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Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants

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  • Ryuhei Nagata

    (Kyoto University)

  • Masahiro Fujihashi

    (Kyoto University)

  • Takaaki Sato

    (Kyoto University, Katsura)

  • Haruyuki Atomi

    (Kyoto University, Katsura)

  • Kunio Miki

    (Kyoto University)

Abstract

Almost all kinases utilize ATP as their phosphate donor, while a few kinases utilize pyrophosphate (PPi) instead. PPi-dependent kinases are often homologous to their ATP-dependent counterparts, but determinants of their different donor specificities remain unclear. We identify a PPi-dependent member of the ribokinase family, which differs from known PPi-dependent kinases, and elucidate its PPi-binding mode based on the crystal structures. Structural comparison and sequence alignment reveal five important residues: three basic residues specifically recognizing PPi and two large hydrophobic residues occluding a part of the ATP-binding pocket. Two of the three basic residues adapt a conserved motif of the ribokinase family for the PPi binding. Using these five key residues as a signature pattern, we discover additional PPi-specific members of the ribokinase family, and thus conclude that these residues are the determinants of PPi-specific binding. Introduction of these residues may enable transformation of ATP-dependent ribokinase family members into PPi-dependent enzymes.

Suggested Citation

  • Ryuhei Nagata & Masahiro Fujihashi & Takaaki Sato & Haruyuki Atomi & Kunio Miki, 2018. "Identification of a pyrophosphate-dependent kinase and its donor selectivity determinants," Nature Communications, Nature, vol. 9(1), pages 1-8, December.
    • Handle: RePEc:nat:natcom:v:9:y:2018:i:1:d:10.1038_s41467-018-04201-z
    DOI: 10.1038/s41467-018-04201-z
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