Crystal structure of human RNA helicase A (DHX9): structural basis for unselective nucleotide base binding in a DEAD-box variant protein

J Mol Biol. 2010 Jul 23;400(4):768-82. doi: 10.1016/j.jmb.2010.05.046. Epub 2010 May 25.


RNA helicases of the DExD/H-box superfamily are critically involved in all RNA-related processes. No crystal structures of human DExH-box domains had been determined previously, and their structures were difficult to predict owing to the low level of homology among DExH-motif-containing proteins from diverse species. Here we present the crystal structures of the conserved domain 1 of the DEIH-motif-containing helicase DHX9 and of the DEAD-box helicase DDX20. Both contain a RecA-like core, but DHX9 differs from DEAD-box proteins in the arrangement of secondary structural elements and is more similar to viral helicases such as NS3. The N-terminus of the DHX9 core contains two long alpha-helices that reside on the surface of the core without contributing to nucleotide binding. The RNA-polymerase-II-interacting minimal transactivation domain sequence forms an extended loop structure that resides in a hydrophobic groove on the surface of the DEIH domain. DHX9 lacks base-selective contacts and forms an unspecific but important stacking interaction with the base of the bound nucleotide, and our biochemical analysis confirms that the protein can hydrolyze ATP, guanosine 5'-triphosphate, cytidine 5'-triphosphate, and uridine 5'-triphosphate. Together, these findings allow the localization of functional motifs within the three-dimensional structure of a human DEIH helicase and show how these enzymes can bind nucleotide with high affinity in the absence of a Q-motif.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Crystallography, X-Ray
  • DEAD Box Protein 20 / chemistry
  • DEAD-box RNA Helicases / chemistry*
  • DEAD-box RNA Helicases / metabolism*
  • Humans
  • Models, Molecular
  • Molecular Sequence Data
  • Neoplasm Proteins / chemistry*
  • Neoplasm Proteins / metabolism*
  • Nucleotides / metabolism*
  • Protein Structure, Secondary
  • Protein Structure, Tertiary
  • Sequence Alignment


  • Neoplasm Proteins
  • Nucleotides
  • DDX20 protein, human
  • DEAD Box Protein 20
  • DHX9 protein, human
  • DEAD-box RNA Helicases

Associated data

  • PDB/2OXC
  • PDB/3LLM
  • RefSeq/NP_071282
  • SWISSPROT/P60842
  • SWISSPROT/Q08211
  • SWISSPROT/Q13206
  • SWISSPROT/Q14147
  • SWISSPROT/Q14562