Structures of the pleiotropic translational regulator Hfq and an Hfq-RNA complex: a bacterial Sm-like protein

EMBO J. 2002 Jul 1;21(13):3546-56. doi: 10.1093/emboj/cdf322.

Abstract

In prokaryotes, Hfq regulates translation by modulating the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences. To elucidate the mechanisms of target recognition and translation regulation by Hfq, we determined the crystal structures of the Staphylococcus aureus Hfq and an Hfq-RNA complex to 1.55 and 2.71 A resolution, respectively. The structures reveal that Hfq possesses the Sm-fold previously observed only in eukaryotes and archaea. However, unlike these heptameric Sm proteins, Hfq forms a homo-hexameric ring. The Hfq-RNA structure reveals that the single-stranded hepta-oligoribonucleotide binds in a circular conformation around a central basic cleft, whereby Tyr42 residues from adjacent subunits stack with six of the bases, and Gln8, outside the Sm motif, provides key protein-base contacts. Such binding suggests a mechanism for Hfq function.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Research Support, U.S. Gov't, P.H.S.

MeSH terms

  • Amino Acid Motifs
  • Amino Acid Sequence
  • Carrier Proteins / chemistry*
  • Carrier Proteins / metabolism
  • Carrier Proteins / ultrastructure
  • Cryoelectron Microscopy
  • Crystallography, X-Ray
  • Gene Expression Regulation, Bacterial
  • Host Factor 1 Protein
  • Integration Host Factors
  • Macromolecular Substances
  • Models, Molecular
  • Molecular Sequence Data
  • Nucleic Acid Conformation
  • Protein Binding
  • Protein Biosynthesis
  • Protein Conformation
  • Protein Structure, Tertiary
  • RNA, Bacterial / chemistry*
  • RNA, Bacterial / metabolism
  • RNA, Bacterial / ultrastructure
  • RNA, Messenger / chemistry*
  • RNA, Messenger / metabolism
  • RNA, Messenger / ultrastructure
  • Recombinant Fusion Proteins / chemistry
  • Sequence Alignment
  • Sequence Homology, Amino Acid
  • Staphylococcus aureus / chemistry*
  • Substrate Specificity

Substances

  • Carrier Proteins
  • Host Factor 1 Protein
  • Integration Host Factors
  • Macromolecular Substances
  • RNA, Bacterial
  • RNA, Messenger
  • Recombinant Fusion Proteins

Associated data

  • PDB/1QK1
  • PDB/1QK2