Structural motif of phosphate-binding site common to various protein superfamilies: All-against-all structural comparison of protein-mononucleotide complexes

Kengo Kinoshita, Keishi Sadanami, Akinori Kidera, Nobuhiro Go

Research output: Contribution to journalArticlepeer-review

97 Citations (Scopus)

Abstract

In order to search for a common structural motif in the phosphate-binding sites of protein-mononucleotide complexes, we investigated the structural variety of phosphate-binding schemes by an all-against-all comparison of 491 binding sites found in the Protein Data Bank. We found four frequently occurring structural motifs composed of protein atoms interacting with phosphate groups, each of which appears in different protein superfamilies with different folds. The most frequently occurring motif, which we call the structural P-loop, is shared by 13 superfamilies and is characterized by a four-residue fragment, GXXX, interacting with a phosphate group through the backbone atoms. Various sequence motifs, including Walker's A motif or the P-loop, turn out to be a structural P-loop found in a few specific superfamilies. The other three motifs are found in pairs of superfamilies: protein kinase and glutathione synthetase ATPase domain like, actin-like ATPase domain and nucleotidyltransferase, and FMN-linked oxido-reductase and PRTase.

Original languageEnglish
Pages (from-to)11-14
Number of pages4
JournalProtein Engineering
Volume12
Issue number1
DOIs
Publication statusPublished - 1999
Externally publishedYes

Keywords

  • Convergent evolution
  • Phosphate-binding site
  • Structural motif
  • Three-dimensional structure comparison

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology

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