Two singular types of CCCH tandem zinc finger in Nab2p contribute to polyadenosine RNA recognition

Structure. 2013 Oct 8;21(10):1800-11. doi: 10.1016/j.str.2013.07.019. Epub 2013 Aug 29.

Abstract

The seven C-terminal CCCH-type zinc fingers of Nab2p bind the poly(A) tail of mRNA (∼A25). Using NMR, we demonstrated that the first four (Zf1-Zf4) contain two structurally independent tandems (TZF12 and TZF34) and bind A12 with moderate affinity (KD = 2.3 μM). Nab2p TZF12 contains a long α helix that contacts the zinc fingers Zf1 and Zf2 to arrange them similarly to Zf6-7 in the Nab2p Zf5-7 structure. Nab2p TZF34 exhibits a distinctive two-fold symmetry of the zinc centers with mutual recognition of histidine ligands. Our mutagenesis and NMR data demonstrate that the α helix of TZF12 and Zf3 of TZF34 define the RNA-binding interface, while Zf1, Zf2, and Zf4 seem to be excluded. These results further our understanding of polyadenosine RNA recognition by the CCCH domain of Nab2p. Moreover, we describe a hypothetical mechanism for controlling poly(A) tail length with specific roles for TZF12, TZF34, and Zf5-7 domains.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Amino Acid Substitution
  • Binding Sites
  • Conserved Sequence
  • Coordination Complexes / chemistry
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular
  • Nucleocytoplasmic Transport Proteins / chemistry*
  • Nucleocytoplasmic Transport Proteins / genetics
  • Protein Binding
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • RNA-Binding Proteins / chemistry*
  • RNA-Binding Proteins / genetics
  • Saccharomyces cerevisiae Proteins / chemistry*
  • Saccharomyces cerevisiae Proteins / genetics
  • Saccharomyces cerevisiae*
  • Structural Homology, Protein
  • Thermodynamics
  • Zinc Fingers

Substances

  • Coordination Complexes
  • NAB2 protein, S cerevisiae
  • Nucleocytoplasmic Transport Proteins
  • RNA-Binding Proteins
  • Saccharomyces cerevisiae Proteins

Associated data

  • PDB/3ZJ1
  • PDB/3ZJ2