

  2. Department of Biochemistry, Massey University, Palmerston North, New Zealand

    Massimo Paoli, Heather M. Baker & Edward N. Baker

  3. Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand

    Bryan F. Anderson

  4. Division of Molecular Biology and Biochemistry, School of Biological Sciences, University of Missouri-Kansas City, Kansas City, 64110-2499, Missouri, USA

    William T. Morgan & Ann Smith

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Correspondence to Edward N. Baker.

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Paoli, M., Anderson, B., Baker, H. et al. Crystal structure of hemopexin reveals a novel high-affinity heme site formed between two β-propeller domains. Nat Struct Mol Biol 6, 926–931 (1999). https://doi.org/10.1038/13294

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