Protein-RNA and protein-protein recognition by dual KH1/2 domains of the neuronal splicing factor Nova-1

Structure. 2011 Jul 13;19(7):930-44. doi: 10.1016/j.str.2011.05.002.

Abstract

Nova onconeural antigens are neuron-specific RNA-binding proteins implicated in paraneoplastic opsoclonus-myoclonus-ataxia (POMA) syndrome. Nova harbors three K-homology (KH) motifs implicated in alternate splicing regulation of genes involved in inhibitory synaptic transmission. We report the crystal structure of the first two KH domains (KH1/2) of Nova-1 bound to an in vitro selected RNA hairpin, containing a UCAG-UCAC high-affinity binding site. Sequence-specific intermolecular contacts in the complex involve KH1 and the second UCAC repeat, with the RNA scaffold buttressed by interactions between repeats. Whereas the canonical RNA-binding surface of KH2 in the above complex engages in protein-protein interactions in the crystalline state, the individual KH2 domain can sequence-specifically target the UCAC RNA element in solution. The observed antiparallel alignment of KH1 and KH2 domains in the crystal structure of the complex generates a scaffold that could facilitate target pre-mRNA looping on Nova binding, thereby potentially explaining Nova's functional role in splicing regulation.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alternative Splicing
  • Amino Acid Sequence
  • Antigens, Neoplasm* / chemistry
  • Antigens, Neoplasm* / genetics
  • Antigens, Neoplasm* / metabolism
  • Base Sequence
  • Binding Sites
  • Crystallization
  • Crystallography, X-Ray
  • Electrophoretic Mobility Shift Assay
  • Humans
  • Magnetic Resonance Spectroscopy
  • Models, Molecular
  • Molecular Sequence Data
  • Nerve Tissue Proteins* / chemistry
  • Nerve Tissue Proteins* / genetics
  • Nerve Tissue Proteins* / metabolism
  • Neuro-Oncological Ventral Antigen
  • Neurons / cytology
  • Neurons / metabolism*
  • Opsoclonus-Myoclonus Syndrome / metabolism*
  • Opsoclonus-Myoclonus Syndrome / physiopathology
  • Protein Binding
  • Protein Structure, Tertiary
  • RNA Precursors / chemistry
  • RNA Precursors / metabolism*
  • RNA, Small Interfering / chemistry
  • RNA, Small Interfering / metabolism*
  • RNA-Binding Proteins* / chemistry
  • RNA-Binding Proteins* / genetics
  • RNA-Binding Proteins* / metabolism
  • Sequence Homology, Amino Acid
  • Solutions / chemistry
  • Solutions / metabolism
  • Synaptic Transmission / physiology*
  • Syndrome

Substances

  • Antigens, Neoplasm
  • Nerve Tissue Proteins
  • Neuro-Oncological Ventral Antigen
  • RNA Precursors
  • RNA, Small Interfering
  • RNA-Binding Proteins
  • Solutions

Associated data

  • PDB/2ANN
  • PDB/2ANR