Structure and RNA binding of the third KH domain of poly(C)-binding protein 1

Nucleic Acids Res. 2005 Feb 24;33(4):1213-21. doi: 10.1093/nar/gki265. Print 2005.

Abstract

Poly(C)-binding proteins (CPs) are important regulators of mRNA stability and translational regulation. They recognize C-rich RNA through their triple KH (hn RNP K homology) domain structures and are thought to carry out their function though direct protection of mRNA sites as well as through interactions with other RNA-binding proteins. We report the crystallographically derived structure of the third domain of alphaCP1 to 2.1 A resolution. alphaCP1-KH3 assumes a classical type I KH domain fold with a triple-stranded beta-sheet held against a three-helix cluster in a betaalphaalphabetabetaalpha configuration. Its binding affinity to an RNA sequence from the 3'-untranslated region (3'-UTR) of androgen receptor mRNA was determined using surface plasmon resonance, giving a K(d) of 4.37 microM, which is indicative of intermediate binding. A model of alphaCP1-KH3 with poly(C)-RNA was generated by homology to a recently reported RNA-bound KH domain structure and suggests the molecular basis for oligonucleotide binding and poly(C)-RNA specificity.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • 3' Untranslated Regions / chemistry*
  • 3' Untranslated Regions / metabolism
  • Amino Acid Sequence
  • Binding Sites
  • Models, Molecular*
  • Molecular Sequence Data
  • Oligonucleotides / chemistry
  • Poly C / chemistry
  • Protein Structure, Tertiary
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / metabolism
  • Sequence Alignment
  • Surface Plasmon Resonance

Substances

  • 3' Untranslated Regions
  • Oligonucleotides
  • RNA-Binding Proteins
  • Poly C