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Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation

Nature Structural Biology volume 8, pages 42–46 (2001)Cite this article

Abstract

Molybdenum cofactor (Moco) biosynthesis is an evolutionarily conserved pathway present in eubacteria, archaea and eukaryotes, including humans. Genetic deficiencies of enzymes involved in Moco biosynthesis in humans lead to a severe and usually fatal disease. Moco contains a tricyclic pyranopterin, termed molybdopterin (MPT), that bears the cis-dithiolene group responsible for molybdenum ligation. The dithiolene group of MPT is generated by MPT synthase, which consists of a large and small subunits. The 1.45 Å resolution crystal structure of MPT synthase reveals a heterotetrameric protein in which the C-terminus of each small subunit is inserted into a large subunit to form the active site. In the activated form of the enzyme this C-terminus is present as a thiocarboxylate. In the structure of a covalent complex of MPT synthase, an isopeptide bond is present between the C-terminus of the small subunit and a Lys side chain in the large subunit. The strong structural similarity between the small subunit of MPT synthase and ubiquitin provides evidence for the evolutionary antecedence of the Moco biosynthetic pathway to the ubiquitin dependent protein degradation pathway.

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Figure 1: Second step of Moco biosynthesis and sequence conservation of MPT synthase.
Figure 2: Mass spectrometric analysis of a, inactive and b, partially active MPT synthase, and c, MPT synthase in which ∼50% of molecules have formed an intersubunit covalent complex.
Figure 3: Structure of MPT synthase.
Figure 4: Active site of MPT synthase.

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Acknowledgements

Supported by National Institutes of Health Grants to H.S. and K.V.R. M.W. would like to thank H. Sage and R. Stevens (Duke University) for performing sedimentation equilibrium centrifugation and mass spectrometry experiments. The National Synchrotron Light Source at Brookhaven is supported by the United States Department of Energy and National Institutes of Health, and beamline X26C is supported in part by the State University of New York at Stony Brook and its Research Foundation.

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Authors and Affiliations

  1. Department of Biochemistry and Center for Structural Biology, State University of New York at Stony Brook, Stony Brook, 11794-5215, New York, USA

    Michael J. Rudolph & Hermann Schindelin

  2. Department of Biochemistry, Duke University Medical Center, Durham, 27710, North Carolina, USA

    Margot M. Wuebbens & K.V. Rajagopalan

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  1. Michael J. Rudolph
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  2. Margot M. Wuebbens
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  3. K.V. Rajagopalan
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  4. Hermann Schindelin
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Correspondence to Hermann Schindelin.

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Rudolph, M., Wuebbens, M., Rajagopalan, K. et al. Crystal structure of molybdopterin synthase and its evolutionary relationship to ubiquitin activation. Nat Struct Mol Biol 8, 42–46 (2001). https://doi.org/10.1038/83034

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