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

• Published in: Nature communications 2018-05, Vol.9 (1), p.1765-8, Article 1765
• Main Authors: Nagata, Ryuhei, Fujihashi, Masahiro, Sato, Takaaki, Atomi, Haruyuki, Miki, Kunio
• Format: Article
• Language: English
• Subjects: 631/45; 631/535; 631/92; Amino Acid Sequence; Amino Acids - chemistry; Amino Acids - genetics; Amino Acids - metabolism; ATP; Base Sequence; Binding; Binding sites; Binding Sites - genetics; Carbohydrates; Conserved sequence; Crystal structure; Crystallography, X-Ray; Determinants; Diphosphates - chemistry; Diphosphates - metabolism; Enzymes; Homology; Humanities and Social Sciences; Hydrophobicity; Kinases; Kinetics; Models, Molecular; multidisciplinary; Mutation; Nucleotide sequence; Phosphorylation; Phosphotransferases (Alcohol Group Acceptor) - chemistry; Phosphotransferases (Alcohol Group Acceptor) - genetics; Phosphotransferases (Alcohol Group Acceptor) - metabolism; Protein Domains; Residues; Ribokinase; Science; Science (multidisciplinary); Sequence Homology, Amino Acid
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-018-04201-z

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. While most kinases are ATP-dependent some utilize pyrophosphate (PPi) instead. Here the authors structurally characterize a PPi-dependent kinase, identify its key recognition residues and find further PPi-dependent ribokinase family members with this signature pattern.