Nucleic acid recognition by OB-fold proteins

Annu Rev Biophys Biomol Struct. 2003;32:115-33. doi: 10.1146/annurev.biophys.32.110601.142506. Epub 2003 Feb 18.

Abstract

The OB-fold domain is a compact structural motif frequently used for nucleic acid recognition. Structural comparison of all OB-fold/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these OB-folds. Loops connecting the secondary structural elements in the OB-fold core are extremely variable in length and in functional detail. However, certain features of ligand binding are conserved among OB-fold complexes, including the location of the binding surface, the polarity of the nucleic acid with respect to the OB-fold, and particular nucleic acid-protein interactions commonly used for recognition of single-stranded and unusually structured nucleic acids. Intriguingly, the observation of shared nucleic acid polarity may shed light on the longstanding question concerning OB-fold origins, indicating that it is unlikely that members of this family arose via convergent evolution.

Publication types

  • Research Support, U.S. Gov't, P.H.S.
  • Review

MeSH terms

  • Amino Acid Motifs
  • DNA / chemistry*
  • DNA / metabolism
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Humans
  • Macromolecular Substances
  • Models, Molecular*
  • Oligonucleotides / metabolism*
  • Oligosaccharides / metabolism*
  • Peptide Fragments / chemistry
  • Peptide Fragments / metabolism
  • Protein Binding
  • Protein Conformation
  • Protein Folding*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Proteins / chemistry
  • Proteins / classification
  • Proteins / metabolism
  • RNA / chemistry*
  • RNA / metabolism

Substances

  • DNA-Binding Proteins
  • Macromolecular Substances
  • Oligonucleotides
  • Oligosaccharides
  • Peptide Fragments
  • Proteins
  • RNA
  • DNA