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Crystal structure of a member of a novel family of dioxygenases (PF10014) reveals a conserved cupin fold and active site

Authors

  • Qingping Xu,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
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  • Joanna Grant,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California
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  • Hsiu-Ju Chiu,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
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  • Carol L. Farr,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
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  • Lukasz Jaroszewski,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Center for Research in Biological Systems, University of California, San Diego, La Jolla, California
    3. Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California
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  • Mark W. Knuth,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California
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  • Mitchell D. Miller,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
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  • Scott A. Lesley,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Protein Sciences Department, Genomics Institute of the Novartis Research Foundation, San Diego, California
    3. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
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  • Adam Godzik,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Center for Research in Biological Systems, University of California, San Diego, La Jolla, California
    3. Program on Bioinformatics and Systems Biology, Sanford-Burnham Medical Research Institute, La Jolla, California
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  • Marc-André Elsliger,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
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  • Ashley M. Deacon,

    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California
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  • Ian A. Wilson

    Corresponding author
    1. Joint Center for Structural Genomics, La Jolla, California (http://www.jcsg.org)
    2. Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California
    • Correspondence to: Ian A. Wilson, Department of Integrative Structural and Computational Biology, BCC206, 10550 N. Torrey Pines Rd., La Jolla, California 92037. E-mail: wilson@scripps.edu

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ABSTRACT

PF10014 is a novel family of 2-oxyglutarate-Fe2+-dependent dioxygenases that are involved in biosynthesis of antibiotics and regulation of biofilm formation, likely by catalyzing hydroxylation of free amino acids or other related ligands. The crystal structure of a PF10014 member from Methylibium petroleiphilum at 1.9 Å resolution shows strong structural similarity to cupin dioxygenases in overall fold and active site, despite very remote homology. However, one of the β-strands of the cupin catalytic core is replaced by a loop that displays conformational isomerism that likely regulates the active site. Proteins 2014; 82:164–170. © 2013 Wiley Periodicals, Inc.

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