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

Ryuhei Nagata, Masahiro Fujihashi (), Takaaki Sato, Haruyuki Atomi and Kunio Miki ()
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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

Nature Communications, 2018, vol. 9, issue 1, 1-8

Abstract: 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.

Date: 2018
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DOI: 10.1038/s41467-018-04201-z

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