Treble clef finger--a functionally diverse zinc-binding structural motif

Nucleic Acids Res. 2001 Apr 15;29(8):1703-14. doi: 10.1093/nar/29.8.1703.

Abstract

Detection of similarity is particularly difficult for small proteins and thus connections between many of them remain unnoticed. Structure and sequence analysis of several metal-binding proteins reveals unexpected similarities in structural domains classified as different protein folds in SCOP and suggests unification of seven folds that belong to two protein classes. The common motif, termed treble clef finger in this study, forms the protein structural core and is 25-45 residues long. The treble clef motif is assembled around the central zinc ion and consists of a zinc knuckle, loop, beta-hairpin and an alpha-helix. The knuckle and the first turn of the helix each incorporate two zinc ligands. Treble clef domains constitute the core of many structures such as ribosomal proteins L24E and S14, RING fingers, protein kinase cysteine-rich domains, nuclear receptor-like fingers, LIM domains, phosphatidylinositol-3-phosphate-binding domains and His-Me finger endonucleases. The treble clef finger is a uniquely versatile motif adaptable for various functions. This small domain with a 25 residue structural core can accommodate eight different metal-binding sites and can have many types of functions from binding of nucleic acids, proteins and small molecules, to catalysis of phosphodiester bond hydrolysis. Treble clef motifs are frequently incorporated in larger structures or occur in doublets. Present analysis suggests that the treble clef motif defines a distinct structural fold found in proteins with diverse functional properties and forms one of the major zinc finger groups.

MeSH terms

  • ADP-Ribosylation Factors / chemistry
  • ADP-Ribosylation Factors / metabolism
  • Amino Acid Sequence
  • Binding Sites
  • Cysteine / metabolism
  • DNA-Binding Proteins / chemistry
  • DNA-Binding Proteins / metabolism
  • Endonucleases / chemistry
  • Endonucleases / metabolism
  • GTPase-Activating Proteins / chemistry
  • GTPase-Activating Proteins / metabolism
  • Models, Molecular
  • Molecular Sequence Data
  • Phosphatidylinositol Phosphates / metabolism
  • Protein Folding
  • Protein Kinases / chemistry
  • Protein Kinases / metabolism
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry*
  • Proteins / metabolism*
  • Receptors, Cytoplasmic and Nuclear / chemistry
  • Ribosomal Proteins / chemistry
  • Ribosomal Proteins / metabolism
  • Sequence Alignment
  • Smad Proteins
  • Structure-Activity Relationship
  • Trans-Activators / chemistry
  • Trans-Activators / metabolism
  • Zinc / metabolism*
  • Zinc Fingers*

Substances

  • DNA-Binding Proteins
  • GTPase-Activating Proteins
  • Phosphatidylinositol Phosphates
  • Proteins
  • Receptors, Cytoplasmic and Nuclear
  • Ribosomal Proteins
  • Smad Proteins
  • Trans-Activators
  • phosphatidylinositol 3-phosphate
  • Protein Kinases
  • Endonucleases
  • ADP-Ribosylation Factors
  • Zinc
  • Cysteine