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Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA

Nature Structural & Molecular Biology volume 16, pages 740–746 (2009)Cite this article

Abstract

Box H/ACA small nucleolar and Cajal body ribonucleoprotein particles comprise the most complex pseudouridine synthases and are essential for ribosome and spliceosome maturation. The multistep and multicomponent-mediated enzyme mechanism remains only partially understood. Here we report a crystal structure at 2.35 Å of a substrate-bound functional archaeal enzyme containing three of the four proteins, Cbf5, Nop10 and L7Ae, and a box H/ACA RNA that reveals detailed information about the protein-only active site. The substrate RNA, containing 5-fluorouridine at the modification position, is fully docked and catalytically rearranged by the enzyme in a manner similar to that seen in two stand-alone pseudouridine synthases. Structural analysis provides a mechanism for plasticity in the diversity of guide RNA sequences used and identifies a substrate-anchoring loop of Cbf5 that also interacts with Gar1 in unliganded structures. Activity analyses of mutated proteins and RNAs support the structural findings and further suggest a role of the Cbf5 loop in regulation of enzyme activity.

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Figure 1: Overview of the structure.
Figure 2: Comparison of active site structure.
Figure 3: Interactions of the RNA with Cbf5.
Figure 4: Structural features of the wild-type ψ-pocket important for substrate docking examined by fluorescence analysis.
Figure 5: Structure and activity analysis of variously assembled wild-type and mutant RNPs reveal mechanisms for plasticity and the sensitivity of β7_β10 loop to substrate and Gar1 binding.

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Acknowledgements

This work was supported in part by the US National Institutes of Health grants R01 GM66958-01 (H.L.) and R01 GM54682 (M.T. and R.T.). B.L. (0815118E) and J.Z. (0815267E) are supported by the American Heart Association, Greater Southeast Affiliate. X-ray diffraction data were collected by the Southeast Regional Collaborative Access Team (SER-CAT) 22-ID beamline at the Advanced Photon Source (APS), Argonne National Laboratory. Supporting institutions for APS beamlines may be found at http://necat.chem.cornell.edu and http://www.ser-cat.org/members.html. Use of the APS was supported by the US Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-Eng-38.

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Authors and Affiliations

  1. Institute of Molecular Biophysics, Tallahassee, Florida, USA

    Bo Liang & Hong Li

  2. Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, USA

    Jing Zhou, Elliot Kahen & Hong Li

  3. Department of Biochemistry and Molecular Biology, University of Georgia at Athens, Athens, Georgia, USA

    Rebecca M Terns & Michael P Terns

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Contributions

B.L. determined the crystal structure; J.Z. prepared samples; E.K. performed fluorescence assays; M.P.T. and R.M.T. prepared the manuscript; H.L. supervised the project and prepared the manuscript.

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Correspondence to Hong Li.

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Liang, B., Zhou, J., Kahen, E. et al. Structure of a functional ribonucleoprotein pseudouridine synthase bound to a substrate RNA. Nat Struct Mol Biol 16, 740–746 (2009). https://doi.org/10.1038/nsmb.1624

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