Solution structure of the R3H domain from human Smubp-2

J Mol Biol. 2003 Feb 7;326(1):217-23. doi: 10.1016/s0022-2836(02)01381-5.


The R3H domain is a conserved sequence motif, identified in over 100 proteins, that is thought to be involved in polynucleotide-binding, including DNA, RNA and single-stranded DNA. In this work the 3D structure of the R3H domain from human Smubp-2 was determined by NMR spectroscopy. It is the first 3D structure determination of an R3H domain. The fold presents a small motif, consisting of a three-stranded antiparallel beta-sheet and two alpha-helices, which is related to the structures of the YhhP protein and the C-terminal domain of the translational initiation factor IF3. The similarities are non-trivial, as the amino acid identities are below 10%. Three conserved basic residues cluster on the same face of the R3H domain and could play a role in nucleic acid recognition. An extended hydrophobic area at a different site of the molecular surface could act as a protein-binding site. A strong correlation between conservation of hydrophobic amino acids and side-chain solvent protection indicates that the structure of the Smubp-2 R3H domain is representative of R3H domains in general.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Bacterial Proteins / chemistry
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / metabolism
  • Escherichia coli Proteins*
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Nuclear Magnetic Resonance, Biomolecular*
  • Prokaryotic Initiation Factor-3 / chemistry
  • Protein Structure, Tertiary
  • Sequence Alignment
  • Solutions
  • Structure-Activity Relationship
  • Transcription Factors / chemistry*
  • Transcription Factors / metabolism


  • Bacterial Proteins
  • DNA-Binding Proteins
  • Escherichia coli Proteins
  • IGHMBP2 protein, human
  • Prokaryotic Initiation Factor-3
  • SirA protein, E coli
  • Solutions
  • Transcription Factors

Associated data

  • PDB/1MSZ